This entry represents the N-terminal domain of YopH protein tyrosine phosphatase (PTP). This domain has a compact structure composed of four α-helices and two β-hairpins. Helices alpha-1 and alpha-3 are parallel to each other and antiparallel to helices alpha-2 and alpha-4. This domain targets YopH for secretion from the bacterium and translocation into eukaryotic cells, and has phosphotyrosyl peptide-binding activity, allowing for recognition of p130Cas and paxillin []. YopH from Yersinia sp. is essential for pathogenesis, as it allows the bacteria to resist phagocytosis by host macrophages through its ability to dephosphorylate host proteins, thereby interfering with the host signalling process. Yersinia has one of the most active PTP enzymes known. YopH contains a loop of ten amino acids (the WPD loop) that covers the entrance of the active site of the enzyme during substrate binding []. A homologous domain is found in YscM (Yop secretion protein M or Yop proteins translocation protein M), which acts as a Yop protein translocation protein. Several Yop proteins are involved in pathogenesis. YscM is produced by the virulence operon virC, which encodes thirteen genes, yscA-M []. Transcription of the virC operon was subjected to the same regulation as the yop genes.
The glycine-tyrosine-phenylalanine (GYF) domain is an around 60-amino acid domain which contains a conserved GP[YF]xxxx[MV]xxWxxx[GN]YF motif. It was identified in the human intracellular protein termed CD2 binding protein 2 (CD2BP2), which binds to a site containing two tandem PPPGHR segments within the cytoplasmic region of CD2. Binding experiments and mutational analyses have demonstrated the critical importance of the GYF tripeptide in ligand binding. A GYF domain is also found in several other eukaryotic proteins of unknown function []. It has been proposed that the GYF domain found in these proteins could also be involved in proline-rich sequence recognition [].Resolution of the structure of the CD2BP2 GYF domain by NMR spectroscopy revealed a compact domain with a β-β-α-β-beta topology, where the single α-helix is tilted away from the twisted, anti-parallel β-sheet. The conserved residues of the GYF domain create a contiguous patch of predominantly hydrophobic nature which forms an integral part of the ligand-binding site []. There is limited homology within the C-terminal 20-30 amino acids of various GYF domains, supporting the idea that this part of the domain is structurally but not functionally important [].
Tuberous sclerosis (TSC) is an autosomal dominant disorder caused by a mutation in either the TSC1 or TSC2 tumour suppressor genes. The disease ischaracterised by hamartomas in one or more organs (including brain, skin,heart and kidney) giving rise to a broad phenotypic spectrum (including seizures, mental retardation, renal dysfunction and dermatological abnormalities. TSC2 encodes tuberin, a putative GTPase activatingprotein for rap1 and rab5. The TSC1 gene was recently identified and codesfor hamartin, a novel protein with no significant similarity to tuberin orany other known vertebrate protein []. Hamartin and tuberin have been shown to associate physically in vivo, their interaction being mediated by predicted coiled-coil domains. It is thought that hamartin and tuberin function in the same complex, rather than in separate pathways.Moreover, because oligomerisation of the hamartin C-terminal coiled coildomain is inhibited by the presence of tuberin, it is possible that tuberinacts as a chaperone, preventing hamartin self-aggregation [].Tuberin is a widely expressed 1784-amino-acid protein. Expression of the wild-type gene in TSC2 mutant tumour cells inhibits proliferation andtumorigenicity. This "suppressor"activity is encoded by a functionaldomain in the C terminus that shares similarity with the GTPase activatingprotein Rap1GAP []. It is thought that tuberin functions as a Rab5GAP in vivo to negatively regulate Rab5-GTP activity in endocytosis []. It also acts as a GTPase-activating protein (GAP) for the small GTPase RheB, a direct activator of the protein kinase activity of mTORC1 [, ].
This entry consists of the SWR1-complex protein 4 (Swc4) from yeast, also known as EAF2, and its mammalian homologue DNA methyltransferase 1-associated protein 1 (Dmap1) []. They are components of the NuA4 histone acetyltransferase (HAT) complex, which is highly conserved in eukaryotes. NuA4 acetylates the nucleosomal histones H4 and H2A and plays primary roles in transcription, DNA repair, and cell cycle control [, ].The subunits of the NuA4 complex are shared by the ATP-dependent chromatin-remodeling SWR1 complex in yeast and its human orthologue, Snf 2-related CREB-binding protein (CBP) activator protein (SRCAP) complex. The mammalian NuA4 complex includes the SRCAP complex, and thus combines the functions of the yeast NuA4 and Swr1 complexes []. The SWR1/SRCAP complex mediates the ATP-dependent exchange of histone H2A for the H2A variant HZT1 leading to transcriptional regulation of selected genes by chromatin remodeling [, , ]. Dmap1 was originally identified as an interacting molecule with DNA methyltransferase 1 (DNMT1) and plays a crucial role in DNA repair. It is indispensable for the maintenance of chromosomal integrity and might function as a tumor suppressor [].
Nuclear respiratory factor-1 is a transcriptional activator that has been implicated in the nuclear control of respiratory chain expression in vertebrates. The first 26 amino acids of nuclear respiratory factor-1 are required for the binding of dynein light chain. The interaction with dynein light chain is observed for both ewg and Nrf-1, transcription factors that are structurally and functionally similar between humans and Drosophila [].In Drosophila, the erect wing (ewg) protein is required for proper development of the central nervous system and the indirect flight muscles. The fly ewg gene encodes a novel DNA-binding domain that is also found in four genes previously identified in sea urchin, chicken, zebrafish, and human [].The highest level of expression of both ewg and Nrf-1 was found in the central nervous system, somites, first branchial arch, optic vesicle, and otic vesicle. In the mouse Nrf-1 protein, , there is also an NLS domain at 88-116, and a DNA binding and dimerisation domain at 127-282. Ewg is a site-specific transcriptional activator, and evolutionarily conserved regions of ewg contribute both positively and negatively to transcriptional activity [].
BRCA2 participates in homologous recombination-mediated repair of double-strand DNA breaks [, ]. It stimulates the displacement of Replication protein A (RPA), the most abundant eukaryotic ssDNA binding protein []. Mutations that map throughout the BRCA2 protein are associated with breast cancer susceptibility []. BRCA2 is a large nuclear protein and its most conserved region is the C-terminal BRCA2DBD. BRCA2DBD binds ssDNA in vitro, and is composed of five structural domains, three of which are OB folds (OB1, OB2, and OB3). BRCA2DBD OB2 and OB3 are arranged in tandem, and their mode of binding can be considered qualitatively similar to two OB folds of RPA1, DBD-A and DBD-B (the major DBDs of RPA) []. This entry represents OB1, which consists of a highly curved five-stranded β-sheet that closes on itself to form a β-barrel. OB1 has a shallow groove formed by one face of the curved sheet and is demarcated by two loops, one between beta 1 and beta 2 and another between beta 4 and beta 5, which allows for weak single strand DNA binding. The domain also binds the 70-amino acid DSS1 (deleted in split-hand/split foot syndrome) protein, which was originally identified as one of three genes that map to a 1.5-Mb locus deleted in an inherited developmental malformation syndrome [].
This entry represents pleckstrin homology (PH) domain found in the Pleckstrin homology domain-containing family A members 4-7 (PKHA4-7) from humans. This domain is involved in targeting these proteins to appropriate cellular compartments or enabling them to interact with other components of the signal transduction pathways. Some PH domains are responsible for the protein binding to phosphoinositide phosphates (PIPs) with high affinity and specificity, others display strong specificity in lipid binding. Its specificity is usually determined by loop regions or insertions in the N terminus of the domain, which are not conserved across all PH domains. Proteins included in this entry are predominantly found in chordates. Some members also contain WW (also known as WWP) domains, also occurring in proteins involved in signal transduction processes [, , , ]. PKHA4 (PEPP-1) binds specifically to phosphatidylinositol 3-phosphate (PtdIns3P) and was reported to be involved in ubiquitination [, ]. In humans, PKHA6 (PEPP-3) has been related to the pathophysiology of schizophrenia and the therapy response towards antipsychotics []. PKHA7, required for zonula adherens biogenesis and maintenance, has been identified as one of the host factors mediating death by S. aureus alpha-toxin []and related to hypertension, glaucoma and cancer [, , , , ].
Hakai is an E3 ubiquitin ligase that disrupts cell-cell contacts in epithelial cells and is upregulated in human colon and gastric adenocarcinomas. It was identified to mediate the posttranslational downregulation of E-cadherin (CDH1), a major component of adherens junctions in epithelial cells and a potent tumour suppressor [, , ]. It also promotes ubiquitination of several other tyrosine-phosphorylated Src substrates, including cortactin (CTTN) and DOK1 []. Hakai acts as a homodimer with a novel HYB (Hakai pTyr-binding) domain that forms a phosphotyrosine-binding pocket upon, and consists of a pair of monomers arranged in an anti-parallel configuration. Each monomer contains a C3HC4-type RING-HC finger and a short pTyr-B domain that incorporates a novel, atypical C2H2-type Zn-finger coordination motif. Both domains are important for dimerization [, ]. ZNF645, also known as CBLL2, is a novel testis-specific E3 ubiquitin-protein ligase that plays a role in sperm production and quality control []. It has a structure similar to that of the c-Cbl-like protein Hakai. In contrast to Hakai, its HYB domain demonstrates different target specificities. It interacts with v-Src-phosphorylated E-cadherin, but not to cortactin [].
Hakai is an E3 ubiquitin ligase that disrupts cell-cell contacts in epithelial cells and is upregulated in human colon and gastric adenocarcinomas. It was identified to mediate the posttranslational downregulation of E-cadherin (CDH1), a major component of adherens junctions in epithelial cells and a potent tumour suppressor [, , ]. It also promotes ubiquitination of several other tyrosine-phosphorylated Src substrates, including cortactin (CTTN) and DOK1 []. Hakai acts as a homodimer with a novel HYB (Hakai pTyr-binding) domain that forms a phosphotyrosine-binding pocket upon, and consists of a pair of monomers arranged in an anti-parallel configuration. Each monomer contains a C3HC4-type RING-HC finger and a short pTyr-B domain that incorporates a novel, atypical C2H2-type Zn-finger coordination motif. Both domains are important for dimerization [, ]. ZNF645, also known as CBLL2, is a novel testis-specific E3 ubiquitin-protein ligase that plays a role in sperm production and quality control []. It has a structure similar to that of the c-Cbl-like protein Hakai. In contrast to Hakai, its HYB domain demonstrates different target specificities. It interacts with v-Src-phosphorylated E-cadherin, but not to cortactin [].
Formin homology (FH) proteins play a crucial role in the reorganisation of the actin cytoskeleton, which mediates various functions of thecell cortex including motility, adhesion, and cytokinesis []. Formins are multidomain proteins that interact with diverse signalling molecules and cytoskeletal proteins, although some formins have been assigned functions within the nucleus. Formins are characterised by the presence of three FH domains (FH1, FH2 and FH3), although members of the formin family do not necessarily contain all three domains []. The proline-rich FH1 domain mediates interactions with a variety of proteins, including the actin-binding protein profilin, SH3 (Src homology 3) domain proteins, and WW domain proteins. The FH2 domain is required for the self-association of formin proteins through the ability of FH2 domains to directly bind each other [], and may also act to inhibit actin polymerisation []. The FH3 domain () is less well conserved and may be important for determining intracellular localisation of formin family proteins. In addition, some formins can contain a GTPase-binding domain (GBD) () required for binding to Rho small GTPases, and a C-terminal conserved Dia-autoregulatory domain (DAD).This entry represents the FH2 domain, which was shown by X-ray crystallography to have an elongated, crescent shape containing three helical subdomains [].
The anti-apoptotic protein p35 from baculovirus is thought to prevent the suicidal response ofinfected insect cells by inhibiting caspases. Ectopic expression of p35 in a number of transgenic animals or cell lines is also anti-apoptotic, giving rise to the hypothesis that the protein is a general inhibitor of caspases. This protein belongs to MEROPS proteinase inhibitor family I50, clan IQ. Purified recombinant p35 inhibits human caspase-1, -3, -6, -7, -8, and -10 but does not significantly inhibit unrelated serine or cysteine proteases, implying that p35 is a potent caspase-specific inhibitor. The interaction of p35 with caspase-3, as a model of the inhibitory mechanism,revealed classic slow-binding inhibition, with both active-sites of the caspase-3 dimer acting equally and independently. Inhibition resulted from complex formation between the enzyme and inhibitor, which could be visualised under non-denaturing conditions, but was dissociated by SDS to give p35 cleaved at Asp87, the P1 residue of the inhibitor. Complex formation requires the substrate-binding cleft to be unoccupied [].Infecting the insect cell line IPLB-Ld652Y with the baculovirus Autographa californica nuclear polyhedrosis virus (AcMNPV) results in global translation arrest, which correlates with the presence of the AcMNPV apoptotic suppressor, p35. However, the anti-apoptotic function of p35 in translation arrest is not solely due to caspase inactivation, but its activity enhances signalling to a separate translation arrest pathway, possibly by stimulating the late stages of the baculovirus infection cycle [].
Members of the potato peptidase inhibitor II family are proteinase inhibitors that belong to MEROPS inhibitor family I20, clan IA and are restricted to plants. They inhibit serine peptidases belonging to MEROPS peptidase family S1 [](). They have a multidomain structure [], which permits circular permutation of the sequences. It was been shown that some naturally occurring Pin2 proteins, have an `ancestral' circularly permuted structure []. Circular permutation/ rearrangements of sequences has also been observed between species, such as favin from Vicia faba and the lectin concanavalin A from Canavalia ensiformis []or amongst members of the plant aspartyl proteinases and human lung surfactant proteins []. This family of proteinase inhibitors are present in seeds, leaves and other organs. Perhaps the best known representatives are the wound-induced proteinase inhibitors [, ], which contain up to eight sequence-repeats (the `IP repeats'). The sequence of the IP repeats is quite variable, only the cysteines constituting the four disulphide bridges and a single proline residue are conserved throughout all the known repeat sequences. The structure of the proteinase inhibitor complex is known [].
Transcription factor IIS (TFIIS) is a transcription elongation factor that increases the overall transcription rate of RNA polymerase II by reactivating transcription elongation complexes that have arrested transcription. The three structural domains of TFIIS are conserved from yeast to human. The 80 or so N-terminal residues form a protein interaction domain containing a conserved motif, which has been called the LW motif because of the invariant leucine and tryptophan residues it contains. This N-terminal domain is not required for transcriptional activity, and while a similar sequence has been identified in other transcription factors, and proteins that are predominantly nuclear localized [, ], the domain is also found in proteins not directly involved in transcription. This domain is found in (amongst others):MED26 (also known as CRSP70 and ARC70), a subunit of the Mediator complex, which is required for the activity of the enhancer-binding protein Sp1. Elongin A, a subunit of a transcription elongation factor previously known as SIII. It increases the rate of transcription by suppressing transient pausing of the elongation complex. PPP1R10, a nuclear regulatory subunit of protein phosphatase 1 that was previously known as p99, FB19 or PNUTS. IWS1, which is thought to function in both transcription initiation and elongation. The TFIIS N-terminal domain is a compact four-helix bundle. The hydrophobic core residues of helices 2, 3, and 4 are well conserved among TFIIS domains, although helix 1 is less conserved [].
Phospholamban (PLB) is a small protein (52 amino acids) that regulates the affinity of the cardiac sarcoplasmic reticulum Ca2+-ATPase (SERCA2a) for calcium. PLB is present in cardiac myocytes, in slow-twitch and smooth muscle and is expressed also in aorta endothelial cells in which it could play a role in tissue relaxation. The phosphorylation/dephosphorylation of phospholamban removes and restores, respectively, its inhibitory activity on SERCA2a. It has in fact been shown that phospholamban, in its non-phosphorylated form, binds to SERCA2a and inhibits this pump by lowering its affinity for Ca2+, whereas the phosphorylated form does not exert the inhibition. PLB is phosphorylated at two sites, namely at Ser-16 for acAMP-dependent phosphokinase and at Thr-17 for a Ca2+/calmodulin-dependent phosphokinase, phosphorylation at Ser-16 being a prerequisite for the phosphorylation at Thr-17. The structure of a 36-amino-acid-long N-terminal fragment of human phospholamban phosphorylated at Ser-16 and Thr-17 and Cys36Ser mutated was determined from nuclear magnetic resonance data. The peptide assumes a conformation characterised by two α-helices connected by an irregular strand, whichcomprises the amino acids from Arg-13 to Pro-21. The proline is in a trans conformation. The two phosphate groups on Ser-16 and Thr-17 are shown to interact preferably with the side chains of Arg-14 and Arg-13, respectively [].Mutations of the phospholamban gene cause cardiomyopathy, such as Cardiomyopathy, dilated 1P (CMD1P) [, ]and Cardiomyopathy, familial hypertrophic 18 (CMH18) [].
The complete DNA sequence of the genome of Vaccinia virus has been determined []. 198 "major"protein-coding regions and 65 overlapping "minor"regions have been identified, with a total of 263 potential genes. The genes are compactly organised along the genome, with few noncoding regions []. The function of the majority of proteins encoded by these open reading frames is so far undetermined. The DNA sequence of the Fowlpox virus genome corresponding to the vaccinia virus D6-A1 region has been deduced []. Translation of the sequence reveals fowlpox virus gene homologues corresponding to the D6, D7, D9, D10, D11, D12, D13 and A1 genes of vaccinia virus. Insertion of a gene cartridge comprising the vaccinia virus p7.5 promoter and the lacZ gene into the fowlpox virus D8, D9 and D10 genes was carried out in vitro, followed by recombination into fowlpox virus []. No stable insertion mutants were obtained for D10, suggesting that this gene probably encodes a function essential to virus replication []. D10, like the D9 protein, contains an evolutionarily conserved MutT domain core, which is a characteristic of the NUDIX hydrolase family [].
Herpesviruses are large and complex DNA viruses, widely found in nature. Human cytomegalovirus (HCMV), an important human pathogen, defines the betaherpesvirus family. Mouse cytomegalovirus (MCMV) and rat cytomegalovirus serve as biological model systems for HCMV. HCMV, MCMV, and rat CMV display the largest genomes among the herpesviruses and are essentially co-linear over the central 180 kb of the 230-kb genomes. Betaherpesviruses, which include the CMVs as well as human herpesviruses 6 and 7, differ from alpha- and gammaherpesviruses by the presence of additional gene families such as the US22 gene family, which are mainly clustered at the ends of the genome. The US22 family was first described in HCMV. This gene family comprises 12 members in both HCMV and MCMV and 11 in rat CMV [].US22 proteins have been found across many animal DNA viruses and some vertebrates []. The name sake of this family US22 () is an early nuclear protein that is secreted from cells []. The US22 family may have a role in virus replication and pathogenesis []. Domain analysis showed that US22 proteins usually contain two copies of conserved modules which is homologous to several other families like SMI1 and SYD (commonly called SUKH superfamily). Bacterial operon analysis revealed that all bacterial SUKH members function as immunity proteins against various toxins. Thus US22 family is predicted to counter diverse anti-viral responses by interacting with specific host proteins [].
The homeobox domain or homeodomain was first identified in a number of Drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two α-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA. The first helix helps to stabilise the structure.The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the β-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.
Metallothioneins (MT) are small proteins that bind heavy metals, such as zinc, copper, cadmium, nickel, etc. They have a high content of cysteine residues that bind the metal ions through clusters of thiolate bonds [, ]. An empirical classification into three classes has been proposed by Fowler and coworkers []and Kojima []. Members of class I are defined to include polypeptides related in the positions of their cysteines to equine MT-1B, and include mammalian MTs as well as from crustaceans and molluscs. Class II groups MTs from a variety of species, including sea urchins,fungi, insects and cyanobacteria. Class III MTs are atypical polypeptides composed of gamma-glutamylcysteinyl units [].This original classification system has been found to be limited, in the sense that it does not allow clear differentiation of patterns of structural similarities, either between or within classes. Subsequently, a new classification was proposed on the basis of sequence similarity derived from phylogenetic relationships, which basically proposes an MT family for each main taxonomic group of organisms []. Echinoidea (sea urchin, family 4) MTs are 64-67 residue proteins. Members of this family are recognised by the sequence pattern P-D-x-K-C-[V,F]-C-C-x(5)-C-x-C-x(4)-C-C-x(4)-C-C-x(4,6)-C-C located near the N terminus. The taxonomic range of the members extends to sea urchins (echinodea). The protein sequence is divided into two structural domains, each containing 9 and 11 Cys residues binding 3 and 4 bivalent metal ions, respectively.Family 4 includes subfamilies: e1, e2, they are separate phylogenetic groups. This entry includes the sea urchin proteins, and related sequences from worms.
Metallothioneins (MT) are small proteins that bind heavy metals, such as zinc, copper, cadmium, nickel, etc. They have a high content of cysteine residues that bind the metal ions through clusters of thiolate bonds [, ]. An empirical classification into three classes has been proposed by Fowler and coworkers []and Kojima []. Members of class I are defined to include polypeptides related in the positions of their cysteines to equine MT-1B, and include mammalian MTs as well as from crustaceans and molluscs. Class II groups MTs from a variety of species, including sea urchins,fungi, insects and cyanobacteria. Class III MTs are atypical polypeptides composed of gamma-glutamylcysteinyl units [].This original classification system has been found to be limited, in the sense that it does not allow clear differentiation of patterns of structural similarities, either between or within classes. Subsequently, a new classification was proposed on the basis of sequence similarity derived from phylogenetic relationships, which basically proposes an MT family for each main taxonomic group of organisms []. Echinoidea (sea urchin, family 4) MTs are 64-67 residue proteins. Members of this family are recognised by the sequence pattern P-D-x-K-C-[V,F]-C-C-x(5)-C-x-C-x(4)-C-C-x(4)-C-C-x(4,6)-C-C located near the N terminus. The taxonomic range of the members extends to sea urchins (echinodea). The protein sequence is divided into two structural domains, each containing 9 and 11 Cys residues binding 3 and 4 bivalent metal ions, respectively.Family 4 includes subfamilies: e1, e2, they are separate phylogenetic groups.
The bone morphogenetic protein (BMP) is part of the transforming growth factor-beta superfamily. Transforming growth factor-beta (TGF-beta) is a multifunctional peptide that controls proliferation, differentiation and other functions in many cell types. TGF-beta-1 is a peptide of 112 amino acid residues derived by proteolytic cleavage from the C-terminal of a precursor protein.A number of proteins are known to be related to TGF-beta-1 [, ]. Proteins from the TGF-beta family are only active as homo- or heterodimer; the two chains being linked by a single disulphide bond. From X-ray studies of TGF-beta-2 [], it is known that all the other cysteines are involved in intrachain disulphide bonds. As shown in the following schematic representation, there are four disulphide bonds in the TGF-beta's and in inhibin beta chains, while the other members of lack the first bond.BMP-15 (or GDF-9B) has been identified by in the mouse and in humans []. BMP15 protein is encoded by 2 exons []. Homo sapiens (Human) GDF9B transcripts could be detected only in the gonads by RT-PCR analysis, and in situ hybridization studies indicated that GDF9B is not expressed in small primary follicles but rather in the oocytes of late primary follicles []. It was shown that BMP15 is a selective modulator of FSH function []. Male BMP-15 knockout mice are normal and fertile while the females demonstrate decreased ovulation and fertilization rate [].
This family is composed of ornithine decarboxylases (ODC), arginine decarboxylases (ADC) and lysinedecarboxylases (LDC), and belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase domainsuperfamily (fold I) []. These enzymes catalyse the decarboxylation of ornithine,arginine, or lysine, respectively using PLP as a co-factor. ODC is active as a dimer and catalyses thedecarboxylation of tryptophan []. ADC catalyses the decarboxylation of arginine and LDCcatalyses the decarboxylation of lysine. The PLP combines with the alpha-amino acid to form a Schiff base, whichacts as the substrate in the decarboxylation (COOH group removal) reaction [].Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha,beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction theycatalysed. The availability of several structures allowed a comprehensive analysis of the evolutionaryclassification of PLP dependent enzymes, and it was found that the functional classification did not alwaysagree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLPdependent enzymes can be classified into four major groups of different evolutionary origin: aspartateaminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanineracemase superfamily (fold type III), D-amino acid superfamily (fold type IV) and glycogen phophorylase family(fold type V) [, ].For additional information please see[, ].
TIMP-1 (also known as metalloproteinase inhibitor 1) was originally knocked-out and found to be indistinguishable from wild-type mice in metastasis assays with all tumourgenic cells tested []. Since then, studies have demonstrated that myocardial TIMP-1 plays a regulatory role in post-myocardial infarction remodeling and that myocardial remodeling is accelerated induced TIMP-1 gene deletion []. Transfer and over expression of the Timp1 gene may be a promising therapeutic strategy to target tumour-associated angiogenesis in cancer gene therapy []. Also, TIMP-1-deficient mice are resistant to Pseudomonas aeruginosa corneal and respiratory infections []. Tissue inhibitors of metalloproteinases (TIMPs) are natural inhibitors of matrix metalloproteinases (MMPs) found in most tissues and body fluids. By inhibiting MMPs activities, they participate in tissue remodeling of the extracellular matrix (ECM). The balance between MMPs and TIMPs activities is involved in both normal and pathological events such as wound healing, tissue remodeling, angiogenesis, invasion, tumourigenesis and metastasis []. TIMPs also exhibit functions that appear to be independent of their metalloproteinase inhibitory capacity []. There are four mammalian TIMPs (TIMP-1 to -4), and each TIMP has its own profile of metalloproteinase inhibition.
This is the N-terminal domain found in archaeal actin homologue Ta0583 found in thermophilic archaeon Thermoplasma acidophilum. Structural analysis indicate that the fold of Ta0583 contains the core structure of actin indicating that it belongs to the actin/Hsp70 superfamily of ATPases. Furthermore,Ta0583 co-crystallised with ADP shows that the nucleotide binds at the interface between the subdomains of Ta0583 in a manner similar to that of actin. It has been suggested that Ta0583 might function in the cellular organisation of T. acidophilum []. Other family members include ParM another actin-like protein found in Staphylococcus aureus. Crystal structure co-ordinates revealed that this protein is most structurally related to the chromosomally encoded Actin-like proteins (Alp) Ta0583 from the archaea Thermoplasma acidophilum. Furthermore, biophysical analyses have suggested that ParM filaments undergo a treadmilling-like mechanism of motion in vitro similar to that of F-actin. The recruitment of ParM to the segrosome complex, was shown to be required for the conversion of static ParM filaments to a dynamic form proficient for active segregation and facilitated by the C terminus of ParR [].
The Orange domain is a motif of ~35 amino acids present in eukaryoticDNA-binding transcription repressors, which regulate cell differentiation,embryonic patterning and other biological processes in both vertebrates andinvertebrates. The Orange domain is located just C-terminal to a basichelix-loop-helix (bHLH) domain in the bHLH-Orange (bHLH-O) proteins. Thisfamily of bHLH repressors is related to the Drosophila hairy andEnhancer-of-split proteins, wherein the Orange domain was first described andalso named helix III/IV region [, ]. The transcription of many vertebrate bHLH-O genes is regulated by the Notch signaling pathway, which controls fate decisions and other developmental processes. Orange domain proteins function as transcription repressors involved in the regulation of differentiation, anteroposterior segmentation and sex determination in flies [].Four subfamilies of bHLH-Orange proteins have been identified, i.e. hairy,Enhancer of split, Hey (also named HRT or Hesr) and Stra13 (also named SHARP,DEC, CLAST or BHLHB2) [, ]. All these Orange domain proteins have the bHLH domain and except for the Stra13 subfamily, the othersubfamily members have a conserved tetrapeptide motif in the C-terminalextremity. The C-terminal motif of the hairy and Enhancer of split proteins isWRPW and this binds the transcriptional corepressor groucho/TLE. For the Heysubfamily members the C-terminal motif is YXXW. The Orange domain may conferspecificity of function to different family members and/or it may be involvedin dimerization [, ].
This entry included insecticidal toxin complex proteins (TcaA, TccA, TcbA, TcdA) from Photorhabdus luminescens subsp. laumondii and Xenorhabdus nematophilus (Achromobacter nematophilus) [], and virulence proteins from Salmonella typhimurium that are encoded on a 90kb plasmid.P. luminescens and X. nematophilus are Gram-negative bacteria that form entomopathogenic symbioses with soil nematodes. The bacteria are found in the gut of entomopathogenic nematodes that invade and kill insects. When the nematode invades an insect host the bacteria are released into the insect haemocoel (the open circulatory system), both the bacteria and the nematode undergo multiple rounds of replication which kills the insect host. Mapping of the insecticidal toxin loci and studies on knockout mutants in P. luminescens showed that deletion of either tca or tcd loci dramatically reduced toxicity, while the double mutant tca/tcd abolished toxicity []. However the biology of toxin action is unclear as is the species range of insects the toxins are active against.S. typhimurium contains a 90kb plasmid that is associated withvirulence. This plasmid encodes at least 6 genes needed by thebacterium for invading host macrophages during infection. These includethe 70kDa mkaA protein [], a recognised virulence factor, and more recently described, four spv genes under the control of a regulator [].Deletion studies on the virulence plasmid have shown that an open reading frame encoding a 28kDa protein was needed for successful invasion of the host. This protein, designated mkfA [], VRP4 []or VirA []by differentgroups, is utilised by the microbe upon entry into macrophages, although the exact mechanism is unclear.
A number of receptors for lymphokines, hematopoietic growth factors and growth hormone-related molecules have been found to share a common binding domain. These receptors are designated as hematopoietin receptors []and the corresponding ligands as hematopoietins. Further, hematopoietins have been subdivided into two major structural groups: Large/long and small/short hematopoietins.One subset of individual receptor chains that are part of receptor complexes for large hematopoietins contain common structural elements in their extracellular parts: an immunoglobulin-like domain, an hematopoietin-receptor domain, and 3 fibronectin type-III domains (2 in the leptin receptor). This subgroup was designated as "Gp130 family of receptors"[]and contains the following chains: Leptin receptor (LPTR), Granulocyte colony stimulating factor receptor (GCSFR), Interleukin-6/-11/LIF/OSM/CNTF common beta chain (Gp130), Leukemia inhibiting factor receptor (LIFR), Oncostatin-M receptor beta chain (OSMR), Interleukin-12 receptor beta-1 chain (IL12RB1), Interleukin-12 receptor beta-2 chain (IL12RB2). A schematic representation of the structure of these receptors is shown below: +-------+-------------------------+-----------------xxxxxxx-----------------+|Ig-like| C C C C Extracellular | FnIII (x3) XXXXXXX Cytoplasmic |+-------+-|-|--|--|---------------+-----------------xxxxxxx-----------------+| | | | Transmembrane+-+ +--+These receptor chains homodimerize (GCSFR, Gp130, LPTR) or heterodimerize (Gp130 with LIFR or OSMR, IL12RB1 with IL12RB2) upon binding of the cognate cytokine: G-CSF, LIF, OSM, LPT, or the cytokine/alpha chain complex: IL-6/IL6RA, IL-11/IL11RA, CNTF/CNTFRA, IL-12 (p35/p40) [, ].
X-linked lissencephaly is a severe brain malformation affecting males. Recently it has been demonstrated that the doublecortin gene is implicated in this disorder []. Doublecortin was found to bind to the microtubule cytoskeleton. In vivo and in vitro assays show that Doublecortin stabilises microtubules and causes bundling []. Doublecortin is a basic protein with an iso-electric point of 10, typical of microtubule-binding proteins. However, its sequence contains no known microtubule-binding domain(s).The detailed sequence analysis of Doublecortin and Doublecortin-like proteins allowed the identification of an evolutionarily conserved Doublecortin (DC) domain, which is ubiquitin-like. This domain is found in the N terminus of proteins and consists of one or two tandemly repeated copies of an around 80 amino acids region. It has been suggested that the first DC domain of Doublecortin binds tubulin and enhances microtubule polymerisation [].Some proteins known to contain a DC domain are listed below:Doublecortin. It is required for neuronal migration []. A large number of point mutations in the human DCX gene leading to lissencephaly are located within the DC domains [].Human serine/threonine-protein kinase DCAMKL1. It is a probable kinase that may be involved in a calcium-signaling pathway controlling neuronal migration in the developing brain [, ].Retinitis pigmentosa 1 protein. It is required for the differentiation of photoreceptor cells. Mutation in the human RP1 gene cause retinitis pigmentosa of type 1 [, ].
The jacalin-like mannose-binding lectin domain has a β-prism fold consisting of three 4-stranded β-sheets, with an internal pseudo 3-fold symmetry. Some proteins with this domain stimulate distinct T- and B- cell functions, such as the plant lectin jacalin, which binds to the T-antigen and acts as an agglutinin. The domain can occur in tandem-repeat arrangements with up to six copies, and in architectures combined with a variety of other functional domains. While the family was initially named after an abundant protein found in the jackfruit seed, taxonomic distribution is not restricted to plants. The domain is also found in the salt-stress induced protein from rice and an animal prostatic spermine-binding protein. Proteins containing this domain include:Jacalin, a tetrameric plant seed lectin and agglutinin from Artocarpus heterophyllus (jackfruit), which is specific for galactose [].Artocarpin, a tetrameric plant seed lectin from A. heterophyllus [].Lectin MPA, a tetrameric plant seed lectin and agglutinin from Maclura pomifera (Osage orange), [].Heltuba lectin, a plant seed lectin and agglutinin from Helianthus tuberosus (Jerusalem artichoke) [].Agglutinin from Calystegia sepium (Hedge bindweed) [].Griffithsin, an anti-viral lectin from red algae (Griffithsia species) [].
Jacalin-like lectins are sugar-binding protein domains mostly found in plants. They adopt a β-prism topology consistent with a circularly permuted three-fold repeat of a structural motif. Proteins containing this domain may bind mono- or oligosaccharides with high specificity. The domain can occur in tandem-repeat arrangements with up to six copies, and in architectures combined with a variety of other functional domains. While the family was initially named after an abundant protein found in the jackfruit seed, taxonomic distribution is not restricted to plants. The domain is also found in the salt-stress induced protein from rice and an animal prostatic spermine-binding protein. Proteins containing this domain include:Jacalin, a tetrameric plant seed lectin and agglutinin from Artocarpus heterophyllus (jackfruit), which is specific for galactose [].Artocarpin, a tetrameric plant seed lectin from A. heterophyllus [].Lectin MPA, a tetrameric plant seed lectin and agglutinin from Maclura pomifera (Osage orange), [].Heltuba lectin, a plant seed lectin and agglutinin from Helianthus tuberosus (Jerusalem artichoke) [].Agglutinin from Calystegia sepium (Hedge bindweed) [].Griffithsin, an anti-viral lectin from red algae (Griffithsia species) [].Ipomoelin, a Jacalin-related lectin from sweet potato (Ipomoea batatas cv. Tainung 57) []. This entry refers to jacalin-like lectin domains found in plants.
The proteins in this family are a component of the acetyl coenzyme A carboxylase complex() and are involved in the first step in long-chain fatty acid synthesis. Inplants this is usually located in the chloroplast. In the first step, biotin carboxylase catalyses the carboxylation of the carrier protein to form an intermediate. Next, the transcarboxylase complex transfers the carboxyl group from the intermediate to acetyl-CoA forming malonyl-CoA. This protein functions in the transfer of CO2from one site to another, the biotin binding site locates to the C-terminal of this protein. The biotin is specifically attached to a lysine residue in the sequence AMKM.The structure of the C-terminal domain of the biotin carboxyl carrier (BCC) protein was shown to be a flattened β-barrel structure comprising two four-stranded beta sheets interrupted by a structural loop forming a thumb structure. The biotinyl-lysine is located on a tight β-turn on the opposite end of the molecule. The thumb structure has been shown to attached biotin, thus stabilising the structure.
The ARFGAP domain was first identified in the cell cycle control GTPase activating protein (GAP) GCS1 []. GCS1 is important for the inactivation of the ADP ribosylation factor ARF a member of the Ras superfamily of GTP-binding proteins. GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF, a process dependent on the ARFGAP domain of GCS1 [].The ARFGAP domain contains a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-Cys-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. However a C4-type zinc finger is also found in the ARD1 GAP domain []. This entry represents a structure domain containing the zinc finger motif that can also be found in bacterial protein RecO. RecO is a DNA repair protein involved in damage avoidance-tolerance pathway(s) [].
Two closely related neuropeptide precursors, which share no significant sequence similarity with other known neuropeptides, have recently been identified and named preproneuropeptide B and preproneuropeptide W [, , ]. In humans, each precursor contains a signal sequence and two dibasic cleavage sites. Alternative cleavage of these sites results in long (29 or 30 amino acid) and short (23 amino acid) forms of the resultant neuropeptides [, ]. Murine, rat and bovine versions of preproneuropeptide B, however, contain only the second cleavage site, resulting in only the long form of neuropeptide B [, ]. Neuropeptide B is expressed in both the central nervous system (CNS) and in the periphery. In the CNS, highest levels of the peptide are found in the substantia nigra and hypothalamus, suggesting a possible role in locomotor control and the release of pituitary hormones []. In the periphery, the peptide is most abundant in testis, ovary, uterus, placenta, spleen, lymph nodes and peripheral blood leukocytes, indicating potential roles in the reproductive and immune systems []. Unusually, neuropeptide B purified from bovine hypothalamus was found to be brominated at its N terminus []. This entry represents the neuropeptide B precursor.
Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins. The translocase protein subunits are encoded on the bacterial chromosome.The translocase itself comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecCY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. The chaperone protein SecB []is a highly acidic homotetrameric protein that exists as a "dimer of dimers"in the bacterial cytoplasm. SecB maintains preproteins in an unfolded state after translation, and targets these to the peripheral membrane protein ATPase SecA for secretion [].The tertiary structure of Haemophilus influenzae SecB () was resolved by means of X-ray crystallography to 2.5A []. The chaperone comprises four chains, forming a tetramer, each chain of which has a simple alpha+beta fold arrangement. While one binding site on the homotetramer recognises unfolded polypeptides by hydrophobic interactions, the second binds to SecA through the latter's C-terminal 22 residues.
The SRAP (SOS-response associated peptidase) family is characterised by the SRAP domain with a novel thiol autopeptidase activity, whose active site in human HMCES is comprised of the catalytic triad residues C2, E127, and H210 []. SRAP proteins are evolutionarily conserved in all domains of life. For instance, human HMCES and E. coli YedK are similar in both sequence and structure []. HMCES was originally identified as a possible reader of 5hmC in embryonic stem cell extracts using a double-stranded DNA molecule containing 5hmC as bait []. The bacterial members have operonic associations with the SOS DNA damage response, mutagenic translesion DNA polymerases, non-homologous DNA-ending-joining networks that employ Ku and an ATP-dependent ligase, and other repair systems []. Abasic (AP) sites are one of the most common DNA lesions that block replicative polymerases. SRAP proteins shield the AP site from endonucleases and error-prone polymerases []. Both HMCES and YedK have been found to preferentially bind ssDNA and efficiently form DNA-protein crosslinks (DPCs) to AP sites in ssDNA. They crosslink to AP sites via a stable thiazolidine DNA-protein linkage formed with the N-erminal cysteine and the aldehyde form of the AP deoxyribose []. In B Cells, HMCES has also been shown to mediate microhomology-mediated alternative-end-joining through its SRAP domain [].
Nucleotide excision repair (NER) is a conserved DNA repair pathway that enables the repair of chemically and structurally distinct DNA lesions. In prokaryotes, the UvrA, UvrB and UvrC proteins mediate NER in a multistep, ATP-dependent reaction. UvrC catalyses the first incision on the fourth or fifth phosphodiester bond 3' and on the eighth phosphodiester bond 5' from the damage that is to be excised. UvrC proteins contain conserved regions: the GIY-YIG domain, the cys-rich region, the UvrBC domain which interacts with uvrB, the RNAse H endonuclease domain and the Helix hairpin Helix (HhH)2 domain [].This entry represents the RNAse H endonuclease domain, located at the C-terminal, between the UvrBC and the (HhH)2 domains, nearby the N-terminal of the HhH. Despite the lack of sequence homology, the endonuclease domain has an RNase H-like fold, which is characteristic of enzymes with nuclease or polynucleotide transferase activities. RNase H-related enzymes typically contain a highly conserved carboxylate triad, usually DDE, in their catalytic centre. However, instead of a third carboxylate, UvrC of Thermotoga maritima was found to contain a highly conserved histidine (H488) on helix-4 in close proximity to two aspartates [].
This entry represents the homeo-prospero domain superfamily. This domain consists of a homeodomain-homology N-terminal region and the prospero-specific C-terminal region. The structure of these two regions consists of a single structural unit (a homeo-prospero domain), in which the prospero domain region is in position to contribute to DNA binding and also to mask a defined nuclear export signal that is within the putative homeodomain region. It is proposed that the homeo-prospero domain coordinately regulates prospero nuclear localisation and DNA binding specificity [].Prospero is a large Drosophila transcription factor protein that is expressed in all neural lineages of Drosophila embryos. It is needed for correct expression of several neural proteins and in determining the cell fates of neural stem cells. Homologues of prospero are found in a wide range of animals including humans with the highest level of similarity being found in the C-terminal 160 amino acids. This region was identified as containing an atypical homeobox domain followed by a prospero domain. However, the structure shows that these two regions form a single stable structural domain as defined here []. This homeo-prospero domain binds to DNA.
RNA cyclases are a family of RNA-modifying enzymes that are conserved in eukaryotes, bacteria and archaea. Type 1 RNA 3'-terminal phosphate cyclases () [, ]catalyse the conversion of 3'-phosphate to a 2',3'-cyclic phosphodiester at the end of RNA:ATP + RNA 3'-terminal-phosphate = AMP + diphosphate + RNA terminal-2',3'-cyclic-phosphateThe physiological function of the cyclase is not known, but the enzyme could be involved in the maintenance of cyclic ends in tRNA splicing intermediates or in the cyclisation of the 3' end of U6 snRNA [].A second subfamily of RNA 3'-terminal phosphate cyclases (type 2) that do not have cyclase activity have been identified in eukaryotes. They are localised to the nucleolus and are involved in ribosomal modification [].The crystal structure of RNA 3'-terminal phosphate cyclase shows that each molecule consists of two domains. The larger domain contains three repeats of a folding unit comprising two parallel alpha helices and a four-stranded beta sheet; this fold was previously identified in translation initiation factor 3 (IF3). The large domain is similar to one of the two domains of 5-enolpyruvylshikimate-3-phosphate synthase and UDP-N-acetylglucosamine enolpyruvyl transferase. The smaller domain uses a similar secondary structure element with different topology, observed in many other proteins such as thioredoxin []. Although the active site of this enzyme has not been unambiguously assigned, it can be mapped to a region surrounding His309, an adenylate acceptor, in which a number of amino acids are highly conserved in the enzyme from different sources [].
Dynein is a multisubunit microtubule-dependent motor enzyme that acts as the force generating protein of eukaryotic cilia and flagella. The cytoplasmic isoform of dynein acts as a motor for the intracellular retrograde motility of vesicles and organelles along microtubules.Dynein is composed of a number of ATP-binding large subunits (see ), intermediate size subunits and small subunits. Among the small subunits, there is a family of highly conserved proteins which make up this family [, , ]. Proteins in this family act as one of several non-catalytic accessory components of the cytoplasmic dynein 1 complex that are thought to be involved in linking dynein to cargos and to adapter proteins that regulate dynein function and may play a role in changing or maintaining the spatial distribution of cytoskeletal structures. In yeast, it was identified as a component of the nuclear pore complex where it may contribute to the stable association of the Nup82 subcomplex with the nuclear pore complex [].Both type 1 (DLC1) and 2 (DLC2) dynein light chains have a similar two-layer α-β core structure consisting of beta-alpha(2)-beta-X-beta(2) [, ].
This entry represents the SH3 domain of MPP1, which is a ubiquitously-expressed scaffolding protein that plays roles in regulating neutrophil polarity, cell shape, hair cell development, and neural development and patterning of the retina [, ]. It was originally identified as an erythrocyte protein that stabilizes the actin cytoskeleton to the plasma membrane by forming a complex with 4.1R protein and glycophorin C [, ]. MPP1 belongs to the membrane-associated guanylate kinase (MAGUK) p55 subfamily.The membrane-associated guanylate kinase (MAGUK) p55 subfamily (also known as MPP subfamily) members include the Drosophila Stardust protein and its vertebrate homologues, MPP1-7. They contain the core of three domains characteristic of MAGUK (membrane-associated guanylate kinase) proteins: PDZ, SH3, and guanylate kinase (GuK). In addition, they also contain the Hook (Protein 4.1 Binding) motif in between the SH3 and GuK domains []. MPP2-7 have two additional L27 domains at their N terminus. The GuK domain in MAGUK proteins is enzymatically inactive; instead, the domain mediates protein-protein interactions and associates intramolecularly with the SH3 domain [].
Arylamine N-acetyltransferase (NAT) facilitates the transfer of an acetyl group from acetyl coenzyme A on to a wide range of arylamine, N-hydroxyarylamines and hydrazines. Acetylation of these compounds generally results in inactivation. NAT is found in many species from Mycobacteria (Mycobacterium tuberculosis, Mycobacterium smegmatis etc) to Homo sapiens (Human). It was the first enzyme to be observed to have polymorphic activity amongst human individuals. NAT is also responsible for the inactivation of Isoniazid (a drug used to treat tuberculosis) in humans [, ]. NAT catalyses the reaction:Acetyl-coA + arylamine = coA + N-acetylarylamineNAT is the target of a common genetic polymorphism of clinical relevance in humans. The N-acetylation polymorphism is determined by low or high NAT activity in liver. NAT has been implicated in the action and toxicity of amine-containing drugs, and in the susceptibility to cancer and systematic lupus erythematosus [, , , ]. Two highly similar human genes for NAT, termed NAT1 and NAT2, encode genetically invariant and variant NAT proteins, respectively. The structure of both proteins is similar to each other and to their prokaryotic orthologues, showing three domains: the N-terminal domain is mostly α-helical, the central domain consists of nine β-strands and the C-terminal has has four anti-parallel β-strands and one α-helix. However, in the human central domain there is a specific insertion []. N-malonyltransferase FDB2 from the fungal fitopathogen Fusarium pseudograminearum also belongs to this family. It is involved in the degradation of benzoxazolinones produced by the host plant [, , ].
Kelch is a 50-residue motif, named after the Drosophila mutant in which it was first identified []. This sequence motif represents one β-sheet blade, and several of these repeats can associate to form a β-propeller. For instance, the motif appears 6 times in Drosophila egg-chamber regulatory protein (also known as ring canal kelch protein), creating a 6-bladed β-propeller. The motif is also found in mouse protein MIPP []and in a number of poxviruses. In addition, kelch repeats have been recognised in alpha- and beta-scruin [, ], and in galactose oxidase from the fungus Dactylium dendroides [, ]. The structure of galactose oxidase reveals that the repeated sequence corresponds to a 4-stranded antiparallel β-sheet motif that forms the repeat unit in a super-barrel structural fold [].The known functions of kelch-containing proteins are diverse: scruin is an actin cross-linking protein; galactose oxidase catalyses the oxidation of the hydroxyl group at the C6 position in D-galactose; and kelch may have a cytoskeletal function, as it is localised to the actin-rich ring canals that connect the 15 nurse cells to the developing oocyte in Drosophila []. Nevertheless, based on the location of the kelch pattern in the catalytic unit in galactose oxidase, functionally important residues have been predicted in glyoxal oxidase [].This entry represents the 6-bladed Kelch β-propeller, which consists of six 4-stranded β-sheet motifs (or six Kelch repeats).
Uridylate kinases (also known as UMP kinases) are key enzymes in the synthesis of nucleoside triphosphates. They catalyse the reversible transfer of the gamma-phosphoryl group from an ATP donor to UMP, yielding UDP, which is the starting point for the synthesis of all other pyrimidine nucleotides. The eukaryotic enzyme has a dual specificity, phosphorylating both UMP and CMP, while the bacterial enzyme is specific to UMP. The bacterial enzyme shows no sequence similarity to the eukaryotic enzyme or other nucleoside monophosphate kinases, but rather appears to be part of the amino acid kinase family. It is dependent on magnesium for activity and is activated by GTP and repressed by UTP [, ]. In many bacterial genomes, the gene tends to be located immediately downstream of elongation factor T and upstream of ribosome recycling factor. A related protein family, believed to be equivalent in function is found in the archaea and in spirochetes.Structurally, the bacterial and archaeal proteins are homohexamers centred around a hollow nucleus and organised as a trimer of dimers [, ]. Each monomer within the protein forms the amino acid kinase fold and can be divided into an N-terminal region which binds UMP and mediates intersubunit interactions within the dimer, and a C-terminal region which binds ATP and contains a mobile loop covering the active site. Inhibition of enzyme activity by UTP appears to be due to competition for the binding site for UMP, not allosteric inhibition as was previously suspected.This entry represents both the bacterial and archaeal enzymes.
Dynein is a multisubunit microtubule-dependent motor enzyme that acts as the force generating protein of eukaryotic cilia and flagella. The cytoplasmic isoform of dynein acts as a motor for the intracellular retrograde motility of vesicles and organelles along microtubules.Dynein is composed of a number of ATP-binding large subunits (see ), intermediate size subunits and small subunits. Among the small subunits, there is a family of highly conserved proteins which make up this family [, , ]. Proteins in this family act as one of several non-catalytic accessory components of the cytoplasmic dynein 1 complex that are thought to be involved in linking dynein to cargos and to adapter proteins that regulate dynein function and may play a role in changing or maintaining the spatial distribution of cytoskeletal structures. In yeast, it was identified as a component of the nuclear pore complex where it may contribute to the stable association of the Nup82 subcomplex with the nuclear pore complex [].Both type 1 (DLC1) and 2 (DLC2) dynein light chains have a similar two-layer α-β core structure consisting of beta-alpha(2)-beta-X-beta(2) [, ].
HR1 was first described as a three times repeated homology region of the N-terminal non-catalytic part of protein kinase PRK1(PKN) []. The first two of these repeats were later shownto bind the small G protein rho [, ]known to activate PKN in its GTP-bound form. Similar rho-binding domains also occur in a number of other protein kinases and in the rho-binding proteins rhophilin and rhotekin. Recently, the structure of the N-terminal HR1 repeat complexed with RhoA has been determined by X-ray crystallography. This domain contains two long alpha helices forming a left-handed antiparallel coiled-coil fold termed the antiparallel coiled- coil (ACC) finger domain. The two long helices encompass the basic region and the leucine repeat region, which are identified as the Rho-binding region [, , ].This entry also includes Transducer of Cdc42-dependent actin assembly protein (TOCA) family proteins which contains a central HR1 (also known as Rho effector motif class 1, REM-1) which is closely related to Cdc42-interacting protein 4 (CIP4), effectors of the Rho family small G protein Cdc2 [].
This is the C-terminal domain of CpnT secreted by Mycobacterium tuberculosis (Mtb). It induces necrosis of infected cells to evade immune responses. Mtb utilizes the protein CpnT to kill human macrophages by secreting its C-terminal domain (CTD), named tuberculosis necrotizing toxin (TNT), that induces necrosis. It acts as a NAD+ glycohydrolase which hydrolyzes the essential cellular coenzyme NAD+ in the cytosol of infected macrophages resulting in necrotic cell death []. CpnT transports its toxic CTD from the cell surface of M. tuberculosis by proteolytic cleavage, where the toxin is cleaved to induce host cell death [].Structural analysis determined that the TNT core contains only six β-strands as opposed to seven found in all known NAD+-utilizing toxins, and is significantly smaller, with only two short α-helices and two 3/10 helices. Furthermore, the putative NAD+ binding pocket identified Q822, Y765 and R757 as residues possibly involved in NAD+-binding and hydrolysis based on similar positions of catalytic amino acids of ADP-ribosylating toxins. Glutamine 822 residue was detected to be highly conserved among TNT homologues [].
The phosphotyrosine-binding domain (PTB, also phosphotyrosine-interaction or PI domain) of tensin tends to be found at the C terminus. Tensin is a multi-domain protein that binds to actin filaments and functions as a focal-adhesion molecule (focal adhesions are regions of plasma membrane through which cells attach to the extracellular matrix). Human tensin has actin-binding sites, an SH2 () domain and a region similar to the tumour suppressor PTEN []. The PTB domain interacts with the cytoplasmic tails of beta integrin by binding to an NPXY motif []. The PTB domain is also found in the epidermal growth factor receptor kinase substrate 8 (EPS8).PTB domains have a common PH-like fold and are found in various eukaryotic signaling molecules []. This domain was initially shown to binds peptides with a NPXY motif with differing requirements for phosphorylation of the tyrosine, although more recent studies have found that some types of PTB domains can bind to peptides lack tyrosine residues altogether []. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine []. PTB domains are classified into three groups: phosphotyrosine-dependent Shc-like, phosphotyrosine-dependent IRS-like, and phosphotyrosine-independent Dab-like PTB domains [].
This entry represents the homeo-prospero domain. This domain consists of a homeodomain-homology N-terminal region and the prospero-specific C-terminal region. The structure of these two regions consists of a single structural unit (a homeo-prospero domain), in which the prospero domain region is in position to contribute to DNA binding and also to mask a defined nuclear export signal that is within the putative homeodomain region. It is proposed that the homeo-prospero domain coordinately regulates prospero nuclear localisation and DNA binding specificity [].Prospero is a large Drosophila transcription factor protein that is expressed in all neural lineages of Drosophila embryos. It is needed for correct expression of several neural proteins and in determining the cell fates of neural stem cells. Homologues of prospero are found in a wide range of animals including humans with the highest level of similarity being found in the C-terminal 160 amino acids. This region was identified as containing an atypical homeobox domain followed by a prospero domain. However, the structure shows that these two regions form a single stable structural domain as defined here []. This homeo-prospero domain binds to DNA.
The paired domain is a ~126 amino acid DNA-binding domain, which is found in eukaryotic transcription regulatory proteins involved in embryogenesis. The domain was originally described as the 'paired box' in the Drosophila protein paired (prd) [, ]. The paired DNA-binding domain is generally located in the N-terminal part. An octapeptide []and/or a homeodomain can occur C-terminal to the paired DNA-binding domain, as well as a Pro-Ser-Thr-rich C-terminal. Paired DNA-binding domain proteins can function as transcription repressors or activators. The paired DNA-binding domain contains three subdomains, which show functional differences in DNA-binding.The crystal structures of prd and Pax proteins show that the DNA-bound paired domain is bipartite, consisting of an N-terminal subdomain (PAI or NTD) and a C-terminal subdomain (RED or CTD), connected by a linker. PAI and RED each form a three-helical fold, with the most C-terminal helicescomprising a helix-turn-helix (HTH) motif that binds the DNA major groove. In addition, the PAI subdomain encompasses an N-terminal β-turn andβ-hairpin, also named 'wing', participating in DNA-binding. The linker can bind into the DNA minor groove. Different Pax proteins and their alternatively spliced isoforms use different (sub)domains for DNA-binding to mediate the specificity of sequence recognition [, ].This entry represents the paired DNA-binding domain. This conserved region spans the DNA-binding HTH located in the N-terminal subdomain.
The ERM family consists of three closely-related proteins, ezrin, radixin and moesin []. Ezrin was first identified as a constituent of microvilli [], radixin as a barbed, end-capping actin-modulating protein from isolated junctional fractions [], and moesin as a heparin binding protein [], which is particularly important in immunity acting on both T and B-cells homeostasis and self-tolerance [, ]. Members of this family have been associated with axon-associated Schwann cell (SC) motility and the maintenance of the polarity of these cells []. A tumour suppressor molecule responsible for neurofibromatosis type 2 (NF2) is highly similar to ERM proteins and has been designated merlin (moesin-ezrin-radixin-like protein) []. ERM molecules contain 3 domains, an N-terminal globular domain, an extended α-helical domain and a charged C-terminal domain []. Ezrin, radixin and merlin also contain a polyproline region between the helical and C-terminal domains. The N-terminal domain is highly conserved, and is also found in merlin, band 4.1 proteins and members of the band 4.1 superfamily, designated the FERM domain []. ERM proteins crosslink actin filaments with plasma membranes. They co-localise with CD44 at actin filament plasma membrane interaction sites, associating with CD44 via their N-terminal domains and with actin filaments via their C-terminal domains []. The α-helical region is involved in intramolecular masking of protein-protein interaction sites which regulates the activity of this proteins [].This entry represents the C-terminal domain of ERM family of proteins which corresponds to the actin-binding tail domain [, ].
The core of the bacterial RNA polymerase (RNAP) consists of four subunits, two alpha, a beta and a beta', which are conserved from bacteria to mammals. The alpha subunit (RpoA) initiates RNAP assembly by dimerising to form a platform on which the beta subunits can interact. The alpha subunit consists of a N-terminal domain (NTD) and a C-terminal domain (CTD), connected by a short linker. The NTD is essential for RNAP assembly, while the CTD is necessary for transcription regulation, interacting with transcription factors and promoter upstream elements. In Escherichia coli, the catabolite activator protein (CAP or CRP) was shown to exert its effect through its interactions with the CTD, where CAP binding to CTD promotes RNAP binding to promoter DNA, thereby stimulating transcription initiation at class I CAP-dependent promoters. At class II CAP-dependent promoters, the interaction of CAP with CTD is one of multiple interactions involved in activation [].The CTD has a compact structure of four helices and two long arms enclosing its hydrophobic core, making its folding topology distinct from most other binding proteins. The upstream promoter element-binding site is formed from helices 1 and 4 [].
RNA cyclases are a family of RNA-modifying enzymes that are conserved in eukaryotes, bacteria and archaea. RNA 3'-terminal phosphate cyclase () [, ]catalyses the conversion of 3'-phosphate to a 2',3'-cyclic phosphodiester at the end of RNA.ATP + RNA 3'-terminal-phosphate = AMP + diphosphate + RNA terminal-2',3'-cyclic-phosphateThese enzymes might be responsible for production of the cyclic phosphate RNA ends that are known to be required by many RNA ligases in both prokaryotes and eukaryotes.RNA cyclase is a protein of from 36 to 42kDa. The best conserved region is aglycine-rich stretch of residues located in the central part of the sequence and which is reminiscent of various ATP, GTP or AMP glycine-rich loops.The crystal structure of RNA 3'-terminal phosphate cyclase shows that each molecule consists of two domains. The larger domain contains three repeats of a folding unit comprising two parallel alpha helices and a four-stranded beta sheet; this fold was previously identified in translation initiation factor 3 (IF3). The large domain is similar to one of the two domains of 5-enolpyruvylshikimate-3-phosphate synthase and UDP-N-acetylglucosamine enolpyruvyl transferase. The smaller insert domain disrupts the large domain, and uses a similar secondary structure element with different topology, observed in many other proteins such as thioredoxin []. Although the active site of this enzyme could not be unambiguously assigned, it can be mapped to a region surrounding His309, an adenylate acceptor, in which a number of amino acids are highly conserved in the enzyme from different sources []. This entry represents the small insert domain that interrupts the large repetitive domain.
The chlamydial inclusion membrane is extensively modified by the insertion of type III secreted effector proteins []. These inclusion membrane proteins (Incs) have two major characteristics: an N-terminal type III secretion signal that is necessary for their secretion out of the bacterium and a hydrophobic region consisting of at least two trans-membrane helices that allows insertion into the inclusion membrane. Generally, both the N- and C-terminal regions of the Inc are exposed to the host cell cytosol [].This family has members such as the IncE (also known as CT116) proteins found in Chlamydia trachomatis. IncE Interacts with Retromer-Associated Sorting Nexins (SNXs) directly binding the PX-domains of SNX5/6. It is expressed within the first 2 hours of C. trachomatis infection. IncE region 101-132 is the binding site for SNX5/6 causing re-localization of SNX5/6 from endosomes to the inclusion membrane. IncE101-132 expression was shown to be sufficient to maintain CI-MPR (Cation-Independent Mannose-6-Phosphate Receptor) in retromer-containing compartments, thereby disrupting efficient CI-MPR trafficking to the trans-Golgi. It has been suggested that SNX5/6 bind directly to IncE independently of phosphoinositides and that the predicted IncE C-terminal β-hairpin is required. IncE-mediated sequestration of retromer SNX-BAR proteins may promote Golgi fragmentation, a process that facilitates lipid acquisition by C. trachomatis and enhances progeny production [].
Formylmethanofuran:tetrahyromethanopterin formyltransferase (Ftr) is involved in C1 metabolism in methanogenic archaea, sulphate-reducing archaea and methylotrophic bacteria. It catalyses the following reversible reaction:N-formylmethanofuran + 5,6,7,8-tetrahydromethanopterin = methanofuran + 5-formyl-5,6,7,8-tetrahydromethanopterinFtr from the thermophilic methanogen Methanopyrus kandleri (optimum growth temperature 98 degrees C) is a hyperthermophilic enzyme that is absolutely dependent on the presence of lyotropic salts for activity and thermostability. The crystal structure of Ftr reveals a homotetramer composed essentially of two dimers. Each subunit is subdivided into two tightly associated lobes both consisting of a predominantly antiparallel beta sheet flanked by alpha helices forming an alpha/beta sandwich structure. The approximate location of the active site was detected in a region close to the dimer interface []. Ftr from the mesophilic methanogen Methanosarcina barkeri and the sulphate-reducing archaeon Archaeoglobus fulgidus have a similar structure [].In the methylotrophic bacterium Methylobacterium extorquens, Ftr interacts with three other polypeptides to form an Ftr/cyclohydrolase complex which catalyses the hydrolysis of formyl-tetrahydromethanopterin to formate during growth on C1 substrates [].This superfamily represents two ferredoxin-like domains found in Ftr.
Kelch is a 50-residue motif, named after the Drosophila mutant in which it was first identified []. This sequence motif represents one β-sheet blade, and several of these repeats can associate to form a β-propeller. For instance, the motif appears 6 times in Drosophila egg-chamber regulatory protein (also known as ring canal kelch protein), creating a 6-bladed β-propeller. The motif is also found in mouse protein MIPP []and in a number of poxviruses. In addition, kelch repeats have been recognised in alpha- and beta-scruin [, ], and in galactose oxidase from the fungus Dactylium dendroides [, ]. The structure of galactose oxidase reveals that the repeated sequence corresponds to a 4-stranded antiparallel β-sheet motif that forms the repeat unit in a super-barrel structural fold [].The known functions of kelch-containing proteins are diverse: scruin is an actin cross-linking protein; galactose oxidase catalyses the oxidation of the hydroxyl group at the C6 position in D-galactose; and kelch may have a cytoskeletal function, as it is localised to the actin-rich ring canals that connect the 15 nurse cells to the developing oocyte in Drosophila []. Nevertheless, based on the location of the kelch pattern in the catalytic unit in galactose oxidase, functionally important residues have been predicted in glyoxal oxidase [].This entry represents a type of kelch sequence motif that comprises one β-sheet blade.
PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. PI3Ks play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation and apoptosis [, ]. They can be divided into three main classes (I, II, and III), defined by their substrate specificity, regulation, and domain structure. Class I PI3Ks are the only enzymes capable of converting PtdIns(4,5)P2 to the critical second messenger PtdIns(3,4,5)P3. Class I enzymes are heterodimers and exist in multiple isoforms consisting of one catalytic subunit (out of four isoforms) and one of several regulatory subunits []. Class II PI3Ks comprise three catalytic isoforms that do not associate with any regulatory subunits. They selectively use PtdIns as a substrate to produce PtsIns(3)P []. Class III PI3K was first identified as a vacuolar sorting protein in yeast known as Vps34. Unlike other PI3Ks, the Vps34 lipid kinase specifically utilizes phosphatidylinositol as a substrate, producing the single lipid product PtdIns3P [].
The cyanobacterial clock proteins KaiA, KaiB and SasA are proposed as regulators of the circadian rhythm in cyanobacteria [, ]. Mutations in both proteins have been reported to alter or abolish circadian rhythmicity. KaiB adopts an α-β meander motif and is found to be a dimer []. KaiB was originally discovered from the cyanobacterium Synechococcus as part of the circadian clock gene cluster, kaiABC. KaiB attenuates KaiA-enhanced KaiC autokinase activity by interacting with KaiA-KaiC complexes in a circadian fashion [, ]. KaiB is membrane-associated as well as cytosolic. The amount of membrane-associated protein peaks in the evening (at circadian time (CT) 12-16) while the cytosolic form peaks later (at CT 20). The rhythmic localization of KaiB may function in regulating the formation of Kai complexes. SasA is a sensory histidine kinase which associates with KaiC []. Although it is not an essential oscillator component, it is important in enhancing kaiABC expression and is important in metabolic growth control under day/night cycle conditions. SasA contains an N-terminal sensory domain with a TRX fold which is involved in the SasA-KaiC interaction []. This domain shows high sequence similarity with KaiB []. However, the KaiB structure does not show a classical TRX fold. The N-terminal half of KaiB shares the same beta-α-β topology as TRX, but the topology of its C-terminal half diverges.
This is a family of nucleoporins conserved from yeast to human.Nup85 Nucleoporin is an essential component of the nuclear pore complex (NPC) that seems to be required for NPC assembly and maintenance. As part of the NPC Nup107-160 subcomplex plays a role in RNA export and in tethering NUP98/Nup98 and NUP153 to the nucleus. The Nup107-160 complex seems to be required for spindle assembly during mitosis. NUP85 is required for membrane clustering of CCL2-activated CCR2. Seems to be involved in CCR2-mediated chemotaxis of monocytes and may link activated CCR2 to the phosphatidyl-inositol-3-kinase-Rac-lammellipodium protrusion cascade [, , ]. The Nup84 complex is composed of one copy each of Nup84, Nup85, Nup120, Nup133, Nup145C, Sec13, and Seh1. The structure of a complex of Nup85 and Seh1 was solved []. The N terminus of Nup85 is inserted and forms a three-stranded blade that completes the Seh1 6-bladed β-propeller in trans. Following its N-terminal insertion blade, Nup85 forms a compact cuboid structure composed of 20 helices, with two distinct modules, referred to as crown and trunk [].
Pyridoxamine 5'-phosphate oxidase (PNPOx; ) is a FMN flavoprotein that catalyses the oxidation of pyridoxamine-5-P (PMP) and pyridoxine-5-P (PNP) to pyridoxal-5-P (PLP). This reaction serves as the terminal step in the de novo biosynthesis of PLP in Escherichia coli and as a part of the salvage pathway of this coenzyme in both E. coli and mammalian cells [, ]. The binding sites for FMN and for substrate have been highly conserved throughout evolution.This entry represents a domain with putative PNPOx (Pyridoxamine 5'-phosphate oxidase) function. The domain was initially predicted to encode pyridoxamine 5'-phosphate oxidase, based on sequence similarity. However, there is no experimental data to validate the predicted activity and purified proteins, such as and its paralogs, do not possess this activity, nor do they bind to flavin mononucleotide (FMN). To date, the only time functional oxidase activity has been experimentally demonstrated is when the sequences contain both and . Moreover, some of the family members that contain both domains have been shown to be involved in phenazine biosynthesis. While some molecular function has been experimentally validated for the proteins containing both domains, the role performed by each domain on its own is unknown [].
Metallothioneins (MT) are small proteins that bind heavy metals, such as zinc, copper, cadmium, nickel, etc. They have a high content of cysteine residues that bind the metal ions through clusters of thiolate bonds [, ]. An empirical classification into three classes has been proposed by Fowler and coworkers []and Kojima []. Members of class I are defined to include polypeptides related in the positions of their cysteines to equine MT-1B, and include mammalian MTs as well as from crustaceans and molluscs. Class II groups MTs from a variety of species, including sea urchins,fungi, insects and cyanobacteria. Class III MTs are atypical polypeptides composed of gamma-glutamylcysteinyl units [].This original classification system has been found to be limited, in the sense that it does not allow clear differentiation of patterns of structural similarities, either between or within classes. Subsequently, a new classification was proposed on the basis of sequence similarity derived from phylogenetic relationships, which basically proposes an MT family for each main taxonomic group of organisms []. This superfamily represents the domain found in vertebrates [].
The chorismate synthase AroC consists of two DCoH-like beta(2)-α-β(2)-alpha structural repeats.Chorismate synthase (CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; 1-carboxyvinyl-3-phosphoshikimate phosphate-lyase; E.C. 4.2.3.5) catalyzes the seventh and final step in the shikimate pathway which is used in prokaryotes, fungi and plants for the biosynthesis of aromatic amino acids. It catalyzes the 1,4-trans elimination of the phosphate group from 5-enolpyruvylshikimate-3-phosphate (EPSP) to form chorismate which can then be used in phenylalanine, tyrosine or tryptophan biosynthesis. Chorismate synthase requires the presence of a reduced flavin mononucleotide (FMNH2 or FADH2) for its activity. Chorismate synthase from various sources shows a high degree of sequence conservation [, ]. It is a protein of about 360 to 400 amino-acid residues.Depending on the capacity of these enzymes to regenerate the reduced form of FMN, chorismate synthases are divided into two groups: enzymes, mostly from plants and eubacteria, that sequester CS from the cellular environment, are monofunctional, while those that can generate reduced FMN at the expense of NADPH, such as found in fungi and the ciliated protozoan Euglena gracilis, are bifunctional, having an additional NADPH:FMN oxidoreductase activity. Recently, bifunctionality of the Mycobacterium tuberculosis enzyme (MtCS) was determined by measurements of both chorismate synthase and NADH:FMN oxidoreductase activities. Since shikimate pathway enzymes are present in bacteria, fungi and apicomplexan parasites (such as Toxoplasma gondii, Plasmodium falciparum, and Cryptosporidium parvum) but absent in mammals, they are potentially attractive targets for the development of new therapy against infectious diseases such as tuberculosis (TB) [, , , , , , , , , ].
Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector binding or oligomerisation domain at the C terminus. The winged-helix DNA-binding domain is well conserved in structure for the whole of the GntR family (), and is similar in structure to other transcriptional regulator families. The C-terminal effector-binding and oligomerisation domains are more variable and are consequently used to define the subfamilies. Based on the sequence and structure of the C-terminal domains, the GtnR family can be divided into four major groups, as represented by FadR (), HutC, MocR and YtrA, as well as some minor groups such as those represented by AraR and PlmA [].This entry represents the C-terminal ligand binding domain of many members of the GntR family. This domain probably binds to a range of effector molecules that regulate the transcription of genes through the action of the N-terminal DNA-binding domain. This domain is found in and that are regulators of sugar biosynthesis operons.
RNA cyclases are a family of RNA-modifying enzymes that are conserved in eukaryotes, bacteria and archaea. Type 1 RNA 3'-terminal phosphate cyclases () [, ]catalyse the conversion of 3'-phosphate to a 2',3'-cyclic phosphodiester at the end of RNA:ATP + RNA 3'-terminal-phosphate = AMP + diphosphate + RNA terminal-2',3'-cyclic-phosphateThe physiological function of the cyclase is not known, but the enzyme could be involved in the maintenance of cyclic ends in tRNA splicing intermediates or in the cyclisation of the 3' end of U6 snRNA [].A second subfamily of RNA 3'-terminal phosphate cyclases (type 2) that do not have cyclase activity have been identified in eukaryotes. They are localised to the nucleolus and are involved in ribosomal modification [].The crystal structure of RNA 3'-terminal phosphate cyclase shows that each molecule consists of two domains. The larger domain contains three repeats of a folding unit comprising two parallel alpha helices and a four-stranded beta sheet; this fold was previously identified in translation initiation factor 3 (IF3). The large domain is similar to one of the two domains of 5-enolpyruvylshikimate-3-phosphate synthase and UDP-N-acetylglucosamine enolpyruvyl transferase. The smaller domain uses a similar secondary structure element with different topology, observed in many other proteins such as thioredoxin []. Although the active site of this enzyme has not been unambiguously assigned, it can be mapped to a region surrounding His309, an adenylate acceptor, in which a number of amino acids are highly conserved in the enzyme from different sources [].
Uridylate kinases (also known as UMP kinases) are key enzymes in the synthesis of nucleoside triphosphates. They catalyse the reversible transfer of the gamma-phosphoryl group from an ATP donor to UMP, yielding UDP, which is the starting point for the synthesis of all other pyrimidine nucleotides. The eukaryotic enzyme has a dual specificity, phosphorylating both UMP and CMP, while the bacterial enzyme is specific to UMP. The bacterial enzyme shows no sequence similarity to the eukaryotic enzyme or other nucleoside monophosphate kinases, but rather appears to be part of the amino acid kinase family. It is dependent on magnesium for activity and is activated by GTP and repressed by UTP [, ]. In many bacterial genomes, the gene tends to be located immediately downstream of elongation factor T and upstream of ribosome recycling factor. A related protein family, believed to be equivalent in function is found in the archaea and in spirochetes.Structurally, the bacterial and archaeal proteins are homohexamers centred around a hollow nucleus and organised as a trimer of dimers [, ]. Each monomer within the protein forms the amino acid kinase fold and can be divided into an N-terminal region which binds UMP and mediates intersubunit interactions within the dimer, and a C-terminal region which binds ATP and contains a mobile loop covering the active site. Inhibition of enzyme activity by UTP appears to be due to competition for the binding site for UMP, not allosteric inhibition as was previously suspected.This entry represents the archaeal and spirochete proteins.
This entry represents Prokaryotic ubiquitin-like protein Pup from Mycobacterium tuberculosis and similar short proteins, of 50-90 residues in length, predominantly found in Actinobacteria. Pup is covalently conjugated to the e-NH2 groups of lysines on several target proteins (pupylation) such as the malonyl CoA acyl carrier protein (FabD) []. Pupylation of FabD was shown to result in its recruitment to the mycobacterial proteasome and subsequent degradation analogous to eukaryotic ubiquitin-conjugated proteins. Searches recovered Pup orthologous in all major actinobacteria lineages including the basal bifidobacteria and also sporadically in certain other bacterial lineages [].Members of this protein family, formerly known as DUF797, have a conserved motif with a G [EQ]signature at the C terminus and are suitable for conjugation via the terminal glutamate or the deamidated glutamine (as shown in the case of the Mycobacterium Pup []). Pup is structurally unrelated to the ubiquitin fold and has convergently evolved the function of protein modifier. It has a binding-induced folding recognition mechanism that is different from substrate recognition in the ubiquitin-proteasome system []. This protein, intrinsically disordered, links to target proteins via the ligase PafA, acquiring an ordered assembly to form two helices connected by a linker, positioning the C-terminal glutamate in the active site of this ligase [].
Siderophores are low molecular weight iron-chelating compounds synthesised by many bacteria to aid in the aquisition of this vital trace element []. Proteins in this entry are adenylation components of non-ribosomal peptide synthases (NRPSs) involved in the biosynthesis of siderophores. These proteins belong to the AMP-binding family and are mostly thought to activate 2,3-dihydroxybenzoate (DHB) by ligation of AMP from ATP with the release of pyrophosphate (ATP-PPi exchange). Enzymatic studies on the purified enzyme, 2,3DHB-AMP ligase of Escherichia coli, show that 2,3DHB efficiently supports the ATP-PPi exchange while other analogues can replace 2,3DHB, for example: salicyclic acid (o-hydrobenzoate); 2,4DHB and 2,5DHB; though the natural substrate 2,3DHB is by far the most efficient. Substrates such as 2,6DHB and 2,4,6THB do not support the ATP-PPi exchange and suggest significant steric interference by the 6-hyroxy side chain [].The crystal structure of 2,3-dihydroxybenzoate-AMP ligase () from Bacillus subtilis has been examined []. This protein is composed of a large N-terminal domain (~420 aa) and a more compact C-terminal domain (~110 aa), with an overall "hammer-and-anvil"fold similar to that of firefly luciferase []. The active site is located in a deep compartment located at the interface of the domains, with a p-loop thought to be involved in catalysis located at the entrance to the cavity. Relatively little conformational change was observed during catalysis.
Striated fibre assemblin (SFA), an acidic 33kDa protein, is the majorcomponent of striated microtubule-associated fibres (SMAFs) in the flagellarbasal apparatus of green flagellates. In Chlamydomonas, and other greenflagellates, the SMAFs form a cross-like pattern and run alongside theproximal parts of four bundles of flagellar root microtubules.The sequence of SFA contains two structurally distinct domains []. Thehead domain, with ~30 residues, contains all the prolines (3-8 depending onspecies) and is rich in hydroxyamino acids. This non-helical domain isfurther characterised by the presence of repetitive SP-motifs, some of themin the context SP(M/T)R, which is a putative substrate for p34-CDC2 kinase. The rod domain, with ~250 residues, is predicted to be mostly alpha-helical (the α-helix content was estimated to be 76% for the entiremolecule or 85% for the postulated rod domain). This domain shows apronounced coiled-coil-forming ability and contains a 29-residue repeatpattern based on four heptads, followed by a skip residue. The rod domains of SF-assemblin and beta-giardin from protozoan Giardia have the same length and display 42% sequence similarity [, ].
Glucose-fructose oxidoreductase (GFOR) catalyses the formation of D-gluconolactone and D-glucitol from D-glucose and D-fructose. It hasone tightly-bound NADP(H) per enzyme subunit, it exists as a homotetramer,and is one of the pivotal proteins in the sorbitol-gluconate pathway. It istargeted to the periplasm of the Gram-negative cell envelope, and belongs tothe GFO/IDH/MOCA superfamily. First discovered in Zymomonas mobilis, homologues have also been found in Caulobacter crescentus and Deinococcus radiodurans.GFOR is of great interest as its mechanism of secretion into the bacterialperiplasm differs from other precursor proteins of the Twin ArginineTranslocation (TAT) pathway []. Although it exhibits the consensus TAT signal motif (S/T-R-R-x-L-F-K) at its N terminus, unlike other TAT proteins that can be universally secreted across a number of Gram-negative microbes, GFOR is only translocated in Z. mobilis. However, replacing the Z. mobilis signal peptide with one from Escherichia coli restores this function. This observation has led to the suggestion that TAT-dependent precursors are optimally adapted only to their particular cognate secretion apparatus [].Recently, the crystal structure of Z. mobilis GFOR was resolved to 2.5A bymeans of X-ray crystallography. This revealed that the protein indeed exists as a homotetramer, and has 4 active sites. There are 2 distinct domains: a classical dinucleotide binding fold at the N terminus and a 9-stranded β-sheet at the C terminus. NADP(H) is bound to the N terminus of the first α-helix.
Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins. The translocase protein subunits are encoded on the bacterial chromosome.The translocase itself comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecCY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. The chaperone protein SecB []is a highly acidic homotetrameric protein that exists as a "dimer of dimers"in the bacterial cytoplasm. SecB maintains preproteins in an unfolded state after translation, and targets these to the peripheral membrane protein ATPase SecA for secretion [].The tertiary structure of Haemophilus influenzae SecB () was resolved by means of X-ray crystallography to 2.5A []. The chaperone comprises four chains, forming a tetramer, each chain of which has a simple alpha+beta fold arrangement. While one binding site on the homotetramer recognises unfolded polypeptides by hydrophobic interactions, the second binds to SecA through the latter's C-terminal 22 residues.
Stomatin is also known as erythrocyte membrane protein band 7.2b. It is a 31kDa membrane protein [], and was named after the rare human disease: haemolytic anaemia hereditary stomatocytosis. The protein contains a single hydrophobic domain, close to the N terminus, and is phosphorylated [].Stomatin is believed to be involved in regulating monovalent cation transport through lipid membranes. Absence of the protein in hereditary stomatocytosis is believed to be the reason for the leakage of Na+and K+ions into and from erythrocytes [].A second function of stomatin is to act as a cytoskeletal anchor. One possible example of this is its interaction with some anti-malarial drugs. Current opinion speculates that such drugs bind to high density lipoproteins in serum. The lipoproteins are delivered to erythrocytes, where it is believed they Interact with stomatin as a means of transfer to the intracellular parasite, via a pathway used for the uptake of exogenous phospholipid [].Stomatin-like proteins have been identified in various organisms, including Caenorhabditis elegans and Mus musculus.This domain covers a small conserved region located about 110 residues after the transmembrane domain.
This domain is found in a group of homeodomain containing proteins from animals, including PHTF1/2, and is typically between 101 and 140 amino acids in length. PHTF proteins do not display any sequence similarity to known or predicted proteins, but their conservation among species suggests an essential function. The 84kDa Phtf1 protein is an integral membrane protein, anchored to a cell membrane by six to eight trans-membrane domains, that is associated with a domain of the endoplasmic reticulum (ER) juxtaposed to the Golgi apparatus. It is present during meiosis and spermiogenesis, and, by the end of spermiogenesis, is released from the mature spermatozoon within the residual bodies []. PHTF1 enhances the binding of FEM1B -feminisation homologue 1B - to cell membranes. Fem-1 was initially identified in the signaling pathway for sex determination, as well as being implicated in apoptosis, but its biochemical role is still unclear, and neither FEM1B nor PHTF1 is directly implicated in apoptosis in spermatogenesis. It is the ANK domain of FEM1B that is necessary for the interaction with the N-terminal region of PHTF1 [].
Disulfide bond isomerases DsbC and DsbG are V-shaped homodimeric proteins containing a redox active CXXC motif imbedded in a TRX fold. They function as protein disulfide isomerases and chaperones in the bacterial periplasm to correct non-native disulfide bonds formed by DsbA and prevent aggregation of incorrectly folded proteins []. DsbC and DsbG are kept in their reduced stateby the cytoplasmic membrane protein DsbD, which utilizes the TRX/TRX reductase system in the cytosol as a source of reducing equivalents []. DsbG differ from DsbC in that it has a more limited substrate specificity, and it may preferentially act later in the folding process to catalyze disulfide rearrangements in folded or partially folded proteins [, ].Also included in this entry is the predicted protein TrbB, whose gene was sequenced from the enterohemorrhagic E. coli type IV pilus gene cluster, which is required for efficient plasmid transfer. TrbB may be a disulfide bond isomerase that functions in the conjugative process by facilitating proper folding of a subset of F-plasmid-encoded proteins in the periplasm [].
The malate dehydrogenase (MDH) of some extremophiles is more similar to the L-lactate dehydrogenases (L-LDH; ) from various sources than to other MDHs []. The archaebacterial MDH deviates from the eubacterial and eukaryotic enzymes having a low selectivity for the coenzyme (NAD(H) or NADP(H)) and catalysing the reduction of oxaloacetate to malate more efficiently than the reverse reaction []. It has been suggested that this class of dinucleotide cofactor-dependent dehydrogenases do not contain a Rossman-fold motif, as it was prior believed to be the case [].The enzyme is a dimer, where each subunit consists of three domains: domain I, domain II (NADPH binding domain), and domain III. Domain I contains N- and C-terminal regions and consists of the four-helix bundle []. The NADPH binding domain is formed of a seven-stranded antiparallel β-sheet fold [].This superfamily represents an α-helical domain found in bacterial and archaeal enzymes with malate, L-lactate, L-sulpholactate dehydrogenase activities, and related proteins. This domain has a four-helix barrel topology which forms an antiparallel pack, and is different from the typical four-helix bundle.
The CoV Spike (S) protein is an envelope glycoprotein that plays the most important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesised as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains a hydrophobic fusion peptide and two heptad repeat regions. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-terminal domain (C-domain). Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). Most CoVs, including SARS-CoV-2, SARS-CoV, and MERS-CoV use the C-domain to bind their receptors. However, CoV such as mouse hepatitis virus (MHV) uses the NTD to bind its receptor, mouse carcinoembryonic antigen related cell adhesion molecule 1a (mCEACAM1a). The S1 NTD contributes to the Spike trimer interface [, , , , ].This entry represents the RBD domain of Spike protein S1 subunit from SARS-CoV-2, which binds the extracellular peptidase domain of angiotensin-converting enzyme 2 (ACE2). It has been shown that the receptor binding induces the dissociation of the S1 with ACE2, prompting the S2 to transit from a metastable pre-fusion to a more-stable post-fusion state that is essential for membrane fusion [, , , ]. Recent structures revealed that only a single RBD is necessary for ACE2 binding and it is not yet clear if protrusion of the RBD from the S protein trimer is necessary for binding to ACE2 or the interconversion of the RBD between closed and open states represents an intrinsic property of the S protein []. During the pandemic, many amino acid substitutions have been reported in the S1 segment, being D614G the most commonly observed amino acid change from the reference sequence. Although it was estimated to be slightly destabilizing, it was hypothesized that it increases virus infectivity by increasing the total amount of S protein incorporated into virions. The most prevalent RBD substitution in the RBD is the T478I, located in a portion of a loop that contacts ACE2. However, most substitutions in the interface with ACE2 appear to be neutral or destabilizing, with none improving binding affinity [].SARS-CoV-2 RBD has a core formed by a twisted five-stranded antiparallel β-sheet (β1-7) with short helices and loops connecting them. Between the β4 and β7 strands in the core, there is an extended insertion, the receptor-binding motif (RBM), containing the short β5 and β6 strands, α4 and α5 helices and loops, which contains most of the contacting residues for binding to ACE2. There are nine cysteine residues in the RBD, eight of which form four pairs of disulfide bonds. Among these four pairs, three are in the core which help to stabilise the β-sheet structure, while the remaining pair connects the loops in the distal end of the RBM [].
This entry represents the predicted archaeal type glutamate synthase large subunit, which includes stand-alone proteins corresponding to the N-terminal, FMN-binding, and the C-terminal domains of the large subunit. All members in this entry contain the FMN-binding domain and some have 1-3 copies of 4Fe-4S binding domain in the N-terminal region but they lack the linker domain, found in the bacterial glutamate synthase large subunit [, ].The large (alpha, GltB) subunit of bacterial glutamate synthase (GOGAT) consists of three domains. represents a stand-alone version of the central domain, and this subgoup contains proteins that are predicted to function as part of GOGAT. This stand-alone form occurs in the archaeal type of GOGAT, where the large subunit is represented by three separate proteins, corresponding to the three domains of the "standard"bacterial enzyme []. Similar organization of GOGAT with stand-alone domains has been found in some bacteria (e.g., Sinorhizobium meliloti, Thermotoga maritima), but its function is not clear in those organisms where the "standard"bacterial form is also present (e.g., Sinorhizobium meliloti).The second (central) domain of the bacterial GOGAT large subunit consists of a linker domain and the FMN-binding domain (). The FMN-binding domain has a beta/alpha barrel topology. In this domain, the 2-iminoglutarate intermediate, formed upon the addition of ammonia onto 2-oxoglutarate, is reduced by the FMN cofactor producing the second molecule of L-glutamate []. This domain also contains the enzyme 3Fe-4S cluster [].Originally, only the ORF encoding the central domain of GOGAT was recognised and annotated as GltB in archaea, and the rest of the large subunit was thought to be missing, which may lead to some misannotations []. This led to speculations that the archaeal form of the GOGAT large subunit is the ancestral minimum form of the enzyme. Later analysis showed, however, that in all archaea where the large subunit has been found, its entire sequence is represented by three separate ORFs [].Glutamate synthase (GOGAT, GltS) is a complex iron-sulphur flavoprotein that catalyses the reductive synthesis of L-glutamate from 2-oxoglutarate (2-OG) and L-glutamine via intramolecular channeling of ammonia, a reaction in the bacterial, yeast and plant pathways for ammonia assimilation []. GOGAT is a multifunctional enzyme that functions through three distinct active centres carrying out multiple reaction steps: L-glutamine hydrolysis, conversion of 2-oxoglutarate into L-glutamate, and electron uptake from an electron donor [].There are four classes of GOGAT [, ]: 1. Bacterial NADPH-dependent GOGAT (NADPH-GOGAT, ). This standard bacterial NADPH-GOGAT is composed of a large (alpha, GltB) subunit and a small (beta, GltD) subunit.2. Ferredoxin-dependent form in cyanobacteria and plants (Fd-GOGAT from photosynthetic cells, ) displays a single-subunit structure corresponding to the large bacterial subunit.3. Pyridine-linked form in both photosynthetic and nonphotosynthetic eukaryotes (eukaryotic GOGAT or NADH-GOGAT, ) displays a single-subunit structure corresponding to the fusion of the small and the large bacterial subunits ().4. The archaeal type with stand-alone proteins corresponding to the N-terminal, FMN-binding, and the C-terminal domains of the large subunit [, ](, , ), and to the small subunit.
RNA (C5-cytosine) methyltransferases (RCMTs) catalyse the transfer of a methyl group to the 5th carbon of a cytosine base in RNA sequences to produce C5-methylcytosine. RCMTs use the cofactor S-adenosyl-L-methionine (SAM) as a methyl donor []. The catalytic mechanism of RCMTs involves an attack by the thiolate of a Cys residue on position 6 of the target cytosine base to form a covalent link, thereby activating C5 for methyl-group transfer. Following the addition of the methyl group, a second Cys residue acts as a general base in the beta-elimination of the proton from the methylated cytosine ring. The free enzyme is restored and the methylated product is released [].Numerous putative RCMTs have been identified in archaea, bacteria and eukaryota [, ]; most are predicted to be nuclear or nucleolar proteins []. The Escherichia coli Ribosomal RNA Small-subunit Methyltransferase Beta (RSMB) FMU (FirMicUtes) represents the first protein identified and characterised as a cytosine-specific RNA methyltransferase. RSMB was reported to catalyse the formation of C5-methylcytosine at position 967 of 16S rRNA [, ].A classification of RCMTs has been proposed on the basis of sequence similarity []. According to this classification, RCMTs are divided into 8 distinct subfamilies []. Recently, a new RCMT subfamily, termed RCMT9, was identified []. Members of the RCMT contain a core domain, responsible for the cytosine-specific RNA methyltransferase activity. This 'catalytic' domain adopts the Rossman fold for the accommodation of the cofactor SAM []. The RCMT subfamilies are also distinguished by N-terminal and C-terminal extensions, variable both in size and sequence [].The rRNA small subunit methyltransferase B (RsmB) protein, often referred to as Fmu, has been demonstrated to methylate only C967 of the 16S ribosomal RNA and to produce only m5C at that position []. The structure of the E. coli protein has been determined []. It contains three subdomains which share structural homology to DNA m5C methyltransferases and two RNA binding protein families. The N-terminal sequence shares homology to another (noncatalytic) RNA binding protein, e.g. the ribosomal RNA antiterminator protein NusB (). The catalytic lobe of the N1 domain, comprises the conserved core identified in all of the putative RNA m5C MTase sequences. Although the N1 domain is structurally homologous to known RNA binding proteins, there is no clear sequence motif that defines its role in RNA binding and recognition. At the functional centre of the catalytic lobe is the MTase domain of Fmu (residues 232-429), which adopts a fold typical of known AdoMet-dependent methyltransferases. In spite of the lack of a conserved RNA binding motif in the N1 domain, the close association of the N1 and MTase domains suggest that any RNA bound in the active site of the MTase domain is likely to interact with the N1 domain.Theis entry is specific for the enterobacterial RsmB proteins.
Cytochrome P450 enzymes are a superfamily of haem-containing mono-oxygenases that are found in all kingdoms of life, and which show extraordinary diversity in their reaction chemistry. In mammals, these proteins are found primarily in microsomes of hepatocytes and other cell types, where they oxidise steroids, fatty acids and xenobiotics, and are important for the detoxification and clearance of various compounds, as well as for hormone synthesis and breakdown, cholesterol synthesis and vitamin D metabolism. In plants, these proteins are important for the biosynthesis of several compounds such as hormones, defensive compounds and fatty acids. In bacteria, they are important for several metabolic processes, such as the biosynthesis of antibiotic erythromycin in Saccharopolyspora erythraea (Streptomyces erythraeus).Cytochrome P450 enzymes use haem to oxidise their substrates, using protons derived from NADH or NADPH to split the oxygen so a single atom can be added to a substrate. They also require electrons, which they receive from a variety of redox partners. In certain cases, cytochrome P450 can be fused to its redox partner to produce a bi-functional protein, such as with P450BM-3 from Bacillus megaterium [], which has haem and flavin domains.Organisms produce many different cytochrome P450 enzymes (at least 58 in humans), which together with alternative splicing can provide a wide array of enzymes with different substrate and tissue specificities. Individual cytochrome P450 proteins follow the nomenclature: CYP, followed by a number (family), then a letter (subfamily), and another number (protein); e.g. CYP3A4 is the fourth protein in family 3, subfamily A. In general, family members should share >40% identity, while subfamily members should share >55% identity.Cytochrome P450 proteins can also be grouped by two different schemes. One scheme was based on a taxonomic split: class I (prokaryotic/mitochondrial) and class II (eukaryotic microsomes). The other scheme was based on the number of components in the system: class B (3-components) and class E (2-components). These classes merge to a certain degree. Most prokaryotes and mitochondria (and fungal CYP55) have 3-component systems (class I/class B) - a FAD-containing flavoprotein (NAD(P)H-dependent reductase), an iron-sulphur protein and P450. Most eukaryotic microsomes have 2-component systems (class II/class E) - NADPH:P450 reductase (FAD and FMN-containing flavoprotein) and P450. There are exceptions to this scheme, such as 1-component systems that resemble class E enzymes [, , ]. The class E enzymes can be further subdivided into five sequence clusters, groups I-V, each of which may contain more than one cytochrome P450 family (eg, CYP1 and CYP2 are both found in group I). The divergence of the cytochrome P450 superfamily into B- and E-classes, and further divergence into stable clusters within the E-class, appears to be very ancient, occurring before the appearance of eukaryotes.This entry represents mitochondrial cytochrome P450 proteins. In the mitochondrial system, cytochrome P450 can be reduced by the 2Fe-2S iron-sulphur protein adrenodoxin, which can accept electrons from NADPH-dependent adrenodoxin reductase. Both adrenodoxin and adrenodoxin reductase are soluble, and located in the mitochondrial matrix.
Cytochrome P450 enzymes are a superfamily of haem-containing mono-oxygenases that are found in all kingdoms of life, and which show extraordinary diversity in their reaction chemistry. In mammals, these proteins are found primarily in microsomes of hepatocytes and other cell types, where they oxidise steroids, fatty acids and xenobiotics, and are important for the detoxification and clearance of various compounds, as well as for hormone synthesis and breakdown, cholesterol synthesis and vitamin D metabolism. In plants, these proteins are important for the biosynthesis of several compounds such as hormones, defensive compounds and fatty acids. In bacteria, they are important for several metabolic processes, such as the biosynthesis of antibiotic erythromycin in Saccharopolyspora erythraea (Streptomyces erythraeus).Cytochrome P450 enzymes use haem to oxidise their substrates, using protons derived from NADH or NADPH to split the oxygen so a single atom can be added to a substrate. They also require electrons, which they receive from a variety of redox partners. In certain cases, cytochrome P450 can be fused to its redox partner to produce a bi-functional protein, such as with P450BM-3 from Bacillus megaterium [], which has haem and flavin domains.Organisms produce many different cytochrome P450 enzymes (at least 58 in humans), which together with alternative splicing can provide a wide array of enzymes with different substrate and tissue specificities. Individual cytochrome P450 proteins follow the nomenclature: CYP, followed by a number (family), then a letter (subfamily), and another number (protein); e.g. CYP3A4 is the fourth protein in family 3, subfamily A. In general, family members should share >40% identity, while subfamily members should share >55% identity.Cytochrome P450 proteins can also be grouped by two different schemes. One scheme was based on a taxonomic split: class I (prokaryotic/mitochondrial) and class II (eukaryotic microsomes). The other scheme was based on the number of components in the system: class B (3-components) and class E (2-components). These classes merge to a certain degree. Most prokaryotes and mitochondria (and fungal CYP55) have 3-component systems (class I/class B) - a FAD-containing flavoprotein (NAD(P)H-dependent reductase), an iron-sulphur protein and P450. Most eukaryotic microsomes have 2-component systems (class II/class E) - NADPH:P450 reductase (FAD and FMN-containing flavoprotein) and P450. There are exceptions to this scheme, such as 1-component systems that resemble class E enzymes [, , ]. The class E enzymes can be further subdivided into five sequence clusters, groups I-V, each of which may contain more than one cytochrome P450 family (eg, CYP1 and CYP2 are both found in group I). The divergence of the cytochrome P450 superfamily into B- and E-classes, and further divergence into stable clusters within the E-class, appears to be very ancient, occurring before the appearance of eukaryotes.This family also includes germacrene A hydroxylase (GAO1; ) from plants such as lettuce (Lactuca sativa). GAO1 is required for the biosynthesis of germacrene-derived sesquiterpene lactones, which are characteristic natural products in members of the Asteraceae [].
Cytochrome P450 enzymes are a superfamily of haem-containing mono-oxygenases that are found in all kingdoms of life, and which show extraordinary diversity in their reaction chemistry. In mammals, these proteins are found primarily in microsomes of hepatocytes and other cell types, where they oxidise steroids, fatty acids and xenobiotics, and are important for the detoxification and clearance of various compounds, as well as for hormone synthesis and breakdown, cholesterol synthesis and vitamin D metabolism. In plants, these proteins are important for the biosynthesis of several compounds such as hormones, defensive compounds and fatty acids. In bacteria, they are important for several metabolic processes, such as the biosynthesis of antibiotic erythromycin in Saccharopolyspora erythraea (Streptomyces erythraeus).Cytochrome P450 enzymes use haem to oxidise their substrates, using protons derived from NADH or NADPH to split the oxygen so a single atom can be added to a substrate. They also require electrons, which they receive from a variety of redox partners. In certain cases, cytochrome P450 can be fused to its redox partner to produce a bi-functional protein, such as with P450BM-3 from Bacillus megaterium [], which has haem and flavin domains.Organisms produce many different cytochrome P450 enzymes (at least 58 in humans), which together with alternative splicing can provide a wide array of enzymes with different substrate and tissue specificities. Individual cytochrome P450 proteins follow the nomenclature: CYP, followed by a number (family), then a letter (subfamily), and another number (protein); e.g. CYP3A4 is the fourth protein in family 3, subfamily A. In general, family members should share >40% identity, while subfamily members should share >55% identity.Cytochrome P450 proteins can also be grouped by two different schemes. One scheme was based on a taxonomic split: class I (prokaryotic/mitochondrial) and class II (eukaryotic microsomes). The other scheme was based on the number of components in the system: class B (3-components) and class E (2-components). These classes merge to a certain degree. Most prokaryotes and mitochondria (and fungal CYP55) have 3-component systems (class I/class B) - a FAD-containing flavoprotein (NAD(P)H-dependent reductase), an iron-sulphur protein and P450. Most eukaryotic microsomes have 2-component systems (class II/class E) - NADPH:P450 reductase (FAD and FMN-containing flavoprotein) and P450. There are exceptions to this scheme, such as 1-component systems that resemble class E enzymes [, , ]. The class E enzymes can be further subdivided into five sequence clusters, groups I-V, each of which may contain more than one cytochrome P450 family (eg, CYP1 and CYP2 are both found in group I). The divergence of the cytochrome P450 superfamily into B- and E-classes, and further divergence into stable clusters within the E-class, appears to be very ancient, occurring before the appearance of eukaryotes.This entry represents class B cytochrome P450 proteins, which are part of 3-component systems in bacteria, mitochondria and certain fungal enzymes.
Cytochrome P450 enzymes are a superfamily of haem-containing mono-oxygenases that are found in all kingdoms of life, and which show extraordinary diversity in their reaction chemistry. In mammals, these proteins are found primarily in microsomes of hepatocytes and other cell types, where they oxidise steroids, fatty acids and xenobiotics, and are important for the detoxification and clearance of various compounds, as well as for hormone synthesis and breakdown, cholesterol synthesis and vitamin D metabolism. In plants, these proteins are important for the biosynthesis of several compounds such as hormones, defensive compounds and fatty acids. In bacteria, they are important for several metabolic processes, such as the biosynthesis of antibiotic erythromycin in Saccharopolyspora erythraea (Streptomyces erythraeus).Cytochrome P450 enzymes use haem to oxidise their substrates, using protons derived from NADH or NADPH to split the oxygen so a single atom can be added to a substrate. They also require electrons, which they receive from a variety of redox partners. In certain cases, cytochrome P450 can be fused to its redox partner to produce a bi-functional protein, such as with P450BM-3 from Bacillus megaterium [], which has haem and flavin domains.Organisms produce many different cytochrome P450 enzymes (at least 58 in humans), which together with alternative splicing can provide a wide array of enzymes with different substrate and tissue specificities. Individual cytochrome P450 proteins follow the nomenclature: CYP, followed by a number (family), then a letter (subfamily), and another number (protein); e.g. CYP3A4 is the fourth protein in family 3, subfamily A. In general, family members should share >40% identity, while subfamily members should share >55% identity.Cytochrome P450 proteins can also be grouped by two different schemes. One scheme was based on a taxonomic split: class I (prokaryotic/mitochondrial) and class II (eukaryotic microsomes). The other scheme was based on the number of components in the system: class B (3-components) and class E (2-components). These classes merge to a certain degree. Most prokaryotes and mitochondria (and fungal CYP55) have 3-component systems (class I/class B) - a FAD-containing flavoprotein (NAD(P)H-dependent reductase), an iron-sulphur protein and P450. Most eukaryotic microsomes have 2-component systems (class II/class E) - NADPH:P450 reductase (FAD and FMN-containing flavoprotein) and P450. There are exceptions to this scheme, such as 1-component systems that resemble class E enzymes [, , ]. The class E enzymes can be further subdivided into five sequence clusters, groups I-V, each of which may contain more than one cytochrome P450 family (eg, CYP1 and CYP2 are both found in group I). The divergence of the cytochrome P450 superfamily into B- and E-classes, and further divergence into stable clusters within the E-class, appears to be very ancient, occurring before the appearance of eukaryotes.This entry represents class E cytochrome P450 proteins that fall into sequence cluster group II. Group II enzymes are distributed widely in life, i.e., in bacteria (family CYP102), cyanobacteria (CYP110), fungi (CYP52, CYP53 and CYP56), insects (CYP4 and CYP6) and mammals (CYP3, CYP4 and CYP5). Many group II enzymes catalyse hydroxylation of linear chains, such as alkanes (CYP52), alcohols and fatty acids (CYP4, CYP5, CYP102); Aspergillus niger CYP53 carries out para-hydroxylation of benzoate; yeast CYP56 is possibly involved in oxidation of tyrosine residues; insect CYP6 metabolises a wide range of toxic compounds; and members of the CYP3 family are omnivorous.
Cytochrome P450 enzymes are a superfamily of haem-containing mono-oxygenases that are found in all kingdoms of life, and which show extraordinary diversity in their reaction chemistry. In mammals, these proteins are found primarily in microsomes of hepatocytes and other cell types, where they oxidise steroids, fatty acids and xenobiotics, and are important for the detoxification and clearance of various compounds, as well as for hormone synthesis and breakdown, cholesterol synthesis and vitamin D metabolism. In plants, these proteins are important for the biosynthesis of several compounds such as hormones, defensive compounds and fatty acids. In bacteria, they are important for several metabolic processes, such as the biosynthesis of antibiotic erythromycin in Saccharopolyspora erythraea (Streptomyces erythraeus).Cytochrome P450 enzymes use haem to oxidise their substrates, using protons derived from NADH or NADPH to split the oxygen so a single atom can be added to a substrate. They also require electrons, which they receive from a variety of redox partners. In certain cases, cytochrome P450 can be fused to its redox partner to produce a bi-functional protein, such as with P450BM-3 from Bacillus megaterium [], which has haem and flavin domains.Organisms produce many different cytochrome P450 enzymes (at least 58 in humans), which together with alternative splicing can provide a wide array of enzymes with different substrate and tissue specificities. Individual cytochrome P450 proteins follow the nomenclature: CYP, followed by a number (family), then a letter (subfamily), and another number (protein); e.g. CYP3A4 is the fourth protein in family 3, subfamily A. In general, family members should share >40% identity, while subfamily members should share >55% identity.Cytochrome P450 proteins can also be grouped by two different schemes. One scheme was based on a taxonomic split: class I (prokaryotic/mitochondrial) and class II (eukaryotic microsomes). The other scheme was based on the number of components in the system: class B (3-components) and class E (2-components). These classes merge to a certain degree. Most prokaryotes and mitochondria (and fungal CYP55) have 3-component systems (class I/class B) - a FAD-containing flavoprotein (NAD(P)H-dependent reductase), an iron-sulphur protein and P450. Most eukaryotic microsomes have 2-component systems (class II/class E) - NADPH:P450 reductase (FAD and FMN-containing flavoprotein) and P450. There are exceptions to this scheme, such as 1-component systems that resemble class E enzymes [, , ]. The class E enzymes can be further subdivided into five sequence clusters, groups I-V, each of which may contain more than one cytochrome P450 family (eg, CYP1 and CYP2 are both found in group I). The divergence of the cytochrome P450 superfamily into B- and E-classes, and further divergence into stable clusters within the E-class, appears to be very ancient, occurring before the appearance of eukaryotes.This entry represents the CYP2J family from group I, class E, cytochrome P450 proteins, as well as other CYP2 family proteins. The CYP2 family comprises 15 subfamilies (A-H, J-N, P and Q). The first five (A-E) are present in mammalian liver, but in differing amounts and with different inducibilities. These five subfamilies show varied substrate specificities, with some degree of overlap. CYP3A family enzymes are of major importance in the mammalian (especially human) detoxification of xenobiotics. CYP3A4, CYP3A5 and CYP3A7 catalyses the metabolism of a wide variety of substrates, including over 50% of therapeutic drugs. CYP3A enzymes are predominantly (not exclusively) expressed in the liver and intestine. Both genetic and environmental factors such as diet (especially grapefruit and St John's wort) can affect CYP3A activity, which can alter the efficacy and clearance of drugs []. In addition, CYP3A may play a role in breast and prostate carcinogenesis through its role in controlling the level of se hormones drugs [].
Cytochrome P450 enzymes are a superfamily of haem-containing mono-oxygenases that are found in all kingdoms of life, and which show extraordinary diversity in their reaction chemistry. In mammals, these proteins are found primarily in microsomes of hepatocytes and other cell types, where they oxidise steroids, fatty acids and xenobiotics, and are important for the detoxification and clearance of various compounds, as well as for hormone synthesis and breakdown, cholesterol synthesis and vitamin D metabolism. In plants, these proteins are important for the biosynthesis of several compounds such as hormones, defensive compounds and fatty acids. In bacteria, they are important for several metabolic processes, such as the biosynthesis of antibiotic erythromycin in Saccharopolyspora erythraea (Streptomyces erythraeus).Cytochrome P450 enzymes use haem to oxidise their substrates, using protons derived from NADH or NADPH to split the oxygen so a single atom can be added to a substrate. They also require electrons, which they receive from a variety of redox partners. In certain cases, cytochrome P450 can be fused to its redox partner to produce a bi-functional protein, such as with P450BM-3 from Bacillus megaterium [], which has haem and flavin domains.Organisms produce many different cytochrome P450 enzymes (at least 58 in humans), which together with alternative splicing can provide a wide array of enzymes with different substrate and tissue specificities. Individual cytochrome P450 proteins follow the nomenclature: CYP, followed by a number (family), then a letter (subfamily), and another number (protein); e.g. CYP3A4 is the fourth protein in family 3, subfamily A. In general, family members should share >40% identity, while subfamily members should share >55% identity.Cytochrome P450 proteins can also be grouped by two different schemes. One scheme was based on a taxonomic split: class I (prokaryotic/mitochondrial) and class II (eukaryotic microsomes). The other scheme was based on the number of components in the system: class B (3-components) and class E (2-components). These classes merge to a certain degree. Most prokaryotes and mitochondria (and fungal CYP55) have 3-component systems (class I/class B) - a FAD-containing flavoprotein (NAD(P)H-dependent reductase), an iron-sulphur protein and P450. Most eukaryotic microsomes have 2-component systems (class II/class E) - NADPH:P450 reductase (FAD and FMN-containing flavoprotein) and P450. There are exceptions to this scheme, such as 1-component systems that resemble class E enzymes [, , ]. The class E enzymes can be further subdivided into five sequence clusters, groups I-V, each of which may contain more than one cytochrome P450 family (eg, CYP1 and CYP2 are both found in group I). The divergence of the cytochrome P450 superfamily into B- and E-classes, and further divergence into stable clusters within the E-class, appears to be very ancient, occurring before the appearance of eukaryotes.This entry represents class E cytochrome P450 proteins that fall into sequence cluster group I. Group I is richest in members, consisting of cytochrome P450 families CYP1, CYP2, CYP17, CYP21 and CYP71. The members of the first four families are of vertebrate origin, while those from CYP71 are derived from plants. CYP1 and CYP2 enzymes mainly metabolise exogenous substrates, whereas CYP17 and CYP21 are involved in metabolism of endogenous physiologically-active compounds.In the fungus Gibberella, P450 (FUS8) is a component in the biosynthetic pathway for the mycotoxin fusarin C. FUS8 oxidizes carbon C-20 of the intermediate 20-hydroxy-fusarin to form the penultimate intermediate carboxy-fusarin C [].This entry also includes cytochromes P450 (Noroxomaritidine synthases and p-coumarate 3-hydroxylase) that catalyse an intramolecular para-para' C-C phenol coupling of 4'-O-methylnorbelladine in alkaloids biosynthesis, during the biosynthesis of phenylpropanoids and Amaryllidaceae alkaloids including haemanthamine- and crinamine-type alkaloids, promising anticancer agents [, ].
Cytochrome P450 enzymes are a superfamily of haem-containing mono-oxygenases that are found in all kingdoms of life, and which show extraordinary diversity in their reaction chemistry. In mammals, these proteins are found primarily in microsomes of hepatocytes and other cell types, where they oxidise steroids, fatty acids and xenobiotics, and are important for the detoxification and clearance of various compounds, as well as for hormone synthesis and breakdown, cholesterol synthesis and vitamin D metabolism. In plants, these proteins are important for the biosynthesis of several compounds such as hormones, defensive compounds and fatty acids. In bacteria, they are important for several metabolic processes, such as the biosynthesis of antibiotic erythromycin in Saccharopolyspora erythraea (Streptomyces erythraeus).Cytochrome P450 enzymes use haem to oxidise their substrates, using protons derived from NADH or NADPH to split the oxygen so a single atom can be added to a substrate. They also require electrons, which they receive from a variety of redox partners. In certain cases, cytochrome P450 can be fused to its redox partner to produce a bi-functional protein, such as with P450BM-3 from Bacillus megaterium [], which has haem and flavin domains.Organisms produce many different cytochrome P450 enzymes (at least 58 in humans), which together with alternative splicing can provide a wide array of enzymes with different substrate and tissue specificities. Individual cytochrome P450 proteins follow the nomenclature: CYP, followed by a number (family), then a letter (subfamily), and another number (protein); e.g. CYP3A4 is the fourth protein in family 3, subfamily A. In general, family members should share >40% identity, while subfamily members should share >55% identity.Cytochrome P450 proteins can also be grouped by two different schemes. One scheme was based on a taxonomic split: class I (prokaryotic/mitochondrial) and class II (eukaryotic microsomes). The other scheme was based on the number of components in the system: class B (3-components) and class E (2-components). These classes merge to a certain degree. Most prokaryotes and mitochondria (and fungal CYP55) have 3-component systems (class I/class B) - a FAD-containing flavoprotein (NAD(P)H-dependent reductase), an iron-sulphur protein and P450. Most eukaryotic microsomes have 2-component systems (class II/class E) - NADPH:P450 reductase (FAD and FMN-containing flavoprotein) and P450. There are exceptions to this scheme, such as 1-component systems that resemble class E enzymes [, , ]. The class E enzymes can be further subdivided into five sequence clusters, groups I-V, each of which may contain more than one cytochrome P450 family (eg, CYP1 and CYP2 are both found in group I). The divergence of the cytochrome P450 superfamily into B- and E-classes, and further divergence into stable clusters within the E-class, appears to be very ancient, occurring before the appearance of eukaryotes.This entry represents the CYP1 family from group I, class E, cytochrome P450 proteins. CYP1 enzymes mainly metabolise exogenous substrates and are found in mammalia (1A, 1B), bony fishes (1A), sharks, skates, rays (1A) and birds (1A). CYP1A contains five proteins, namely, CYP1A1, 1A2, 1A3, 1A4 and 1A5. CYP1 family members are closely associated with the metabolic activation of pro-carcinogens and mutagens []. For example, CYP1B1 may play an important role in susceptibility to mammary and ovarian cancer through its involvement in oestrogen metabolism [], as well as with various cancers associated with the activation of polycyclic aromatic hydrocarbons in cigarette smoke [].
Cytochrome P450 enzymes are a superfamily of haem-containing mono-oxygenases that are found in all kingdoms of life, and which show extraordinary diversity in their reaction chemistry. In mammals, these proteins are found primarily in microsomes of hepatocytes and other cell types, where they oxidise steroids, fatty acids and xenobiotics, and are important for the detoxification and clearance of various compounds, as well as for hormone synthesis and breakdown, cholesterol synthesis and vitamin D metabolism. In plants, these proteins are important for the biosynthesis of several compounds such as hormones, defensive compounds and fatty acids. In bacteria, they are important for several metabolic processes, such as the biosynthesis of antibiotic erythromycin in Saccharopolyspora erythraea (Streptomyces erythraeus).Cytochrome P450 enzymes use haem to oxidise their substrates, using protons derived from NADH or NADPH to split the oxygen so a single atom can be added to a substrate. They also require electrons, which they receive from a variety of redox partners. In certain cases, cytochrome P450 can be fused to its redox partner to produce a bi-functional protein, such as with P450BM-3 from Bacillus megaterium [], which has haem and flavin domains.Organisms produce many different cytochrome P450 enzymes (at least 58 in humans), which together with alternative splicing can provide a wide array of enzymes with different substrate and tissue specificities. Individual cytochrome P450 proteins follow the nomenclature: CYP, followed by a number (family), then a letter (subfamily), and another number (protein); e.g. CYP3A4 is the fourth protein in family 3, subfamily A. In general, family members should share >40% identity, while subfamily members should share >55% identity.Cytochrome P450 proteins can also be grouped by two different schemes. One scheme was based on a taxonomic split: class I (prokaryotic/mitochondrial) and class II (eukaryotic microsomes). The other scheme was based on the number of components in the system: class B (3-components) and class E (2-components). These classes merge to a certain degree. Most prokaryotes and mitochondria (and fungal CYP55) have 3-component systems (class I/class B) - a FAD-containing flavoprotein (NAD(P)H-dependent reductase), an iron-sulphur protein and P450. Most eukaryotic microsomes have 2-component systems (class II/class E) - NADPH:P450 reductase (FAD and FMN-containing flavoprotein) and P450. There are exceptions to this scheme, such as 1-component systems that resemble class E enzymes [, , ]. The class E enzymes can be further subdivided into five sequence clusters, groups I-V, each of which may contain more than one cytochrome P450 family (eg, CYP1 and CYP2 are both found in group I). The divergence of the cytochrome P450 superfamily into B- and E-classes, and further divergence into stable clusters within the E-class, appears to be very ancient, occurring before the appearance of eukaryotes.This entry represents the CYP2A family from group I, class E, cytochrome P450 proteins, as well as other CYP2 family proteins. The CYP2 family comprises 15 subfamilies (A-H, J-N, P and Q). The first five (A-E) are present in mammalian liver, but in differing amounts and with different inducibilities. These five subfamilies show varied substrate specificities, with some degree of overlap. CYP2A proteins are responsible of metabolising a variety of drugs, which in pigs appears to be gender-dependent (influenced by sex hormones), the highest activity being in females [].
Cytochrome P450 enzymes are a superfamily of haem-containing mono-oxygenases that are found in all kingdoms of life, and which show extraordinary diversity in their reaction chemistry. In mammals, these proteins are found primarily in microsomes of hepatocytes and other cell types, where they oxidise steroids, fatty acids and xenobiotics, and are important for the detoxification and clearance of various compounds, as well as for hormone synthesis and breakdown, cholesterol synthesis and vitamin D metabolism. In plants, these proteins are important for the biosynthesis of several compounds such as hormones, defensive compounds and fatty acids. In bacteria, they are important for several metabolic processes, such as the biosynthesis of antibiotic erythromycin in Saccharopolyspora erythraea (Streptomyces erythraeus).Cytochrome P450 enzymes use haem to oxidise their substrates, using protons derived from NADH or NADPH to split the oxygen so a single atom can be added to a substrate. They also require electrons, which they receive from a variety of redox partners. In certain cases, cytochrome P450 can be fused to its redox partner to produce a bi-functional protein, such as with P450BM-3 from Bacillus megaterium [], which has haem and flavin domains.Organisms produce many different cytochrome P450 enzymes (at least 58 in humans), which together with alternative splicing can provide a wide array of enzymes with different substrate and tissue specificities. Individual cytochrome P450 proteins follow the nomenclature: CYP, followed by a number (family), then a letter (subfamily), and another number (protein); e.g. CYP3A4 is the fourth protein in family 3, subfamily A. In general, family members should share >40% identity, while subfamily members should share >55% identity.Cytochrome P450 proteins can also be grouped by two different schemes. One scheme was based on a taxonomic split: class I (prokaryotic/mitochondrial) and class II (eukaryotic microsomes). The other scheme was based on the number of components in the system: class B (3-components) and class E (2-components). These classes merge to a certain degree. Most prokaryotes and mitochondria (and fungal CYP55) have 3-component systems (class I/class B) - a FAD-containing flavoprotein (NAD(P)H-dependent reductase), an iron-sulphur protein and P450. Most eukaryotic microsomes have 2-component systems (class II/class E) - NADPH:P450 reductase (FAD and FMN-containing flavoprotein) and P450. There are exceptions to this scheme, such as 1-component systems that resemble class E enzymes [, , ]. The class E enzymes can be further subdivided into five sequence clusters, groups I-V, each of which may contain more than one cytochrome P450 family (eg, CYP1 and CYP2 are both found in group I). The divergence of the cytochrome P450 superfamily into B- and E-classes, and further divergence into stable clusters within the E-class, appears to be very ancient, occurring before the appearance of eukaryotes.This entry represents the CYP2B family from group I, class E, cytochrome P450 proteins, as well as other CYP2 family proteins. The CYP2 family comprises 15 subfamilies (A-H, J-N, P and Q). The first five (A-E) are present in mammalian liver, but in differing amounts and with different inducibilities. These five subfamilies show varied substrate specificities, with some degree of overlap. The structure-function relationships of CYP2B4 reveals that substrate specificity of an individual protein is determined by active site residues as well as non-active site residues that modulate conformational changes important for substrate access []. CYP2B proteins have been linked with toxic effects produced by reactive oxygen species (ROS) via a mechanism known as futile cycling in rodent. The likelihood of toxic activation mediated by CYP2B is minimal in man, as the relevant orthologue is poorly expressed in human liver and is only associated with the toxicity of a very small number of carcinogens and cytotoxic agents.
Cytochrome P450 enzymes are a superfamily of haem-containing mono-oxygenases that are found in all kingdoms of life, and which show extraordinary diversity in their reaction chemistry. In mammals, these proteins are found primarily in microsomes of hepatocytes and other cell types, where they oxidise steroids, fatty acids and xenobiotics, and are important for the detoxification and clearance of various compounds, as well as for hormone synthesis and breakdown, cholesterol synthesis and vitamin D metabolism. In plants, these proteins are important for the biosynthesis of several compounds such as hormones, defensive compounds and fatty acids. In bacteria, they are important for several metabolic processes, such as the biosynthesis of antibiotic erythromycin in Saccharopolyspora erythraea (Streptomyces erythraeus).Cytochrome P450 enzymes use haem to oxidise their substrates, using protons derived from NADH or NADPH to split the oxygen so a single atom can be added to a substrate. They also require electrons, which they receive from a variety of redox partners. In certain cases, cytochrome P450 can be fused to its redox partner to produce a bi-functional protein, such as with P450BM-3 from Bacillus megaterium [], which has haem and flavin domains.Organisms produce many different cytochrome P450 enzymes (at least 58 in humans), which together with alternative splicing can provide a wide array of enzymes with different substrate and tissue specificities. Individual cytochrome P450 proteins follow the nomenclature: CYP, followed by a number (family), then a letter (subfamily), and another number (protein); e.g. CYP3A4 is the fourth protein in family 3, subfamily A. In general, family members should share >40% identity, while subfamily members should share >55% identity.Cytochrome P450 proteins can also be grouped by two different schemes. One scheme was based on a taxonomic split: class I (prokaryotic/mitochondrial) and class II (eukaryotic microsomes). The other scheme was based on the number of components in the system: class B (3-components) and class E (2-components). These classes merge to a certain degree. Most prokaryotes and mitochondria (and fungal CYP55) have 3-component systems (class I/class B) - a FAD-containing flavoprotein (NAD(P)H-dependent reductase), an iron-sulphur protein and P450. Most eukaryotic microsomes have 2-component systems (class II/class E) - NADPH:P450 reductase (FAD and FMN-containing flavoprotein) and P450. There are exceptions to this scheme, such as 1-component systems that resemble class E enzymes [, , ]. The class E enzymes can be further subdivided into five sequence clusters, groups I-V, each of which may contain more than one cytochrome P450 family (eg, CYP1 and CYP2 are both found in group I). The divergence of the cytochrome P450 superfamily into B- and E-classes, and further divergence into stable clusters within the E-class, appears to be very ancient, occurring before the appearance of eukaryotes.This entry represents the CYP2D family from group I, class E, cytochrome P450 proteins, as well as other CYP2 family proteins. The CYP2 family comprises 15 subfamilies (A-H, J-N, P and Q). The first five (A-E) are present in mammalian liver, but in differing amounts and with different inducibilities. These five subfamilies show varied substrate specificities, with some degree of overlap. CYP2D6 metabolises several classes of therapeutic drugs, endogenous neurochemicals and toxins, and can be detected in liver, intestine and kidney []. CYP2D6 is non-inducible, and genomic defects in CYP2D6 that inhibit or induce activity can have serious effects with respect to drug efficacy and clearance [].
Cytochrome P450 enzymes are a superfamily of haem-containing mono-oxygenases that are found in all kingdoms of life, and which show extraordinary diversity in their reaction chemistry. In mammals, these proteins are found primarily in microsomes of hepatocytes and other cell types, where they oxidise steroids, fatty acids and xenobiotics, and are important for the detoxification and clearance of various compounds, as well as for hormone synthesis and breakdown, cholesterol synthesis and vitamin D metabolism. In plants, these proteins are important for the biosynthesis of several compounds such as hormones, defensive compounds and fatty acids. In bacteria, they are important for several metabolic processes, such as the biosynthesis of antibiotic erythromycin in Saccharopolyspora erythraea (Streptomyces erythraeus).Cytochrome P450 enzymes use haem to oxidise their substrates, using protons derived from NADH or NADPH to split the oxygen so asingle atom can be added to a substrate. They also require electrons, which they receive from a variety of redox partners. In certain cases, cytochrome P450 can be fused to its redox partner to produce a bi-functional protein, such as with P450BM-3 from Bacillus megaterium [], which has haem and flavin domains.Organisms produce many different cytochrome P450 enzymes (at least 58 in humans), which together with alternative splicing can provide a wide array of enzymes with different substrate and tissue specificities. Individual cytochrome P450 proteins follow the nomenclature: CYP, followed by a number (family), then a letter (subfamily), and another number (protein); e.g. CYP3A4 is the fourth protein in family 3, subfamily A. In general, family members should share >40% identity, while subfamily members should share >55% identity.Cytochrome P450 proteins can also be grouped by two different schemes. One scheme was based on a taxonomic split: class I (prokaryotic/mitochondrial) and class II (eukaryotic microsomes). The other scheme was based on the number of components in the system: class B (3-components) and class E (2-components). These classes merge to a certain degree. Most prokaryotes and mitochondria (and fungal CYP55) have 3-component systems (class I/class B) - a FAD-containing flavoprotein (NAD(P)H-dependent reductase), an iron-sulphur protein and P450. Most eukaryotic microsomes have 2-component systems (class II/class E) - NADPH:P450 reductase (FAD and FMN-containing flavoprotein) and P450. There are exceptions to this scheme, such as 1-component systems that resemble class E enzymes [, , ]. The class E enzymes can be further subdivided into five sequence clusters, groups I-V, each of which may contain more than one cytochrome P450 family (eg, CYP1 and CYP2 are both found in group I).The divergence of the cytochrome P450 superfamily into B- and E-classes, and further divergence into stable clusters within the E-class, appears to be very ancient, occurring before the appearance of eukaryotes.This entry represents the CYP2E family from group I, class E, cytochrome P450 proteins, as well as other CYP2 family proteins. The CYP2 family comprises 15 subfamilies (A-H, J-N, P and Q). The first five (A-E) are present in mammalian liver, but in differing amounts and with different inducibilities. These five subfamilies show varied substrate specificities, with some degree of overlap. CYP2E1 metabolises several therapeutic drugs, precarcinogens and solvents to reactive metabolites, and as such is appears involved in cancer susceptibility [].
Cytochrome P450 enzymes are a superfamily of haem-containing mono-oxygenases that are found in all kingdoms of life, and which show extraordinary diversity in their reaction chemistry. In mammals, these proteins are found primarily in microsomes of hepatocytes and other cell types, where they oxidise steroids, fatty acids and xenobiotics, and are important for the detoxification and clearance of various compounds, as well as for hormone synthesis and breakdown, cholesterol synthesis and vitamin D metabolism. In plants, these proteins are important for the biosynthesis of several compounds such as hormones, defensive compounds and fatty acids. In bacteria, they are important for several metabolic processes, such as the biosynthesis of antibiotic erythromycin in Saccharopolyspora erythraea (Streptomyces erythraeus).Cytochrome P450 enzymes use haem to oxidise their substrates, using protons derived from NADH or NADPH to split the oxygen so a single atom can be added to a substrate. They also require electrons, which they receive from a variety of redox partners. In certain cases, cytochrome P450 can be fused to its redox partner to produce a bi-functional protein, such as with P450BM-3 from Bacillus megaterium [], which has haem and flavin domains.Organisms produce many different cytochrome P450 enzymes (at least 58 in humans), which together with alternative splicing can provide a wide array of enzymes with different substrate and tissue specificities. Individual cytochrome P450 proteins follow the nomenclature: CYP, followed by a number (family), then a letter (subfamily), and another number (protein); e.g. CYP3A4 is the fourth protein in family 3, subfamily A. In general, family members should share >40% identity, while subfamily members should share >55% identity.Cytochrome P450 proteins can also be grouped by two different schemes. One scheme was based on a taxonomic split: class I (prokaryotic/mitochondrial) and class II (eukaryotic microsomes). The other scheme was based on the number of components in the system: class B (3-components) and class E (2-components). These classes merge to a certain degree. Most prokaryotes and mitochondria (and fungal CYP55) have 3-component systems (class I/class B) - a FAD-containing flavoprotein (NAD(P)H-dependent reductase), an iron-sulphur protein and P450. Most eukaryotic microsomes have 2-component systems (class II/class E) - NADPH:P450 reductase (FAD and FMN-containing flavoprotein) and P450. There are exceptions to this scheme, such as 1-component systems that resemble class E enzymes [, , ]. The class E enzymes can be further subdivided into five sequence clusters, groups I-V, each of which may contain more than one cytochrome P450 family (eg, CYP1 and CYP2 are both found in group I). The divergence of the cytochrome P450 superfamily into B- and E-classes, and further divergence into stable clusters within the E-class, appears to be very ancient, occurring before the appearance of eukaryotes.This entry represents the CYP2J family from group I, class E, cytochrome P450 proteins, as well as other CYP2 family proteins. The CYP2 family comprises 15 subfamilies (A-H, J-N, P and Q). The first five (A-E) are present in mammalian liver, but in differing amounts and with different inducibilities. These five subfamilies show varied substrate specificities, with some degree of overlap. Several CYP2J isoforms have been reported, including rabbit CYP2J1; human CYP2J2, the only member of the human CYP2J subfamily known for its role as arachidonic acid epoxygenase and antihistamine drugs are also substrates of it []; rat CYP2J3 and CYP2J4; mouse CYP2J5, CYP2J6, CYP2J7, CYP2J8 and CYP2J9; and rat CYP2J10. Both rat CYP2J3 and human CYP2J2 catalyse vitamin D 25-hydroxylase, but with distinct preferences: rat for vitamin D3 and human for vitamin D2 []. Rat CYP2J4 is expressed in the intestine, where it is active towards all-trans and 9-cis-retinal, producing the corresponding retinoic acids []. Mouse CYP2J5 is abundant in the kidney, where it is active in the metabolism of arachidonic acid to epoxyeicosatrienoic acids, and may be influenced by sex hormones [].
Cytochrome P450 enzymes are a superfamily of haem-containing mono-oxygenases that are found in all kingdoms of life, and which show extraordinary diversity in their reaction chemistry. In mammals, these proteins are found primarily in microsomes of hepatocytes and other cell types, where they oxidise steroids, fatty acids and xenobiotics, and are important for the detoxification and clearance of various compounds, as well as for hormone synthesis and breakdown, cholesterol synthesis and vitamin D metabolism. In plants, these proteins are important for the biosynthesis of several compounds such as hormones, defensive compounds and fatty acids. In bacteria, they are important for several metabolic processes, such as the biosynthesis of antibiotic erythromycin in Saccharopolyspora erythraea (Streptomyces erythraeus).Cytochrome P450 enzymes use haem to oxidise their substrates, using protons derived from NADH or NADPH to split the oxygen so a single atom can be added to a substrate. They also require electrons, which they receive from a variety of redox partners. In certain cases, cytochrome P450 can be fused to its redox partner to produce a bi-functional protein, such as with P450BM-3 from Bacillus megaterium [], which has haem and flavin domains.Organisms produce many different cytochrome P450 enzymes (at least 58 in humans), which together with alternative splicing can provide a wide array of enzymes with different substrate and tissue specificities. Individual cytochrome P450 proteins follow the nomenclature: CYP, followed by a number (family), then a letter (subfamily), and another number (protein); e.g. CYP3A4 is the fourth protein in family 3, subfamily A. In general, family members should share >40% identity, while subfamily members should share >55% identity.Cytochrome P450 proteins can also be grouped by two different schemes. One scheme was based on a taxonomic split: class I (prokaryotic/mitochondrial) and class II (eukaryotic microsomes). The other scheme was based on the number of components in the system: class B (3-components) and class E (2-components). These classes merge to a certain degree. Most prokaryotes and mitochondria (and fungal CYP55) have 3-component systems (class I/class B) - a FAD-containing flavoprotein (NAD(P)H-dependent reductase), an iron-sulphur protein and P450. Most eukaryotic microsomes have 2-component systems (class II/class E) - NADPH:P450 reductase (FAD and FMN-containing flavoprotein) and P450. There are exceptions to this scheme, such as 1-component systems that resemble class E enzymes [, , ]. The class E enzymes can be further subdivided into five sequence clusters, groups I-V, each of which may contain more than one cytochrome P450 family (eg, CYP1 and CYP2 are both found in group I). The divergence of the cytochrome P450 superfamily into B- and E-classes, and further divergence into stable clusters within the E-class, appears to be very ancient, occurring before the appearance of eukaryotes.This entry represents class E cytochrome P450 proteins that fall into sequence cluster group IV. Group IV comprises the CYP7 (cholesterol 7-alpha-hydroxylase) and CYP51 (lanosterol 14-alpha-demethylase) families, which show significant sequence similarity even though there is no apparent functional resemblance. The CYP8 (prostacyclin synthase) family also falls into this group, and shows high sequence similarity to CYP7 members []. Proteins required in the biosynthesis of fungal mycotoxins are also included: cytochrome P450 monooxygenases gloO and gloP from Glarea lozoyensis are required for synthesis of lipohexapeptides of the echinocandin family that prevent fungal cell wall formation by non-competitive inhibition of beta-1,3-glucan synthase [].
Cytochrome P450 enzymes are a superfamily of haem-containing mono-oxygenases that are found in all kingdoms of life, and which show extraordinary diversity in their reaction chemistry. In mammals, these proteins are found primarily in microsomes of hepatocytes and other cell types, where they oxidise steroids, fatty acids and xenobiotics, and are important for the detoxification and clearance of various compounds, as well as for hormone synthesis and breakdown, cholesterol synthesis and vitamin D metabolism. In plants, these proteins are important for the biosynthesis of several compounds such as hormones, defensive compounds and fatty acids. In bacteria, they are important for several metabolic processes, such as the biosynthesis of antibiotic erythromycin in Saccharopolyspora erythraea (Streptomyces erythraeus).Cytochrome P450 enzymes use haem to oxidise their substrates, using protons derived from NADH or NADPH to split the oxygen so a single atom can be added to a substrate. They also require electrons, which they receive from a variety of redox partners. In certain cases, cytochrome P450 can be fused to its redox partner to produce a bi-functional protein, such as with P450BM-3 from Bacillus megaterium [], which has haem and flavin domains.Organisms produce many different cytochrome P450 enzymes (at least 58 in humans), which together with alternative splicing can provide a wide array of enzymes with different substrate and tissue specificities. Individual cytochrome P450 proteins follow the nomenclature: CYP, followed by a number (family), then a letter (subfamily), and another number (protein); e.g. CYP3A4 is the fourth protein in family 3, subfamily A. In general, family members should share >40% identity, while subfamily members should share >55% identity.Cytochrome P450 proteins can also be grouped by two different schemes. One scheme was based on a taxonomic split: class I (prokaryotic/mitochondrial) and class II (eukaryotic microsomes). The other scheme was based on the number of components in the system: class B (3-components) and class E (2-components). These classes merge to a certain degree. Most prokaryotes and mitochondria (and fungal CYP55) have 3-component systems (class I/class B) - a FAD-containing flavoprotein (NAD(P)H-dependent reductase), an iron-sulphur protein and P450. Most eukaryotic microsomes have 2-component systems (class II/class E) - NADPH:P450 reductase (FAD and FMN-containing flavoprotein) and P450. There are exceptions to this scheme, such as 1-component systems that resemble class E enzymes [, , ]. The class E enzymes can be further subdivided into five sequence clusters, groups I-V, each of which may contain more than one cytochrome P450 family (eg, CYP1 and CYP2 are both found in group I). The divergence of the cytochrome P450 superfamily into B- and E-classes, and further divergence into stable clusters within the E-class, appears to be very ancient, occurring before the appearance of eukaryotes.This entry represents the CYP24A (Vitamin D 24-hydroxylase) family from class E, cytochrome P450 proteins. These enzymes are mitochondrial in origin. CYP24A1 has a role in maintaining calcium homeostasis, catalysing the NADPH-dependent 24-hydroxylation of 25-hydroxyvitamin D(3) in the presence of adrenodoxin and NADPH-adrenodoxin reductase. Human CYP24A1 catalyses both C-23 and C-24 oxidation, while the rat enzyme only catalyses C-24 oxidation [].
Cytochrome P450 enzymes are a superfamily of haem-containing mono-oxygenases that are found in all kingdoms of life, and which show extraordinary diversity in their reaction chemistry. In mammals, these proteins are found primarily in microsomes of hepatocytes and other cell types, where they oxidise steroids, fatty acids and xenobiotics, and are important for the detoxification and clearance of various compounds, as well as for hormone synthesis and breakdown, cholesterol synthesis and vitamin D metabolism. In plants, these proteins are important for the biosynthesis of several compounds such as hormones, defensive compounds and fatty acids. In bacteria, they are important for several metabolic processes, such as the biosynthesis of antibiotic erythromycin in Saccharopolyspora erythraea (Streptomyces erythraeus).Cytochrome P450 enzymes use haem to oxidise their substrates, using protons derived from NADH or NADPH to split the oxygen so a single atom can be added to a substrate. They also require electrons, which they receive from a variety of redox partners. In certain cases, cytochrome P450 can be fused to its redox partner to produce a bi-functional protein, such as with P450BM-3 from Bacillus megaterium [], which has haem and flavin domains.Organisms produce many different cytochrome P450 enzymes (at least 58 in humans), which together with alternative splicing can provide a wide array of enzymes with different substrate and tissue specificities. Individual cytochrome P450 proteins follow the nomenclature: CYP, followed by a number (family), then a letter (subfamily), and another number (protein); e.g. CYP3A4 is the fourth protein in family 3, subfamily A. In general, family members should share >40% identity, while subfamily members should share >55% identity.Cytochrome P450 proteins can also be grouped by two different schemes. One scheme was based on a taxonomic split: class I (prokaryotic/mitochondrial) and class II (eukaryotic microsomes). The other scheme was based on the number of components in the system: class B (3-components) and class E (2-components). These classes merge to a certain degree. Most prokaryotes and mitochondria (and fungal CYP55) have 3-component systems (class I/class B) - a FAD-containing flavoprotein (NAD(P)H-dependent reductase), an iron-sulphur protein and P450. Most eukaryotic microsomes have 2-component systems (class II/class E) - NADPH:P450 reductase (FAD and FMN-containing flavoprotein) and P450. There are exceptions to this scheme, such as 1-component systems that resemble class E enzymes [, , ]. The class E enzymes can be further subdivided into five sequence clusters, groups I-V, each of which may contain more than one cytochrome P450 family (eg, CYP1 and CYP2 are both found in group I). The divergence of the cytochrome P450 superfamily into B- and E-classes, and further divergence into stable clusters within the E-class, appears to be very ancient, occurring before the appearance of eukaryotes.This entry represents the CYP52 family from class E, cytochrome P450 proteins. These enzymes should be classed as sequence cluster group II []. Group II proteins are distributed widely amongst the kingdoms of life, but the CYP52 family has been first described only amongst Candida-related species of fungi, and as such may represent a novel development in Candida yeast. CYP52 proteins catalyse the conversion of fatty acids and alkanes to alpha,omega-dicarboxylic acids [, ].
Ca2+ ions are unique in that they not only carry charge but they are also the most widely used of diffusible second messengers. Voltage-dependent Ca2+ channels (VDCC) are a family of molecules that allow cells to couple electrical activity to intracellular Ca2+ signalling. The opening and closing of these channels by depolarizing stimuli, such as action potentials, allows Ca2+ ions to enter neurons down a steep electrochemical gradient, producing transient intracellular Ca2+ signals. Many of the processes that occur in neurons, including transmitter release, gene transcription and metabolism are controlled by Ca2+ influx occurring simultaneously at different cellular locales. The pore is formed by the alpha-1 subunit which incorporates the conduction pore, the voltage sensor and gating apparatus, and the known sites of channel regulation by second messengers, drugs, and toxins []. The activity of this pore is modulated by four tightly-coupled subunits: an intracellular beta subunit; a transmembrane gamma subunit; and a disulphide-linked complex of alpha-2 and delta subunits, which are proteolytically cleaved from the same gene product. Properties of the protein including gating voltage-dependence, G protein modulation and kinase susceptibility can be influenced by these subunits.Voltage-gated calcium channels are classified as T, L, N, P, Q and R, and are distinguished by their sensitivity to pharmacological blocks, single-channel conductance kinetics, and voltage-dependence. On the basis of their voltage activation properties, the voltage-gated calcium classes can be further divided into two broad groups: the low (T-type) and high (L, N, P, Q and R-type) threshold-activated channels.Co-expression of beta subunit mRNA with alpha-1 subunit mRNA in xenopus oocytes produces increased calcium currents, which are accompanied by a shift in the voltage-dependence of activation to more negative membrane potentials. Conversely, microinjection of antisense oligonucleotides to beta subunit mRNA produces decreased calcium currents and shifts voltage-dependent activation to more positive membrane potentials. There are four distinct beta subunits: beta-1, beta-2, beta-3 and beta-4; and the magnitude of the shift in the voltage-dependence of activation of change to membrane potentials varies with the particular subtype [].There are 3 splice variants of the beta-1 subunit: beta-1a, beta-1b and beta 1c. Beta-1a is the most extensively studied of these and is known to be expressed in skeletal muscle and brain, but not in smooth muscle or heart. Beta-1a appears to be important for the functional expression of the alpha-1 subunit in skeletal muscle. It is a 524-residue peripheral membrane protein that associates with a conserved 9-residue motif between repeats I and II of the alpha-1 subunit []. Beta-1b was identified by cloning in rat brain, heart and hippocampus, and differs from beta-1a by having a deletion of ~50 amino acids at residue 209, and having a 120-residue C-terminal elongation. Beta-1c was cloned from human heart and hippocampus and has the same deletion as beta-1b, but lacks the C-terminal extension.
Chemokines (chemotactic cytokines) are a family of chemoattractant molecules. They attract leukocytes to areas of inflammation and lesions, and play a key role in leukocyte activation. Originally defined as host defense proteins, chemokines are now known to play a much broader biological role []. They have a wide range of effects in many different cell types beyond the immune system, including, for example, various cells of the central nervous system [], and endothelial cells, where they may act as either angiogenic or angiostatic factors [].The chemokine family is divided into four classes based on the number and spacing of their conserved cysteines: 2 Cys residues may be adjacent (the CC family); separated by an intervening residue (the CXC family); have only one of the first two Cys residues (C chemokines); or contain both cysteines, separated by three intervening residues (CX3C chemokines).Chemokines exert their effects by binding to rhodopsin-like G protein-coupled receptors on the surface of cells. Following interactionwith their specific chemokine ligands, chemokine receptors trigger a flux in intracellular calcium ions, which cause a cellular response, including the onset of chemotaxis. There are over fifty distinct chemokines and least 18 human chemokine receptors []. Although the receptors bind only a single class of chemokines, they often bind several members of the same class with high affinity. Chemokine receptors are preferentially expressed on important functional subsets of dendritic cells, monocytes and lymphocytes, including Langerhans cells and T helper cells [, ]. Chemokines and their receptors can also be subclassified into homeostatic leukocyte homing molecules (CXCR4, CXCR5, CCR7, CCR9) versus inflammatory/inducible molecules (CXCR1, CXCR2, CXCR3, CCR1-6, CX3CR1).This entry represents the Duffy antigen/chemokine receptor, DARC (Duffy Antigen for Chemokines). It is also known as Fy protein [, ], and was originally identified as a blood group antigen. DARC has been found to act as a multi-specific receptor for chemokines of both the C-C and C-X-C families including CCL2, CCL5, CXCL1 and CXCL4 [, , , , ], it has also been shown to internalise chemokines but not scavenge them []. Although DARC is a 7-transmembrane protein, sharing a high content of α-helical secondary structure typical of chemokine structures [], the characteristic rhodopsin-like signature is virtually absent. As a result, unlike classical chemokine receptors DARC does not signal through G-proteins, so is regarded as an atypical chemokine receptor. DARC was initially described on red blood cells, but subsequent studies have demonstrated DARC protein expression on renal endothelial and epithelial cells and in Purkinje cells of the cerebellum, even in Duffy-negative individuals whose red cells lack DARC [, , , , ]. DARC is believed to play an important role in endothelial cells, since expression on these cell types is highly conserved, whereas the function on RBCs appears to be dispensable in order to confer resistance to malaria []. There is evidence suggesting a role for DARC in neutrophil migration from the blood into the tissues []and in modulating inflammatory response [, , , , ].
Mycobacterial species are usually slender, curved rods with a unique cellwall of complex waxes and glycolipids. They are resistant to acids, alkalisand dehydration, and are very slow to grow in vitro. The humanpathogenic Mycobacteria (Mycobacterium tuberculosis and Mycobacterium leprae) are becoming resistant to conventional treatments and, together with HIV-related diseases, are fast posing a global health threat. An essentialrequirement, particularly of M. tuberculosis, is to gain entrance to, and to resist, the hostile intra-cellular environment of epithelial cells [].The genome of M. tuberculosis contains four mammalian cell entry (mce) operons [], which are widely distributed in both pathogenic and non-pathogenic mycobacteria suggesting that the presence of these putative virulence genes is not an indicator for the pathogenicity of the bacilli. At the 5' end of the transcriptional unit are two genes that have evolved from a tandem duplication, and whose products resemble YrbE, a conserved hypothetical protein found in Escherichia coli, Haemophilus influenzae and Porphyra purpurea. All of the YrbE proteins, including the eight from M. tuberculosis, are probable integral membrane proteins with six TM alpha helices. The next six genes in each operon, the mce genes, are related, their products ranging in size from 275 to 564 amino acid residues. The corresponding protein sequences contain a number of highly conserved motifs that define a 24-member family with a common organisation. Twenty of these proteins have a strongly hydrophobic segment at the NH2-terminal end that could span the lipid bilayer whereas the remaining four, all ofwhich correspond to the seventh gene in their respective operons, mce1E to mce4E, are probably lipoproteinprecursors. In all 24 cases the COOH-terminal domain of themce proteins is predicted to be exposed on the external face of the cytoplasmicmembrane [].The ability to gain entry and resist the antimicrobial intracellular environment of mammalian cells is an essential virulence property of M. tuberculosis. This property is conferred by Mce1A, the third gene of operon 1, which when expressed in E. coli conferred the ability to invade HeLa cells. The recombinant protein when used to coat latex spheres also promoted their uptake into HeLa cells. N terminus deletion constructs of Mce1A identified a domain located between amino acid positions 106 and 163 that was needed for this cell uptake activity. Mce1A contains hydrophobic stretches at the N terminus predictive of a signal sequence, and colloidal gold immunoelectron microscopy indicated that the corresponding native protein is expressed on the surface of M. tuberculosis. Recombinant Mce2A, which had the highest level of identity (67%) to Mce1A, was unable to promote the association of microspheres with HeLa cells and an mce-deletion mutant in Mycobacterium bovis greatly impaired the ability of the microbe to infect epithelial cells in vitro. Although the exact function of Mce1A is still unknown, it appears to serve as an effector molecule expressed on the surface of M. tuberculosis that is capable of eliciting plasma membrane perturbations in non-phagocytic mammalian cells []. The distribution of the mce operons in both pathogenic and non-pathogenic mycobacteria suggests that the presence of these putative virulence genes is not an indicator for the pathogenicity of the bacilli - it may be that pathogenicity is determined by their expression [, ].The members of this family represent all 24 genes associated with the four mammalian cell entry operons of Mycobacterium tuberculosis and their homologues in other Actinomycetales [].
Cytochrome P450 enzymes are a superfamily of haem-containing mono-oxygenases that are found in all kingdoms of life, and which show extraordinary diversity in their reaction chemistry. In mammals, these proteins are found primarily in microsomes of hepatocytes and other cell types, where they oxidise steroids, fatty acids and xenobiotics, and are important for the detoxification and clearance of various compounds, as well as for hormone synthesis and breakdown, cholesterol synthesis and vitamin D metabolism. In plants, these proteins are important for the biosynthesis of several compounds such as hormones, defensive compounds and fatty acids. In bacteria, they are important for several metabolic processes, such as the biosynthesis of antibiotic erythromycin in Saccharopolyspora erythraea (Streptomyces erythraeus).Cytochrome P450 enzymes use haem to oxidise their substrates, using protons derived from NADH or NADPH to split the oxygen so a single atom can be added to a substrate. They also require electrons, which they receive from a variety of redox partners. In certain cases, cytochrome P450 can be fused to its redox partner to produce a bi-functional protein, such as with P450BM-3 from Bacillus megaterium [], which has haem and flavin domains.Organisms produce many different cytochrome P450 enzymes (at least 58 in humans), which together with alternative splicing can provide a wide array of enzymes with different substrate and tissue specificities. Individual cytochrome P450 proteins follow the nomenclature: CYP, followed by a number (family), then a letter (subfamily), and another number (protein); e.g. CYP3A4 is the fourth protein in family 3, subfamily A. In general, family members should share >40% identity, while subfamily members should share >55% identity.Cytochrome P450 proteins can also be grouped by two different schemes. One scheme was based on a taxonomic split: class I (prokaryotic/mitochondrial) and class II (eukaryotic microsomes). The other scheme was based on the number of components in the system: class B (3-components) and class E (2-components). These classes merge to a certain degree. Most prokaryotes and mitochondria (and fungal CYP55) have 3-component systems (class I/class B) - a FAD-containing flavoprotein (NAD(P)H-dependent reductase), an iron-sulphur protein and P450. Most eukaryotic microsomes have 2-component systems (class II/class E) - NADPH:P450 reductase (FAD and FMN-containing flavoprotein) and P450. There are exceptions to this scheme, such as 1-component systems that resemble class E enzymes [, , ]. The class E enzymes can be further subdivided into five sequence clusters, groups I-V, each of which may contain more than one cytochrome P450 family (eg, CYP1 and CYP2 are both found in group I). The divergence of the cytochrome P450 superfamily into B- and E-classes, and further divergence into stable clusters within the E-class, appears to be very ancient, occurring before the appearance of eukaryotes.This entry represents a conserved site based around a highly conserved cysteine residue involved in binding haem iron in the fifth coordination site, which is found in the C-terminal regions of P450 proteins.
POU proteins are eukaryotic transcription factors containing a bipartite DNA-binding domain referred to as the POU domain. The acronym POU (pronounced 'pow') is named after the pituitary-specific Pit-1, octamer-binding proteins Oct-1 and Oct-2, and the neural Unc-86 from Caenorhabditis elegans. The POU domain is a 70 to 75 amino-acid region found upstream of a homeobox domain in some transcription factors. POU domain genes have been described in organisms as divergent as C. elegans, Drosophila melanogaster (Fruit fly), Xenopus laevis (African clawed frog), Danio rerio (Zebrafish) (Brachydanio rerio) and Homo sapiens (Human) but have not been yet identified in plants and fungi. The various members of the POU family have a wide variety of functions, all of which are related to the development of an organism [].The POU domain is a bipartite domain composed of two subunits separated by a non-conserved region of 15-55 amino acids. The N-terminal subunit is known as POU-specific (POUs) domain () and a C-terminal homeodomain. Both subdomains contain the structural motif 'helix-turn-helix', which directly associates with the two components of bipartite DNA-binding sites. The 3-D structure of the POU-domain has been determined by multidimensional NMR []and X-ray crystallography to 3.0 A resolution []. The subdomains are connected by a flexible linker [, , ]. Despite of the lack of sequence homology, 3D structure of POUs is similar to 3D structure of bacteriophage lambda repressor and other members of HTH_3 family [, ].POU domain containing proteins bind to specific DNA sequences to cause temporal and spatial regulation of genes. Including genes: involved in the regulation of neuronal development in the central nervous system of mammals []; immunoglobulin light and heavy chains (Oct-2) []; and those for prolactin and growth hormone (Pit-1). Both elements of the POU-domain are required for high affinity sequence-specific DNA-binding. The domain may also be involved in protein-protein interactions [].POU domain class 5 includes the Oct3/4 gene (POU domain class 5 transcription factor 1). Mice with targeted disruption of the Oct3/4 gene developed to the blastocyst stage; however, the inner cell mass cells were not pluripotent. Instead, they were restricted to differentiation along the extraembryonic trophoblast lineage. Furthermore, in the absence of a true inner cell mass, trophoblast proliferation was not maintained in Oct3/4 -/- embryos. Expansion of trophoblast precursors was restored by addition of fibroblast growth factor-4, an Oct4 target gene product. It is thought that Oct4 determines paracrine growth factor signalling from stem cells to the trophectoderm with the activity of Oct4 essential for the identity of the pluripotential founder cell population in the mammalian embryo. Critical amounts of OCT3/4 are required to sustain stem cell self-renewal, with increased or decreased amounts inducing divergent developmental programs. It has been suggested that OCT3/4 is a master regulator of pluripotency and controls lineage commitment.
G protein-coupled receptors (GPCRs) constitute a vast protein family that encompasses a wide range of functions, including various autocrine, paracrine and endocrine processes. They show considerable diversity at the sequence level, on the basis of which they can be separated into distinct groups []. The term clan can be used to describe the GPCRs, as they embrace a group of families for which there are indications of evolutionary relationship, but between which there is no statistically significant similarity in sequence []. The currently known clan members include rhodopsin-like GPCRs (Class A, GPCRA), secretin-like GPCRs (Class B, GPCRB), metabotropic glutamate receptor family (Class C, GPCRC), fungal mating pheromone receptors (Class D, GPCRD), cAMP receptors (Class E, GPCRE) and frizzled/smoothened (Class F, GPCRF) [, , , , ]. GPCRs are major drug targets, and are consequently the subject of considerable research interest. It has been reported that the repertoire of GPCRs for endogenous ligands consists of approximately 400 receptors in humans and mice []. Most GPCRs are identified on the basis of their DNA sequences, rather than the ligand they bind, those that are unmatched to known natural ligands are designated by as orphan GPCRs, or unclassified GPCRs [].The rhodopsin-like GPCRs (GPCRA) represent a widespread protein family that includes hormone, neurotransmitter and light receptors, all of which transduce extracellular signals through interaction with guanine nucleotide-binding (G) proteins. Although their activating ligands vary widely in structure and character, the amino acid sequences of the receptors are very similar and are believed to adopt a common structural framework comprising 7 transmembrane (TM) helices [, , ].Neurotensin is a 13-residue peptide transmitter, sharing significantsimilarity in its 6 C-terminal amino acids with several other neuropeptides,including neuromedin N. This region is responsible for the biological activity, the N-terminal portion having a modulatory role. Neurotensin is distributed throughout the central nervous system, with highest levels in the hypothalamus, amygdala and nucleus accumbens. It induces a variety of effects, including: analgesia, hypothermia and increased locomotor activity. It is also involved in regulation of dopamine pathways. In the periphery, neurotensin is found in endocrine cells of the small intestine, where it leads to secretion and smooth muscle contraction.The existence of 2 neurotensin receptor subtypes, with differing affinitiesfor neurotensin and differing sensitivities to the antihistamine levocabastine, was originally demonstrated by binding studies in rodent brain. Two neurotensin receptors (NT1 and NT2) with such properties have since been cloned and have been found to be G-protein-coupled receptor family members [].The NT1 receptor was cloned in 1990 from rat brain and found to act as ahigh affinity, levocabastine insensitive receptor for neurotensin []. The affinity of neurotensin for the receptor could be decreased by both sodium ions and guanosine triphosphate (GTP) []. The NT1 receptor is expressed predominantly in the brain and intestine. In the brain, expression has been found in the diagonal band of Broca, medial septal nucleus, nucleus basalis magnocellularis, suprachiasmatic nucleus, supramammillary area, substantia nigra and ventral tegmental area. The receptor is also expressed in the dorsal root ganglion neurones of the spinal cord. The predominant response upon activation of the receptor by neurotensin is activation of phospholipase C, causing an increase in intracellular calcium levels. The receptor can also stimulate cAMP formation, MAP kinase activation and the induction of growth related genes, such as krox-24 [].
G protein-coupled receptors (GPCRs) constitute a vast protein family that encompasses a wide range of functions, including various autocrine, paracrine and endocrine processes. They show considerable diversity at the sequence level, on the basis of which they can be separated into distinct groups []. The term clan can be used to describe the GPCRs, as they embrace a group of families for which there are indications of evolutionary relationship, but between which there is no statistically significant similarity in sequence []. The currently known clan members include rhodopsin-like GPCRs (Class A, GPCRA), secretin-like GPCRs (Class B, GPCRB), metabotropic glutamate receptor family (Class C, GPCRC), fungal mating pheromone receptors (Class D, GPCRD), cAMP receptors (Class E, GPCRE) and frizzled/smoothened (Class F, GPCRF) [, , , , ]. GPCRs are major drug targets, and are consequently the subject of considerable research interest. It has been reported that the repertoire of GPCRs for endogenous ligands consists of approximately 400 receptors in humans and mice []. Most GPCRs are identified on the basis of their DNA sequences, rather than the ligand they bind, those that are unmatched to known natural ligands are designated by as orphan GPCRs, or unclassified GPCRs [].The rhodopsin-like GPCRs (GPCRA) represent a widespread protein family that includes hormone, neurotransmitter and light receptors, all of which transduce extracellular signals through interaction with guanine nucleotide-binding (G) proteins. Although their activating ligands vary widely in structure and character, the amino acid sequences of the receptors are very similar and are believed to adopt a common structural framework comprising 7 transmembrane (TM) helices [, , ].Leukotrienes (LT) are potent lipid mediators derived from arachidonic acid metabolism. They can be divided into two classes, based on the presence or absence of a cysteinyl group. Leukotriene B4 (LTB4) does not contain such a group, whereas LTC4, LTD4, LTE4 and LTF4 are cysteinyl leukotrienes.LTB4 is one of the most effective chemoattractant mediators known, and is produced predominantly by neutrophils and macrophages. It is involved in a number of events, including: stimulation of leukocyte migration from the bloodstream; activation of neutrophils; inflammatory pain; host defence against infection; increased interleukin production and transcription []. It is found in elevated concentrations in a number of inflammatory and allergic conditions, such as asthma, psoriasis, rheumatoid arthritis and inflammatory bowel disease, and has been implicated in the pathogenesis of these diseases [].Binding sites for LTB4 have been observed in membrane preparations from leukocytes, macrophages and spleen. Two receptors for LTB4 have since been cloned (BLT1 and BLT2); both are members of the rhodopsin-like G-protein-coupled receptor superfamily [].The leukotriene B4 type 1 receptor (BLT1) has been cloned from Homo sapiens (Human), Mus musculus (Mouse) and Rattus norvegicus (Rat), and was found to be identical to a previously cloned receptor, P2Y7 [, ]. This receptor was originally thought to be a purinoceptor but is now widely accepted to bind LTB4. BLT1 has also been reported to act as a coreceptor for macrophage-tropic Human immunodeficiency virus 1 (HIV-1) strains []. BLT1 is expressed primarily in peripheral leukocytes and peritoneal macrophages, with lower levels of expression detected in the spleen and thymus of humans []. Activation of the receptor by LTB4 leads to the production of inositol trisphosphate and an increase in intracellular calcium levels. This response is sensitive to pertussis toxin in some cell types. The receptor also causes chemotaxis and inhibition of forskolin-stimulated adenylyl cyclase activity in a pertussis toxin sensitive manner. It has been demonstrated that BLT1 can couple to Gi2 and G16 G-proteins, depending on the cell type in which it is expressed [].
Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK.A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ].Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms [, ]. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water []. The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily. HKs can be roughly divided into two classes: orthodox and hybrid kinases [, ]. Most orthodox HKs, typified by the Escherichia coli EnvZ protein, function as periplasmic membrane receptors and have a signal peptide and transmembrane segment(s) that separate the protein into a periplasmic N-terminal sensing domain and a highly conserved cytoplasmic C-terminal kinase core. Members of this family, however, have an integral membrane sensor domain. Not all orthodox kinases are membrane bound, e.g., the nitrogen regulatory kinase NtrB (GlnL) is a soluble cytoplasmic HK []. Hybrid kinases contain multiple phosphodonor and phosphoacceptor sites and use multi-step phospho-relay schemes instead of promoting a single phosphoryl transfer. In addition to the sensor domain and kinase core, they contain a CheY-like receiver domain and a His-containing phosphotransfer (HPt) domain.The HWE domain is found in a subset of two-component system kinases, belonging to the same superfamily as []. In [], the HWE family was defined by the presence of conserved a H residue and a WXE motifs and was limited to members of the proteobacteria. However, many homologues of this domain are lack the WXE motif. Furthermore, homologues are found in a wide range of Gram-positive and Gram-negative bacteria as well as in several archaea.
Neurotransmitter ligand-gated ion channels are transmembrane receptor-ion channel complexes that open transiently upon binding of specific ligands, allowing rapid transmission of signals at chemical synapses [, ]. Five of these ion channel receptor families have been shown to form a sequence-related superfamily:Nicotinic acetylcholine receptor (AchR), an excitatory cation channel in vertebrates and invertebrates; in vertebrate motor endplates it is composed of alpha, beta, gamma and delta/epsilon subunits; in neurons it is composed of alpha and non-alpha (or beta) subunits [].Glycine receptor, an inhibitory chloride ion channel composed of alpha and beta subunits [].Gamma-aminobutyric acid (GABA) receptor, an inhibitory chloride ion channel; at least four types of subunits (alpha, beta, gamma and delta) are known [].Serotonin 5HT3 receptor, of which there are seven major types (5HT3-5HT7) [].Glutamate receptor, an excitatory cation channel of which at least three types have been described (kainate, N-methyl-D-aspartate (NMDA) and quisqualate) [].These receptors possess a pentameric structure (made up of varying subunits), surrounding a central pore. All known sequences of subunits from neurotransmitter-gated ion-channels are structurally related. They are composed of a large extracellular glycosylated N-terminal ligand-binding domain, followed by three hydrophobic transmembrane regions which form the ionic channel, followed by an intracellular region of variable length. A fourth hydrophobic region is found at the C-terminal of the sequence [, ].Gamma-aminobutyric acid type A (GABAA) receptors are members of the neurotransmitter ligand-gated ion channels: they mediate neuronal inhibition on binding GABA. The effects of GABA on GABAA receptors are modulated by a range of therapeutically important drugs, including barbiturates, anaesthetics and benzodiazepines (BZs) []. The BZs are a diverse range of compounds, including widely prescribed drugs, such as librium and valium, and their interaction with GABAA receptors provides the most potent pharmacological means of distinguishing different GABAA receptor subtypes.GABAA receptors are pentameric membrane proteins that operate GABA-gated chloride channels []. Eight types of receptor subunit have been cloned, with multiple subtypes within some classes: alpha 1-6, beta 1-4, gamma 1-4, delta, epsilon, pi, rho 1-3 and theta [, ]. Subunits are typically 50-60kDa in size and comprise a long N-terminal extracellular domain, containing a putative signal peptide and a disulphide-bonded beta structural loop; 4 putative transmembrane (TM) domains; and a large cytoplasmic loop connecting the third and fourth TM domains. Amongst family members, the large cytoplasmic loop displays the most divergence in terms of primary structure, the TM domains showing the highest level of sequence conservation [].Most GABAA receptors contain one type of alpha and beta subunit, and a single gamma polypeptide in a ratio of 2:2:1 [], though in some cases other subunits such as epsilon or delta may replace gamma. The BZ binding site is located at the interface of adjacent alpha and gamma subunits; therefore, the type of alpha and gamma subunits present is instrumental in determining BZ selectivity and sensitivity. Receptors can be categorised into 3 groups based on their alpha subunit content and, hence, sensitivity to BZs: alpha 1-containing receptors have greatest sensitivity towards BZs (type I); alpha 2, 3 and 5-containing receptors have similar but distinguishable properties (type II); and alpha 4- and 6-containing assemblies have very low BZ affinity []. A conserved histidine residue in the alpha subunit of type I and II receptors is believed to be responsible for BZ affinity []. Delta cDNA was first reported in rat, mouse and humans []. Delta mRNAwas found to be present in regions of the brain that were low in gamma 2, and insensitivity towards "classical"BZs was observed in receptorscontaining the delta subunit. Furthermore, delta subunits are thought to preferentially pair with the alpha 6 polypeptides over other subtypes, and are often found in place of gamma subunits.
This domain occurs in a family of phage (and bacteriocin) proteins related to the phage P2 V gene product, which forms the small spike at the tip of the tail []. Homologs in general are annotated as baseplate assembly protein V. At least one member is encoded within a region of Pectobacterium carotovorum (Erwinia carotovora) described as a bacteriocin, a phage tail-derived module able to kill bacteria closely related to the host strain.It is also found in Vgr-related proteins. Genes encoding type VI secretion systems (T6SS) are widely distributed in pathogenic Gram-negative bacterial species. In Vibrio cholerae, T6SS have been found to secrete three related proteins extracellularly, VgrG-1, VgrG-2, and VgrG-3. VgrG-1 can covalently cross-link actin in vitro, and this activity was used to demonstrate that V. cholerae can translocate VgrG-1 into macrophages by a T6SS-dependent mechanism. VgrG-related proteins likely assemble into a trimeric complex that is analogous to that formed by the two trimeric proteins gp27 and gp5 that make up the baseplate "tail spike"of Escherichia coli bacteriophage T4. The VgrG components of the T6SS apparatus might assemble a "cell-puncturing device"analogous to phage tail spikes to deliver effector protein domains through membranes of target host cells [].Gp5 is an integral component of the virion baseplate of bacteriophage T4. T4 Gp5 consists of 3 domains connected via long linkers: the N-terminal oligosaccharide/oligonucleotide-binding (OB)-fold domain, the middle lysozyme domain, and the C-terminal triplestranded-helix. The equivalent of the Gp5 OB-fold domain in the structure of VgrG is the domain of unknown function comprising residues 380-470 and conserved in all known VgrGs. This entry represents the OB-fold domain which consists of a 5-stranded antiparallel-barrel with a Greek-key topology [].
