Cytochrome c (CytC) proteins can be defined as electron-transfer proteins having one or several haem c groups, bound to the protein by one or, more generally, two thioether bonds involving sulphydryl groups of cysteine residues. The fifth haem iron ligand is always provided by a histidine residue. CytC possess a wide range of properties and function in a large number of different redox processes.Ambler []recognised four classes of cytC.Class I includes the low-spin soluble CytC of mitochondria and bacteria, with the haem-attachment site towards the N terminus, and the sixth ligand provided by a methionine residue about 40 residues further on towards the C terminus. On the basis of sequence similarity, class I CytC were further subdivided into five classes, IA to IE. Class IC, 'split-alpha-band' Cyt C, possess a widened or split alpha-band of lowered absorptivity. This class includes dihaem Cyt C4 and monohaem Cyt C6 (Cyt C-553) and Cyt C-554.The 3D structures of Chlamydomonas reinhardtii Cyt C6 []and Desulfovibrio vulgaris Cyt C-553 []have been determined. The proteins consist of 4 α-helices; three 'core' helices form a 'basket' around the haem group, with one haem edge exposed to the solvent.This entry also includes Cytochrome c6 from Arabidopsis, which functions as an electron carrier between membrane-bound cytochrome b6-f and photosystem I in oxygenic photosynthesis [].
This domain of unknown function is found at the C terminus in a number of Caenorhabditis elegans and briggsae proteins. It may be an extracellular domain. Most copies of the domain contain six conserved cysteine residues. However some copies of the domain are missing cysteine residues 1 and 3 suggesting that these form a disulphide bridge.
Plants normally grow on substrates that are extremely rich in microorganisms, but infection remains a rare event. During evolution, plants have developed a variety of defence systems to protect themselves from potential pathogens. Proteins including thionins, plant defensins and chitinases have been shown to play active roles against pathogen infections. Plants produce a wide array of antimicrobial compounds for escaping from microorganisms, which have antibacterial, anti-fungal activity, etc. Antimicrobial peptides extracted from plants inhibit the growth of a variety of fungi, oomycetes, Gram-positive bacterial phytopathogenes and Saccharomyces cerevisiae (Baker's yeast). Many antimicrobial peptides (AMPs) which contain cysteine residues abundantly have been isolated from plants, and these are classified into the plant defensin family. Plant defensins can be classified broadly into three types (hevein type, C6 type, and C8 type) according to the number and the position of cysteine residues in the molecules. The C6 type of plant defensins are highly basic proteins that contain 6 cysteine residues and a continuous sequence of cysteines (-CC-). All the 6 cysteines are involved in disulphide bond formation for stabilising protein tertiary structure [, , , ].
Radical SAM domain protein TunB is involved in the biosynthesis of tunicamycins. It catalyses the radical coupling reaction in which a 5'-uridyl radical undergoes radical addition at C6 of N-acetyl-galactoseamine-5,6-ene to yield an alpha-alkoxyalkyl radical. Subsequent hydrogen atom abstraction from 5'-deoxyadenosine could lead to UDP-N-acetyl-tunicamine-uracil and the regeneration of SAM [].
Responsible for the methylation of gentamicin at the C6 position. It has recently been shown that GenK () acts at the X2 Branch Point and is essential for the production of G418 and Gentamicins C2a, C2, and C1. It also acts (with the same function) at the A and A2 branch points [, , , ].
DcrB is a bacterial protein required for phages C1 and C6 adsorption [, ]. It may be involved in the opening or formation of diffusion channels in the outer membrane []. It plays a role in cell envelope biogenesis, maintenance of cell envelope integrity and membrane homeostasis [, ]. DcbrB is essential for lipoprotein maturation under conditions where membrane fluidity may be altered []. Structurally, it consist of an antiparallel β-sheet with two α-helical regions.
This superfamily consists of cytochrome b6/f complex subunit 5 (PetG). The cytochrome bf complex, found in green plants, eukaryotic algae and cyanobacteria, connects photosystem I to photosystem II in the electron transport chain, functioning as a plastoquinol:plastocyanin/cytochrome c6 oxidoreductase []. The purified complex from the unicellular alga Chlamydomonas reinhardtii contains seven subunits; namely four high molecular weight subunits (cytochrome f, Rieske iron-sulphur protein, cytochrome b6, and subunit IV) and three approximately miniproteins (PetG, PetL, and PetX) []. Stoichiometry measurements are consistent with every subunit being present as two copies per b6/f dimer. The absence of PetG affects either the assembly or stability of the cytochrome bf complex in C. reinhardtii [].
In Escherichia coli, the trmA protein is a tRNA (uracil-5-)-methyltransferase() that catalyses the S-adenosylmethionine dependent methylation of U54 in all tRNAs. Orthologues of trmA are found in many eubacterial species. A number of uncharacterised homologues of trmA have been found []:Escherichia coli hypothetical protein ygcA and HI0333, the correspondingHaemophilus influenzae protein.Haemophilus influenzae hypothetical protein HI0958.Chlamydia trachomatis protein HOM1.Fission yeast hypothetical protein SpAC4G8.07c.It is probable that ygcA/HI0333 and HI0958 are responsible for themethylation of U747 and U1939 in 23S rRNA. In trmA, a cysteine is known toparticipate in the catalytic mechanism by forming a covalent adduct to C6 ofuracil.This entry represents a conserved region that includes the active site cysteine.
In Escherichia coli, the trmA protein is a tRNA (uracil-5-)-methyltransferase() that catalyses the S-adenosylmethionine dependent methylation of U54 in all tRNAs. Orthologues of trmA are found in many eubacterial species. A number of uncharacterised homologues of trmA have been found []:Escherichia coli hypothetical protein ygcA and HI0333, the correspondingHaemophilus influenzae protein.Haemophilus influenzae hypothetical protein HI0958.Chlamydia trachomatis protein HOM1.Fission yeast hypothetical protein SpAC4G8.07c.It is probable that ygcA/HI0333 and HI0958 are responsible for themethylation of U747 and U1939 in 23S rRNA. In trmA, a cysteine is known toparticipate in the catalytic mechanism by forming a covalent adduct to C6 ofuracil.This entry represents a conserved site located at the C-terminal end. It contains a conserved histidine.
The conversion of dTDP-glucose into dTDP-4-keto-6-deoxyglucose by Escherichia coli dTDP-glucose 4,6-dehydratase takes place in the active site in three steps: dehydrogenation to dTDP-4-ketoglucose, dehydration to dTDP-4-ketoglucose-5,6-ene, and rereduction of C6 to the methyl group. The 4,6-dehydratase makes use of tightly bound NAD+as the coenzyme for transiently oxidizing the substrate, activating it for the dehydration step []. This and other 4,6-dehydratases catalyze the first committed step in all 6-deoxysugar biosynthetic pathways described to date. Numerous 6-deoxysugars are used in bacterial lipopolysaccharide production as well as in the biosynthesis of a diverse array of secondary metabolites.
This superfamily represents the N-terminal domain of the ornithine decarboxylase (), which is involved in putrescine biosynthesis. This domain has a flavodoxin-like fold, and is termed the "wing"domain because of its position in the overall 3D structure. Six dimers related by C6 symmetry compose the enzymatically active dodecamer of ornithine decarboxylase from Lactobacillus 30a (L30a OrnDC, ). The amino-terminal domain consists of a five-stranded β-sheet termed the "wing"domain. Two wing domains of each dimer project inward towards the centre of the dodecamer and contribute to dodecamer stabilisation [].
This family consists of cytochrome b6/f complex subunit 5 (PetG). The cytochrome bf complex, found in green plants, eukaryotic algae and cyanobacteria, connects photosystem I to photosystem II in the electron transport chain, functioning as a plastoquinol:plastocyanin/cytochrome c6 oxidoreductase []. The purified complex from the unicellular alga Chlamydomonas reinhardtii contains seven subunits; namely four high molecular weight subunits (cytochrome f, Rieske iron-sulphur protein, cytochrome b6, and subunit IV) and three approximately miniproteins (PetG, PetL, and PetX) []. Stoichiometry measurements are consistent with every subunit being present as two copies per b6/f dimer. The absence of PetG affects either the assembly or stability of the cytochrome bf complex in C. reinhardtii [].
This domain is found in the non-catalytic carbohydrate binding module 65B (CMB65B) from Eubacterium cellulosolvens. CBMs are present in plant cell wall degrading enzymes and are responsible for targeting, which enhances catalysis. CBM65s display higher affinity for oligosaccharides, such as cellohexaose, and particularly polysaccharides than cellotetraose, which fully occupies the core component of the substrate binding cleft. The concave surface presented by β-sheet 2 comprises the beta-glucan binding site in CBM65s. C6 of all the backbone glucose moieties makes extensive hydrophobic interactions with the surface tryptophans of CBM65s. Three out of the four surface Trp are highly conserved. The conserved metal ion site typical of CBMs is absent in this CBM65 family [].
Cytochrome c (CytC) proteins can be defined as electron-transfer proteins having one or several haem c groups, bound to the protein by one or, more generally, two thioether bonds involving sulphydryl groups of cysteine residues. The fifth haem iron ligand is always provided by a histidine residue. CytC possess a wide range of properties and function in a large number of different redox processes.Ambler []recognised four classes of cytC.Class I includes the low-spin soluble CytC of mitochondria and bacteria, with the haem-attachment site towards the N terminus, and the sixth ligand provided by a methionine residue about 40 residues further on towards the C terminus. On the basis of sequence similarity, class I CytC were further subdivided into five classes, IA to IE. Class IC, 'split-alpha-band' Cyt C, possess a widened or split alpha-band of lowered absorptivity. This class includes dihaem Cyt C4 and monohaem Cyt C6 (Cyt C-553) and Cyt C-554.The 3D structures of Chlamydomonas reinhardtii Cyt C6 []and Desulfovibrio vulgaris Cyt C-553 []have been determined. The proteins consist of 4 α-helices; three 'core' helices form a 'basket' around the haem group, with one haem edge exposed to the solvent.
DcrB is a bacterial protein required for phages C1 and C6 adsorption [, ]. It may be involved in the opening or formation of diffusion channels in the outer membrane []. It plays a role in cell envelope biogenesis, maintenance of cell envelope integrity and membrane homeostasis [, ]. DcbrB is essential for lipoprotein maturation under conditions where membrane fluidity may be altered []. Structurally, it consist of an antiparallel beta sheet with some alpha helical regions. This entry also includes EagT6 from Pseudomonas aeruginosa which has some homology to DcrB []. EagT6 plays an essential role in toxin Tse6 delivery to target cells and specifically in the loading of Tse6 onto VgrG1a [, ].
This family represents a group of Poxvirus Bcl-2-like proteins that function as immunomodulators to evade the host innate immune response through the inhibition of apoptosis or blocking the activation of pro-inflammatory transcription factors, such as interferon (IFN) regulatory factor-3 (IRF-3) and nuclear factor-kappaB (NF-kappaB) []. These proteins have low sequence identity but high structural similarity to the eukaryotic Bcl-2 protein family. They have a Bcl-2 fold which comprises a central hydrophobic α-helix that is surrounded by an additional layer of 6-7 amphipathic α-helices []. Included in this family are proteins B14 [], A52 [, ], A46 [], C6 [], K7, N1, and N2 []. Protein N1 has the unusual dual ability of modulating apoptosis and inflammatory signalling []. Protein K7, in addition to its anti-inflammatory activity, forms a complex with RNA helicase DDX3 and antagonises interferon-beta promoter induction [].
This domain has a flavodoxin-like fold, and is termed the "wing"domain because of its position in the overall 3D structure. Ornithine decarboxylase from Lactobacillus 30a (L30a OrnDC, ) is representative of the large, pyridoxal-5'-phosphate-dependentdecarboxylases that act on lysine, arginine or ornithine. The crystal structure of the L30a OrnDC has been solved to 3.0 A resolution. Six dimers related by C6 symmetry compose the enzymatically activedodecamer (approximately 106Da). Each monomer of L30a OrnDC can be described in terms of five sequential folding domains.The amino-terminal domain, residues 1 to 107, consists of a five-stranded β-sheet termed the "wing"domain. Two wing domains ofeach dimer project inward towards the centre of the dodecamer and contribute to dodecamer stabilisation [].Proteins containing this domain include the ornithine decarboxylase, the lysine decarboxylase and the biodegradative arginine decarboxylase.
C-5 cytosine-specific DNA methylases (C5 Mtase) are enzymes that specifically methylate the C-5 carbon of cytosines in DNA [, , ]. Such enzymes are found in the proteins described below.As a component of type II restriction-modification systems in prokaryotes and some bacteriophages. Such enzymes recognise a specific DNA sequence where they methylate a cytosine. In doing so, they protect DNA from cleavage by type II restriction enzymes that recognise the same sequence. The sequences of a large number of type II C-5 Mtases are known. In vertebrates, there are a number of C-5 Mtases that methylate CpG dinucleotides. The sequence of the mammalian enzyme is known. C-5 Mtases share a number of short conserved regions. This conserved region contains a conserved Pro-Cys dipeptide in which the cysteine has been shown to be involved in the catalytic mechanism; it appears to form a covalent intermediate with the C6 position of cytosine [].
The membrane attack complex/perforin (MACPF) domain is conserved in bacteria, fungi, mammals and plants. It was originally identified and named as being common to five complement components (C6, C7, C8-alpha, C8-beta, and C9) and perforin. These molecules perform critical functions in innate and adaptive immunity. The MAC family proteins and perforin are known to participate in lytic pore formation. In response to pathogen infection, a sequential and highly specific interaction between the constituent elements occurs to form transmembrane channels which are known as the membrane-attack complex (MAC).Only a few other MACPF proteins have been characterised and several are thought to form pores for invasion or protection [, , ]. Examples are proteins from malarial parasites [], the cytolytic toxins from sea anemones [], and proteins that provide plant immunity [, ]. Functionally uncharacterised MACPF proteins are also evident in pathogenic bacteria such as Chlamydia spp []and Photorhabdus luminescens (Xenorhabdus luminescens) [].The MACPF domain is commonly found to be associated with other N- and C-terminal domains, such as TSP1 (see ), LDLRA (see ), EGF-like (see ),Sushi/CCP/SCR (see ), FIMAC or C2 (see ). They probably control or target MACPF function [, ]. The MACPF domain oligomerizes, undergoes conformational change, and is required for lytic activity.The MACPF domain consists of a central kinked four-stranded antiparallel beta sheet surrounded by alpha helices and beta strands, forming two structural segments. Overall, the MACPF domain hasa thin L-shaped appearance. MACPF domains exhibit limited sequence similarity but contain a signature [YW]-G-[TS]-H-[FY]-x(6)-G-G motif [, , ].Some proteins known to contain a MACPF domain are listed below:Vertebrate complement proteins C6 to C9. Complement factors C6 to C9 assemble to form a scaffold, the membrane attack complex (MAC), that permits C9 polymerisation into pores that lyse Gram-negative pathogens [, ].Vertebrate perforin. It is delivered by natural killer cells and cytotoxic T lymphocytes and forms oligomeric pores (12 to 18 monomers) in the plasma membrane of either virus-infected or transformed cells.Arabidopsis thaliana (Mouse-ear cress) constitutively activated cell death 1 (CAD1) protein. It is likely to act as a mediator that recognises plant signals for pathogen infection [].Arabidopsis thaliana (Mouse-ear cress) necrotic spotted lesions 1 (NSL1) protein [].Venomous sea anemone Phyllodiscus semoni (Night anemone) toxins PsTX-60A and PsTX-60B [].Venomous sea anemone Actineria villosa (Okinawan sea anemone) toxin AvTX-60A [].Plasmodium sporozoite microneme protein essential for cell traversal 2 (SPECT2). It is essential for the membrane-wounding activity of the sporozoite and is involved in its traversal of the sinusoidal cell layer prior to hepatocyte-infection [].P. luminescens Plu-MACPF. Although nonlytic, it was shown to bind to cell membranes [].Chlamydial putative uncharacterised protein CT153 [].
The membrane attack complex/perforin (MACPF) domain is conserved in bacteria, fungi, mammals and plants. It was originally identified and named as being common to five complement components (C6, C7, C8-alpha, C8-beta, and C9) and perforin. These molecules perform critical functions in innate and adaptive immunity. The MAC family proteins and perforin are known to participate in lytic pore formation. In response to pathogen infection, a sequential and highly specific interaction between the constituent elements occurs to form transmembrane channels which are known as the membrane-attack complex (MAC).Only a few other MACPF proteins have been characterised and several are thought to form pores for invasion or protection [, , ]. Examples are proteins from malarial parasites [], the cytolytic toxins from sea anemones [], and proteins that provide plant immunity [, ]. Functionally uncharacterised MACPF proteins are also evident in pathogenic bacteria such as Chlamydia spp []and Photorhabdus luminescens (Xenorhabdus luminescens) [].The MACPF domain is commonly found to be associated with other N- and C-terminal domains, such as TSP1 (see ), LDLRA (see ), EGF-like (see ),Sushi/CCP/SCR (see ), FIMAC or C2 (see ). They probably control or target MACPF function [, ]. The MACPF domain oligomerizes, undergoes conformational change, and is required for lytic activity.The MACPF domain consists of a central kinked four-stranded antiparallel beta sheet surrounded by alpha helices and beta strands, forming two structural segments. Overall, the MACPF domain has a thin L-shaped appearance. MACPF domainsexhibit limited sequence similarity but contain a signature [YW]-G-[TS]-H-[FY]-x(6)-G-G motif [, , ].Some proteins known to contain a MACPF domain are listed below:Vertebrate complement proteins C6 to C9. Complement factors C6 to C9 assemble to form a scaffold, the membrane attack complex (MAC), that permits C9 polymerisation into pores that lyse Gram-negative pathogens [, ].Vertebrate perforin. It is delivered by natural killer cells and cytotoxic T lymphocytes and forms oligomeric pores (12 to 18 monomers) in the plasma membrane of either virus-infected or transformed cells.Arabidopsis thaliana (Mouse-ear cress) constitutively activated cell death 1 (CAD1) protein. It is likely to act as a mediator that recognises plant signals for pathogen infection [].Arabidopsis thaliana (Mouse-ear cress) necrotic spotted lesions 1 (NSL1) protein [].Venomous sea anemone Phyllodiscus semoni (Night anemone) toxins PsTX-60A and PsTX-60B [].Venomous sea anemone Actineria villosa (Okinawan sea anemone) toxin AvTX-60A [].Plasmodium sporozoite microneme protein essential for cell traversal 2 (SPECT2). It is essential for the membrane-wounding activity of the sporozoite and is involved in its traversal of the sinusoidal cell layer prior to hepatocyte-infection [].P. luminescens Plu-MACPF. Although nonlytic, it was shown to bind to cell membranes [].Chlamydial putative uncharacterised protein CT153 [].
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.
O-Glycosyl hydrolases () are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) website.Glycoside hydrolase family 36 () occur in prokaryotes, eukaryotes, and archaea with a wide range of hydrolytic activities, including alpha-galactosidase, alpha-N-acetylgalactosaminidase, stachyose synthase, and raffinose synthase [, ]. All GH36 enzymes cleave a terminal carbohydrate moiety from a substrate that varies considerably in size, depending on the enzyme, and may be either a starch or a glycoprotein. GH36 members are retaining enzymes that cleave their substrates via an acid/base-catalyzed, double-displacement mechanism involving a covalent glycosyl-enzyme intermediate []. Two aspartic acid residues have been identified as the catalytic nucleophile and the acid/base, respectively.Proteins in this entry also include AgaSK, a bifunctional protein that contains two domains: one closely related to alpha-galactosidases from glycoside hydrolase family GH36 and the other containing a nucleotide-binding motif. It can hydrolyze melibiose and raffinose to galactose and either glucose or sucrose, respectively, and can specifically phosphorylate sucrose on the C6 position of glucose in the presence of ATP [].
Butanol dehydrogenase (BDH) is involved in the final step of the butanol formation pathway, in which it catalyses the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidised in the process. The NADH-BDH has higher activity with longer chained aldehydes and is inhibited by metabolites containing an adenine moiety. This protein family belongs to the so-called iron-containing alcohol dehydrogenase superfamily. Members in this family use divalent ions, preferentially iron or zinc []. This family also includes E. coli YqhD enzyme, an NADP-dependent dehydrogenase whose activity measurements with several alcohols demonstrate preference for alcohols longer than C3 [, ]. The active site of YqhD contains a zinc atom, and a modified NADPH cofactor bearing OH groups on the saturated C5 and C6 atoms, possibly due to oxygen stress on the enzyme, which would functionally work under anaerobic conditions.This entry also includes Long-chain-alcohol dehydrogenase 2 from Geobacillus thermodenitrificans which is able to oxidise a broad range of alkyl alcohols from methanol to 1-triacontanol (C1 to C30), whose best substrate is 1-octanol. In contrast to other members of the family, it apparently does not use iron or other metals as cofactor [].
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).
This entry represents a β-propeller domain found in galactose oxidase and in Kelch repeat-containing proteins.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; neuraminidase hydrolyses sialic acid residues from glycoproteins; 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 [].Galactose oxidase () is a monomeric enzyme that contains a single copper ion and catalyses the stereospecific oxidation of primary alcohols to their corresponding aldehyde []. The protein contains an unusual covalent thioether bond between a tyrosine and a cysteine that forms during its maturation []. Galactose oxidase is a three-domain protein: the N-terminal domain forms a jelly-roll sandwich, the central domain forms a seven 4-bladed β-propeller, and the C-terminal domain has an immunoglobulin-like fold.
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.
Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Many families of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases [].Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ].The potyviridae are a family of positive strand RNA viruses, members of which include Zucchini yellow mosaic virus, and Turnip mosaic virus (strain Japanese) which cause considerable losses of crops worldwide.This entry represents a C-terminal region from various plant potyvirus P1 proteins (found at the N terminus of the polyprotein). The C terminus of P1 is a serine peptidase belonging to MEROPS peptidase family S30 (clan PA(S)). It is the protease responsible for autocatalytic cleavage between P1 and the helper component protease, which is a cysteine peptidase belonging to MEROPS peptidase family C6 [, ]. The P1 protein may be involved in virus-host interactions [], and evasion of immune responses [].
Potyviruses form one of the most numerous groups of plant viruses and are a major cause of crop loss worldwide. The helper-component proteinase (HC-Pro) is an indispensable, multifunctional protein of members of the genus Potyvirus and other viruses of the family Potyviridae. It is directly involved in diverse steps of viral infection, such as aphid plant-to-plant transmission, polyprotein processing, and suppression of host antiviral RNA silencing. HC-Pro is generally divided into three functional domains: a N-terminal domain, a central region, and a cysteine protease domain (CPD) in the C-terminal region. The HC-Pro CPD domain has a protease activity that autocatalytically cleaves a Gly-Gly dipeptide at its own C terminus to release HC-Pro from the rest of the viral polyprotein. Cysteine and histidine residues form the catalytic dyad at the active site. The HC-Pro CPD domain constitutes the peptidase family C6 of the CA clan [].The HC-Pro CPD domain adopts a compact oval-shaped alpha/beta fold. The secondary structure elements include four α-helices (alpha1-alpha4) and two short β-strands (beta1 and beta2) arranged in the order alpha1-alpha2-alpha3-beta1-beta2-alpha4. In addition, two 3(10) helices are located between alpha3 and beta1 and downstream of alpha4. The four helices form a helix bundle packed against one face of a short β-hairpin formed by strands beta1 and beta2. The catalytic residue Cys is located at the N terminus of helix alpha1, and the other catalytic residue His is located on strand beta2. The substrate binding cleft is lined by the loop connecting helices alpha2 and alpha3 and the N-terminal region of helix alpha1 on one side and by strand beta2 on the other side [].This superfamily represents the CPD domain of the HC-Pro protein.
This entry represents the CPD domain of the HC-Pro protein. Potyviruses form one of the most numerous groups of plant viruses and are a major cause of crop loss worldwide. The helper-component proteinase (HC-Pro) is an indispensable, multifunctional protein of members of the genus Potyvirus and other viruses of the family Potyviridae. It is directly involved in diverse steps of viral infection, such as aphid plant-to-plant transmission, polyprotein processing, and suppression of host antiviral RNA silencing. HC-Pro is generally divided into three functional domains: a N-terminal domain, a central region, and a cysteine protease domain (CPD) in the C-terminal region. The HC-Pro CPD domain has a protease activity that autocatalytically cleaves a Gly-Gly dipeptide at its own C terminus to release HC-Pro from the rest of the viral polyprotein. Cysteine and histidine residues form the catalytic dyad at the active site. The HC-Pro CPD domain constitutes the peptidase family C6 of the CA clan [].The HC-Pro CPD domain adopts a compact oval-shaped alpha/beta fold. The secondary structure elements include four α-helices (alpha1-alpha4) and two short β-strands (beta1 and beta2) arranged in the order alpha1-alpha2-alpha3-beta1-beta2-alpha4. In addition, two 3(10) helices are located between alpha3 and beta1 and downstream of alpha4. The four helices form a helix bundle packed against one face of a short β-hairpin formed by strands beta1 and beta2. The catalytic residue Cys is located at the N terminus of helix alpha1, and the other catalytic residue His is located on strand beta2. The substrate binding cleft is lined by the loop connecting helices alpha2 and alpha3 and the N-terminal region of helix alpha1 on one side and by strand beta2 on the other side [].
This enrry represents the potyvirus helper component protease found in genome polyproteins of potyviruses. It is is a cysteine peptidase belonging to the MEROPS peptidase family C6 (clan CA). The helper component-proteinase is required for aphid transmission.A cysteine peptidase is a proteolytic enzyme that hydrolyses a peptide bond using the thiol group of a cysteine residue as a nucleophile. Hydrolysis involves usually a catalytic triad consisting of the thiol group of the cysteine, the imidazolium ring of a histidine, and a third residue, usually asparagine or aspartic acid, to orientate and activate the imidazolium ring. In only one family of cysteine peptidases, is the role of the general base assigned to a residue other than a histidine: in peptidases from family C89 (acid ceramidase) an arginine is the general base. Cysteine peptidases can be grouped into fourteen different clans, with members of each clan possessing a tertiary fold unique to the clan. Four clans of cysteine peptidases share structural similarities with serine and threonine peptidases and asparagine lyases. From sequence similarities, cysteine peptidases can be clustered into over 80 different families []. Clans CF, CM, CN, CO, CP and PD contain only one family.Cysteine peptidases are often active at acidic pH and are therefore confined to acidic environments, such as the animal lysosome or plant vacuole. Cysteine peptidases can be endopeptidases, aminopeptidases, carboxypeptidases, dipeptidyl-peptidases or omega-peptidases. They are inhibited by thiol chelators such as iodoacetate, iodoacetic acid, N-ethylmaleimide or p-chloromercuribenzoate.Clan CA includes proteins with a papain-like fold. There is a catalytic triad which occurs in the order: Cys/His/Asn (or Asp). A fourth residue, usually Gln, is important for stabilising the acyl intermediate that forms during catalysis, and this precedes the active site Cys. The fold consists of two subdomains with the active site between them. One subdomain consists of a bundle of helices, with the catalytic Cys at the end of one of them, and the other subdomain is a β-barrel with the active site His and Asn (or Asp). There are over thirty families in the clan, and tertiary structures have been solved for members of most of these. Peptidases in clan CA are usually sensitive to the small molecule inhibitor E64, which is ineffective against peptidases from other clans of cysteine peptidases [].Clan CD includes proteins with a caspase-like fold. Proteins in the clan have an α/β/α sandwich structure. There is a catalytic dyad which occurs in the order His/Cys. The active site His occurs in a His-Gly motif and the active site Cys occurs in an Ala-Cys motif; both motifs are preceded by a block of hydrophobic residues []. Specificity is predominantly directed towards residues that occupy the S1 binding pocket, so that caspases cleave aspartyl bonds, legumains cleave asparaginyl bonds, and gingipains cleave lysyl or arginyl bonds.Clan CE includes proteins with an adenain-like fold. The fold consists of two subdomains with the active site between them. One domain is a bundle of helices, and the other a β-barrell. The subdomains are in the opposite order to those found in peptidases from clan CA, and this is reflected in the order of active site residues: His/Asn/Gln/Cys. This has prompted speculation that proteins in clans CA and CE are related, and that members of one clan are derived from a circular permutation of the structure of the other.Clan CL includes proteins with a sortase B-like fold. Peptidases in the clan hydrolyse and transfer bacterial cell wall peptides. The fold shows a closed β-barrel decorated with helices with the active site at one end of the barrel []. The active site consists of a His/Cys catalytic dyad.Cysteine peptidases with a chymotrypsin-like fold are included in clan PA, which also includes serine peptidases. Cysteine peptidases that are N-terminal nucleophile hydrolases are included in clan PB. Cysteine peptidases with a tertiary structure similar to that of the serine-type aspartyl dipeptidase are included in clan PC. Cysteine peptidases with an intein-like fold are included in clan PD, which also includes asparagine lyases.
