This superfamily includes the immunoglobulin-binding protein Sbi domain IV (Sbi-IV) which binds the central complement protein C3. Sbi-IV interacts with Sbi-III to induce a consumption of complement via alternative pathway activation []. When not interacting with Sbi-III, Sbi-IV inhibits the alternative pathway without complement consumption. Sbi-IV structurally comprises a three-helix bundle [].Sbi-IV is similar to Efb-C and Ehp [, , ]. Sbi-IV binds to the thioester-containing domain of native C3. The interaction between Sbi-IV and C3, in the presence of domain III, results in the formation of a covalent Sbi-III-IV-C3 adduct followed by futile fluid phase consumption of C3 [].
This group represents a group of mono-ADP-ribosyltransferases, including Edin (epidermal cell differentiation inhibitor) from Staphylococcus aureus and C3 from phage. Edin inhibits terminal differentiation of cultured mouse keratinocytes []. C3 is an ADP-ribosyltransferase [, ].
The NTR domain found in complement C3 is also known as the C345C domain because it occurs at the C terminus of complement C3, C4 and C5. Complement C3 plays a pivotal role in the activation of the complement systems, as all pathways (classical, alternative, and lectin) result in the processing of C3 by C3 convertase. The larger fragment, activated C3b, contains the NTR/C345C domain and binds covalently, via a reactive thioester, to cell surface carbohydrates including components of bacterial cell walls and immune aggregates. The smaller cleavage product, C3a, acts independently as a diffusible signal to mediate local inflammatory processes. The structure of C3 shows that the NTR/C345C domain is located in an exposed position relative to the rest of the molecule. The function of the domain in complement C3 is poorly understood [, ].This domain is also found in cobra venom factor, a functional analogue of human complement component C3b [].
This domain is MG4 found in thioester-containing proteins (TEPs) such as Alpha-2-macroglobulin, complement C3 and C5 and complement-like proteins [, ].
This entry represents a class of homeobox domain that differs substantially from the typical homeobox domain described in . It is found in both C4 and C3 plants [].
Flavocytochrome C3 (Fcc3) enzymes from a number of Shewanella species, including Shewanella frigidimarina (strain NCIMB 400), have respiratory fumarate reductase activity, which enables the bacteria to respire anaerobically with fumarate as a terminal electron acceptor. Flavocytochrome C3 in S. frigidimarina is a soluble, single chain tetrahaem enzyme found in the periplasm, making it distinct from other bacterial fumarate reductases (), which are membrane-bound, multi-subunit enzymes, even though their function is analogous.Shewanella Fcc3 is composed of three domains: an N-terminal tetrahaem cytochrome domain, a flavin domain and a clamp domain. The cytochrome domain can also occur on its own in some tetrahaem cytochromes implicated in iron oxidation. This entry represents the cytochrome domain, which has a different arrangement of the polypeptide chain in comparison to classical tetra-haem cytochrome C3 [, ].
This entry represents geranylgeranylglyceryl phosphate (GGGP) synthase and Heptaprenylglyceryl phosphate (HepGP) synthase.GGGP synthase is a prenyltransferase that catalyses the transfer of the geranylgeranyl moiety of geranylgeranyl diphosphate (GGPP) to the C3 hydroxyl of sn-glycerol-1-phosphate (G1P). This reaction is the first ether-bond-formation step in the biosynthesis of archaeal membrane lipids. This entry also matches putative glycerol-1-phosphate prenyltransferases that may catalyse the transfer of a prenyl moiety to sn-glycerol-1-phosphate (G1P) []. HepGP synthase is a prenyltransferase that catalyses in vivo the transfer of the heptaprenyl moiety of heptaprenyl pyrophosphate (HepPP; 35 carbon atoms) to the C3 hydroxyl of sn-glycerol-1-phosphate (G1P), producing heptaprenylglyceryl phosphate (HepGP) [].
This entry represents geranylgeranylglyceryl phosphate (GGGP) synthase and Heptaprenylglyceryl phosphate (HepGP) synthase.GGGP synthase is a prenyltransferase that catalyses the transfer of the geranylgeranyl moiety of geranylgeranyl diphosphate (GGPP) to the C3 hydroxyl of sn-glycerol-1-phosphate (G1P). This reaction is the first ether-bond-formation step in the biosynthesis of archaeal membrane lipids. This entry also matches putative glycerol-1-phosphate prenyltransferases that may catalyse the transfer of a prenyl moiety to sn-glycerol-1-phosphate (G1P) []. HepGP synthase is a prenyltransferase that catalyses in vivo the transfer of the heptaprenyl moiety of heptaprenyl pyrophosphate (HepPP; 35 carbon atoms) to the C3 hydroxyl of sn-glycerol-1-phosphate (G1P), producing heptaprenylglyceryl phosphate (HepGP) [].
This group represents complement control proteins, vaccinia virus C3-type. The vaccinia virus complement control protein C3 is involved in modulating the host inflammatory response by blocking both classical and alternative pathways of complement activity through its ability to bind host complement components C3b and C4b (complement 3b and 4b, respectively) []. Protein B5, another member of this group, binds complement components C3 and C1q []. By blocking complement activation at multiple sites, the complement control proteins can down-regulate pro-inflammatory chemotactic factors (C3a, C4a, and C5a), resulting in reduced cellular influx and inflammation..
This domain is found in the C-terminal of lysine-2,3-aminomutase (LAM) and is involved in dimerisation []. LAM catalyses the interconversion of L-alpha-lysine and L-beta-lysine, which proceeds by migration of the amino group from C2 to C3 concomitant with cross-migration of the 3-pro-R hydrogen of L-alpha-lysine to the 2-pro-R position of L-beta-lysine.
SCIN is released by Staphylococcus aureus to counteract the host immune defense. The protein binds to and inhibits C3 convertases on the bacterial surface, reducing phagocytosis and blocking downstream effector functions by C3b deposition on its surface []. An 18 residue stretch 31-48 is crucial for SCIN activity [].
This entry includes complement C3, a major component in the both the classical and alternative complement activation pathways. C3 is cleaved into two chains, known as alpha (C3a) and beta (C3b) by C3 convertases. C3b binds to cell surface carbohydrates or immune aggregates []. C3a is an anaphylatoxin and mediator of a localized inflammatory response, acting as a chemoattractant for neutrophils []. Both alpha and beta chains can be further processed to generate fragments with other properties; for example, C3-beta-c is also a chemoattractant [].This entry also includes complement C3-like proteins from snake venoms, such as AVF-1 and -2 from Austrelaps superbus, which have been shown to activate human complement Factor B in the presence of Factor D and Mg2+, and deplete the complement activity in human and guinea pig serum [].
This entry represents superantigen toxins from Staphylococcus aureus and Streptococcus pyogenes, which share a common core structure consisting of beta(2)-α-β(2). S. aureus toxins with this fold include: enterotoxins A (SEA) [], B (SEB) [], C2 (SEC2) [], C3 (SEC3) []and H (SEH) [], heat shock syndrome toxin-1 [], and superantigen-like proteins SET1 []and SET3 []. S. pyogenes toxins with this fold include: pyrogenic exotoxins A1 []and Spe-J [], and in superantigen proteins Spe-C [], Spe-H [], Smez-2 []and SSA [].
Caliciviruses are positive-stranded ssRNA viruses that cause gastroenteritis []. The calicivirus genome contains two open reading frames, ORF1 and ORF2 [, ]. ORF1 encodes a non-structural polypeptide, which has RNA helicase, cysteine protease and RNA polymerase activity. The cysteine peptidases of the Calciviruses belong to MEROPS peptidase families C3 (subfamilies A to G), C24, C28, C37 and C40. The regions of the poly-protein in which these activities lie are similar to proteins produced by the picornaviruses [, ].
This group represents a complement factor B. Factor B is part of the alternate pathway of the complement system. It is cleaved by factor D into 2 fragments: Ba and Bb. Bb, a serine protease, then combines with complement factor 3b to generate the C3 or C5 convertase. Bb is involved in the proliferation of preactivated B lymphocytes, while Ba inhibits their proliferation [, ].
This entry represents the lysine-2,3-aminomutase (LAM) family of proteins. LAM catalyses the interconversion of L-alpha-lysine and L-beta-lysine, which proceeds by migration of the amino group from C2 to C3 concomitant with cross-migration of the 3-pro-R hydrogen of L-alpha-lysine to the 2-pro-R position of L-beta-lysine. Glutamate 2,3-aminomutase is closely related to LAM, but can be distinguished by architecture (longer N-terminal region, shorter C-terminal region) and replacement of key lysine-binding residues []. Glutamate 2,3-aminomutase catalyses the interconversion of L-glutamate and L-beta-glutamate [].
In proteins belonging to the c-type cytochrome family [], the haem group is covalently attached by thioether bonds to two conserved cysteine residues located in the cytochrome c centre. Cytochromes c typically function in electron transfer, but c-type cytochrome centres are also found in the active sites of many enzymes.This domain contains multiple CxxCH motifs. There are a variable number of helices, as well as a little beta structure present in multihaem cytochromes, but they do not form a true structural fold. Cytochrome (cyt) c3-like proteins are multihaem cytochromes, including cyt c3 with four haem groups [], cyt c7 (cyt c551.5) with three haem groups (deletion of one cyt c3 haem-binding site), nine-haem cyt c (tandem repeat of two cyt c3-like domains with an additional haem-binding site), and 16-haem cyt c HmcA (tandem repeat of four cyt c3-like domains). The photosynthetic reaction centre composed of a cytochrome subunit is also a multihaem cytochrome []. In addition, the di-haem elbow motif shows a similar structure, the main characteristic feature of this motif being the packing of its two haems; many members of this group of proteins contain one or more complete motifs flanked by incomplete motifs and/or other domains. For example, the di-haem elbow motif is present in the multihaem cytochrome domain found in the periplasmic nitrate reductase subunit NapB [], in hydroxylamine oxioreductase HAO (contains 3 complete motifs), in cyt c554 (contains one complete motif), in cyt c nitrite reductase, and in the N-terminal domain of flavocytochrome c3 (respiratory fumarate reductase).
This enzyme, known also as GGGP synthase and GGGPS, is a prenyltransferase that catalyses the transfer of the geranylgeranyl moiety of geranylgeranyl diphosphate (GGPP) to the C3 hydroxyl of sn-glycerol-1-phosphate (G1P). It catalyses the stereospecific first step in the biosynthesis of the characteristic membrane diether lipids of archaea. To a much lesser extent, is also able to use heptaprenyl pyrophosphate (HepPP; 35 carbon atoms) as the prenyl donor. Interestingly, the closest homologues outside this family are not the functionally equivalent enzymes of other archaea, but rather functionally distinct bacterial enzymes [, ].
SR-25, otherwise known as ADP-ribosylation factor-like factor 6-interacting protein 4, is expressed in virtually all tissue types. At the N terminus there is a repeat of serine-arginine (SR repeat), and towards the middle of the protein there are clusters of both serines and of basic amino acids. The presence of many nuclear localisation signals strongly implies that this is a nuclear protein that may contribute to RNA splicing []. SR-25 is also implicated, along with heat-shock-protein-27, as a mediator in the Rac1 (GTPase ras-related C3 botulinum toxin substrate 1; also see ) signalling pathway [].
Cytochromes c (cytC) 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 III comprises the low redox potential multiple haem cytochromes: cyt C7 (trihaem), C3 (tetrahaem),and high-molecular-weight cytC, HMC (hexadecahaem), with only 30-40 residues per haem group. The haem c groups, all bis-histidinyl coordinated,are structurally and functionally nonequivalent and present different redoxpotentials in the range 0 to -400 mV []. The 3D structures of a number of cyt C3 proteins have been determined. The proteinsconsist of 4-5 α-helices and 2 β-strands wrapped around a compactcore of four non-parallel haems, which present a relatively high degree of exposure to the solvent. The overall protein architecture, haem plane orientations and iron-iron distances are highly conserved [].
Cytochromes c (cytC) 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.This family, found in sulphate-reducers, represents a cytochrome containing sixteen haem groups which forms part of a transmembrane protein complex that allows electron flow from the periplasmic hydrogenase to the cytoplasmic enzymes that catalyse reduction of sulphates []. HmcA () from Desulfovibrio vulgaris strain Hildenborough is composed of three distinct regions; an N-terminal three-haem domain homologous to cytochrome c7, a four-haem cyctochrome c3-like domain, and a C-terminal nine-haem cytochrome Hcc-like domain [, ]. This last domain is composed of two cytochrome c3-like domains with an isolated haem group inserted between them. HcmA interacts specifically with cytochrome c3 [], where the last haem group of HcmA and haem four of cytochrome c3 interact to provide the likely site of electron transfer between molecules [].
Cytochromes c (cytC) 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 III comprises the low redox potential multiple haem cytochromes: C3 (tetrahaem),and high-molecular-weight cytC, HMC (hexadecahaem), with only 30-40 residues per haem group. The haem c groups, all bis-histidinyl coordinated,are structurally andfunctionally nonequivalent and present different redoxpotentials in the range 0 to -400 mV []. The 3D structures of a number of cyt C3 proteins have been determined. The proteinsconsist of 4-5 α-helices and 2 β-strands wrapped around a compactcore of four non-parallel haems, which present a relatively high degree of exposure to the solvent. The overall protein architecture, haem plane orientations and iron-iron distances are highly conserved [].
Malate dehydrogenase () (MDH) []catalyzes the interconversionof malate to oxaloacetate utilizing the NAD/NADH cofactor system. The enzymeparticipates in the citric acid cycle and exists in allaerobics organisms.While prokaryotic organisms contains a single form of MDH, in eukaryotic cellsthere are two isozymes: one which is located in the mitochondrial matrix andthe other in the cytoplasm. Fungi and plants also harbor a glyoxysomal formwhich functions in the glyoxylate pathway. In plants chloroplast there is anadditional NADP-dependent form of MDH () which is essential forboth the universal C3 photosynthesis (Calvin) cycle and the more specialisedC4 cycle.The pattern for this enzyme includestwo residues involved in the catalytic mechanism []: an aspartic acid whichis involved in a proton relay mechanism, and an arginine which binds thesubstrate.
This entry represents complement factor 5 (C5; MEROPS identifier I39.952). C5 is a component of the lytic complex consisting of factors C5-C9 which attacks bacterial cell membranes. C5 is synthesized as a precursor and is activated by a C5 convertase. The anaphylatoxin C5a is released and is a mediator of local inflammation. C5a is also a chemokine, directing polymorphonuclear leukocytes to the site of infammation. C5a binds to the receptor C5AR1, which results in intracellular calcium release, smooth muscle contraction, increased vascular permeability, and histamine release from mast cells and basophilic leukocytes []. The tertiary structure of C5 has been solved and the fold is similar to that of complement C3 and the peptidase inhibitor alpha2-macroglobulin [].
Viruses in the order Picornavirales infect different vertebrate, invertebrate, and plant hosts and are responsible for a variety of human, animal, and plant diseases. These viruses have a single-stranded, positive sense RNA genome that generally translates a large precursor polyprotein which is proteolytically cleaved after translation to generate mature functional viral proteins. This process is usually mediated by (more than one) proteases, and a 3C (for the family Picornaviridae) or 3C-like (3CL) protease (for other families) plays a central role in the cleavage of the viral precursor polyprotein. In addition to this key role, 3C/3C-like protease is able to cleave a number of host proteins to remodel the cellular environment for virus reproduction [, , , , , ]. The Picornavirales 3C/3C-like protease domain forms the MEROPS peptidase family C3 (picornain family) of clan PA.The 3C/3CL protease domain adopts a chymotrypsin-like fold with a cysteine nucleophile in place of a commonly found serine which suggests that the cysteine and serine perform an analogous catalytic function. The catalytic triad is made of a histidine, an aspartate/glutamate and the conserved cysteine in this sequential order. The 3C/3CL protease domain folds into two antiparallel beta barrels that are linked by a loop with a short α-helix in its middle, and flanked by two other α-helices at the N- and C-terminal. The two barrels are topologically equivalent and are formed by six antiparallel beta strands with the first four organised into a Greek key motif. The active-site residues are located in the cleft between the two barrels with the nucleophilic Cys from the C-terminal barrel and the general acid base His-Glu/Asp from the N-terminal barrel [, , ].This entry includes cysteine peptidases that belong to MEROPS peptidase family C3 (picornain, clan PA(C)), subfamilies C3A and C3B.
Functionally characterised members of the 6-8 TMS Triose-phosphate Transporter (TPT) family are derived from the inner envelopemembranes of chloroplasts and non-green plastids of plants. Under normal physiological conditions, chloroplast TPTs mediate a strict antiport of substrates, frequently exchanging an organic three carbon compound phosphate ester for inorganic phosphate (Pi) [, ].Normally, a triose-phosphate, 3-phosphoglycerate, or another phosphorylated C3compound made in the chloroplast during photosynthesis, exits the organelle into thecytoplasm of the plant cell in exchange for Pi. However, experiments with reconstituted translocator in artificial membranes indicate that transport can also occur by a channel-like uniport mechanism with up to 10-fold higher transport rates. Channel opening may be induced by a membrane potential of large magnitude and/or by high substrate concentrations. Non-green plastid and chloroplast carriers, such as those from maize endosperm and root membranes, mediate transport of C3 compounds phosphorylated at carbon atom 2, particularly phosphoenolpyruvate, in exchange for Pi. These are the phosphoenolpyruvate:Pi antiporters (PPT). Glucose-6-P has also been shown to be a substrate of some plastid translocators (GPT). The three types of proteins (TPT, PPT and GPT) are divergent in sequence as well as substrate specificity, but their substrate specificities overlap.TPT paralogues are also present in Saccharomyces cerevisiae, which are functionally uncharacterised.
The CLIP domain is a regulatory domain which controls the proteinase action of various proteins of the trypsin family, e.g. easter and pap2. The domain is restricted to the arthropoda and found in varying copy numbers (from one to five in Drosophila proteins). It is always found N-terminal to the chymotrypsin serine protease domain, which belong to MEROPS peptidase family S1A. The CLIP domain remains linked to the protease domain after cleavage of a conserved residue which retains the protein in zymogen form. It is named CLIP because it can be drawn in the shape of a paper clip. It has many disulphide bonds and highly conserved cysteine residues, and so it folds extensively [, ]. The clip domain adopts an α/β mixed fold consisting of two helices and an antiparallel distorted β-sheet made of four strands. The two helices are antiparallel and are almost perpendicular to the β-sheet. Three disulfide bridges (C1-C5, C2-C4, C3-C6) stabilize the β-sheet, C3 being the only cysteine that is not located on a β-strand. The clip domain is located opposite the activation loop and contacts the C-terminal α-helix of the SP domain []. The CLIP domain is present in silkworm prophenoloxidase-activating enzyme [].
These proteins belong to MEROPS peptidase family S1 (chymotrypsin family, clan PA(S)), subfamily S1A.This family contains the mammalian mannan-binding lectin-associated serine proteases 1 and 2 (MASP1 and MASP2) and complement components C1s and C1r. The C1 complex, containing C1q, C1s, and C1r, triggers the classical complement pathway. When C1q interacts with antibody, C1r becomes autocatalytically activated. Activated C1r in turn activates C1s, which then cleaves C2 and C4 in the classical pathway.Mannose-binding lectin (MBL) complexes with MASP1, MASP2, and a smaller alternative splice product of the MASP2 gene. Binding of MBL to carbohydrates on the surface of microorganisms triggers activation of the associated MASPs. Then MASP1 activates C3 and C2, whereas MASP2 activates C4 and C2 []. Based on the fact that the gene structures of MASP1, C1r, and C1s are similar except that C1r and C1s lack introns in the region encoding the trypsin domain, it has been proposed that the MASP proteins evolved earlier than C1r and C1s []. The complement pathway is also involved in development [].These sequences typically contain a signal sequence, followed by a CUB domain, an EGF-like domain (which often is not detected), a second CUB domain, two sushi domains (sometimes only one is detected), and a trypsin domain.
Pyruvate phosphate dikinase (PPDK, or pyruvate orthophosphate dikinase) is found in plants, bacteria and archaea. The amino acid sequence identity between bacterial and plant enzymes is high, and they are similar in sequence to other PEP-utilizing enzymes. PPDK catalyses the reversible conversion of ATP and pyruvate to AMP and PEP (phosphoenolpyruvate). In bacteria such as Clostridium symbiosum (Bacteroides symbiosus), PPDK uses Mg2+ and NH4+ ions as cofactors []. The enzyme has three domains: the N- and C-terminal domains each have an active site centre that catalyses a different step in the reaction, and the middle domain has a carrier histidine residue that moves between the two active centres.In plants, PPDK is localised predominantly in chloroplast stroma where it catalyses the rate-limiting step in the C4 photosynthetic pathway, namely the synthesis of PEP, which acts as the primary CO2 acceptor in C4 photosynthesis []. PPDK activity in C4 plants is strictly regulated by light, its activity decreasing in darkness. This response is regulated by phosphorylation and dephosphorylation of the enzyme using ADP; such regulation is not seen in the bacterial form of the enzyme. PPDK is also found in C3 plants, but it is not known to have a photosynthetic role [].
The CLIP domain is a regulatory domain which controls the proteinase action of various proteins of the trypsin family, e.g. easter and pap2. The domain is restricted to the arthropoda and found in varying copy numbers (from one to five in Drosophila proteins). It is always found N-terminal to the chymotrypsin serine protease domain, which belong to MEROPS peptidase family S1A. The CLIP domain remains linked to the protease domain after cleavage of a conserved residue which retains the protein in zymogen form. It is named CLIP because it can be drawn in the shape of a paper clip. It has many disulphide bonds and highly conserved cysteine residues, and so it folds extensively [, ]. The clip domain adopts an α/β mixed fold consisting of two helices and an antiparallel distorted β-sheet made of four strands. The two helices are antiparallel and are almost perpendicular to the β-sheet. Three disulfide bridges (C1-C5, C2-C4, C3-C6) stabilize the β-sheet, C3 being the only cysteine that is not located on a β-strand. The clip domain is located opposite the activation loop and contacts the C-terminal α-helix of the SP domain []. The CLIP domain is present in silkworm prophenoloxidase-activating enzyme [].
This entry contains serum complement C3 and C4 precursors and alpha-macrogrobulins. The alpha-macroglobulin (aM) family of proteins includes protease inhibitors [], typified by the human tetrameric a2-macroglobulin (a2M); they belong to the MEROPS proteinase inhibitor family I39, clan IL. These protease inhibitors share several defining properties, which include (i) the ability to inhibit proteases from all catalytic classes, (ii) the presence of a 'bait region' and a thiol ester, (iii) a similar protease inhibitorymechanism and (iv) the inactivation of the inhibitory capacity by reaction of the thiol ester with small primary amines. aM protease inhibitors inhibit by steric hindrance []. The mechanism involves protease cleavage of the bait region, a segment of the aM thatis particularly susceptible to proteolytic cleavage, which initiates a conformational change such that the aM collapses about the protease. In the resulting aM-protease complex, the active site of the protease is sterically shielded, thus substantially decreasing access to protein substrates. Two additional events occur as a consequence of bait region cleavage, namely (i) the h-cysteinyl-g-glutamyl thiol ester becomes highly reactive and (ii) a major conformational change exposes a conserved COOH-terminal receptor binding domain [](RBD). RBD exposure allows the aM protease complex to bind to clearance receptors and be removed from circulation []. Tetrameric, dimeric, and, more recently, monomeric aM protease inhibitors have been identified [, ].This entry represents a conserved region, located towards the C terminus, which contains the two residues involved in the thiol ester bond.
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 [].
This entry contains serum complement C3 and C4 precursors and alpha-macrogrobulins. The alpha-macroglobulin (aM) family of proteins includes protease inhibitors [, ], typified by the human tetrameric a2-macroglobulin (a2M); they belong to the MEROPS proteinase inhibitor family I39, clan IL. These protease inhibitors share several defining properties, which include (i) the ability to inhibit proteases from all catalytic classes, (ii) the presence of a 'bait region' and a thioester, (iii) a similar protease inhibitory mechanism and (iv) the inactivation of the inhibitory capacity by reaction of the thiol ester with small primary amines. aM protease inhibitors inhibit by steric hindrance []. The mechanism involves protease cleavage of the bait region, a segment of the aM that is particularly susceptible to proteolytic cleavage, which initiates a conformational change such that the aM collapses about the protease. In the resulting aM-protease complex, the active site of the protease is sterically shielded, thus substantially decreasing access to protein substrates. Two additional events occur as a consequence of bait region cleavage, namely (i) the h-cysteinyl-g-glutamyl thiol ester becomes highly reactive and (ii) a major conformational change exposes a conserved COOH-terminal receptor binding domain [](RBD). RBD exposure allows the aM protease complex to bind to clearance receptors and be removed from circulation []. Tetrameric, dimeric, and, more recently, monomeric aM protease inhibitors have been identified [, ].
(Bovine immunodeficiency virus) (BIV), like the human immunodeficiency virus, is a lentivirus. It shows a great deal of genomic diversity, mostly in the viral envelope gene []. This property of the BIV group of viruses may play an important role in the pathobiology of the virus, particularly the conserved (C) 2, hypervariable (V) 1, V2 and C3 regions [].The surface protein (SU) attaches the virus to the host cell by binding to its receptor. This interaction triggers the refolding of the transmembrane protein (TM) and is thought to activate its fusogenic potential by unmasking its fusion peptide. Fusion occurs at the host cell plasma membrane.The transmembrane protein (TM) acts as a class I viral fusion protein. Under the current model, the protein has at least 3 conformational states: pre-fusion native state, pre-hairpin intermediate state, and post-fusion hairpin state. During viral and target cell membrane fusion, the coiled coil regions (heptad repeats) assume a trimer-of-hairpins structure, positioning the fusion peptide in close proximity to the C-terminal region of the ectodomain. The formation of this structure appears to drive apposition and subsequent fusion of viral and target cell membranes. Membranes fusion leads to delivery of the nucleocapsid into the cytoplasm.
Viruses in the order Picornavirales infect different vertebrate, invertebrate, and plant hosts and are responsible for a variety of human, animal, and plant diseases. These viruses have a single-stranded, positive sense RNA genome that generally translates a large precursor polyprotein which is proteolytically cleaved after translation to generate mature functional viral proteins. This process is usually mediated by (more than one) proteases, and a 3C (for the family Picornaviridae) or 3C-like (3CL) protease (for other families) plays a central role in the cleavage of the viral precursor polyprotein. In addition to this key role, 3C/3C-like protease is able to cleave a number of host proteins to remodel the cellular environment for virus reproduction [, , , , , ]. The Picornavirales 3C/3C-like protease domain forms the MEROPS peptidase family C3 (picornain family) of clan PA.The 3C/3CL protease domain adopts a chymotrypsin-like fold with a cysteine nucleophile in place of a commonly found serine which suggests that the cysteine and serine perform an analogous catalytic function. The catalytic triad is made of a histidine, an aspartate/glutamate and the conserved cysteine in this sequential order. The 3C/3CL protease domain folds into two antiparallel beta barrels that are linked by a loop with a short α-helix in its middle, and flanked by two other α-helices at the N- and C-terminal. The two barrels are topologically equivalent and are formed by six antiparallel beta strands with the first four organised into a Greek key motif. The active-site residues are located in the cleft between the two barrels with the nucleophilic Cys from the C-terminal barrel and the general acid base His-Glu/Asp from the N-terminal barrel [, , ].
Viruses in the order Picornavirales infect different vertebrate, invertebrate, and plant hosts and are responsible for a variety of human, animal, and plant diseases. These viruses have a single-stranded, positive sense RNA genome that generally translates a large precursor polyprotein which is proteolytically cleaved after translation to generate mature functional viral proteins. This process is usually mediated by (more than one) proteases, and a 3C (for the family Picornaviridae) or 3C-like (3CL) protease (for other families) plays a central role in the cleavage of the viral precursor polyprotein. In addition to this key role, 3C/3C-like protease is able to cleave a number of host proteins to remodel the cellular environment for virus reproduction [, , , , , ]. The Picornavirales 3C/3C-like protease domain forms the MEROPS peptidase family C3 (picornain family) of clan PA.The 3C/3CL protease domain adopts a chymotrypsin-like fold with a cysteine nucleophile in place of a commonly found serine which suggests that the cysteine and serine perform an analogous catalytic function. The catalytic triad is made of a histidine, an aspartate/glutamate and the conserved cysteine in this sequential order. The 3C/3CL protease domain folds into two antiparallel beta barrels that are linked by a loop with a short α-helix in its middle, and flanked by two other α-helices at the N- and C-terminal. The two barrels are topologically equivalent and are formed by six antiparallel beta strands with the first four organised into a Greek key motif. The active-site residues are located in the cleft between the two barrels with the nucleophilic Cys from the C-terminal barrel and the general acid base His-Glu/Asp from the N-terminal barrel [, , ].This entry represents a rice tungro spherical waikavirus-type peptidase that belongs to MEROPS peptidase family C3G. It is a picornain 3C-type protease, and is responsible for the self-cleavage of the positive single-stranded polyproteins of a number of plant viral genomes. The location of the protease activity of the polyprotein is at the C-terminal end, adjacent and N-terminal to the putative RNA polymerase [, ].
Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies.A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation [].
Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies.A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the N-terminal domain superfamily. Structurally, this domain has a ferredoxin-like fold, which consists of an alpha+beta sandwich with antiparallel β-sheet.
Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies.A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain superfamily.
Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies.A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain.
Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies.A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation [].
Hydrogenases catalyse the reversible oxidation of molecular hydrogen and play a vital role in anaerobic metabolism. Metal-containing hydrogenases are subdivided into three classes: Fe ('iron only') hydrogenases; Ni-Fe hydrogenases; and Ni-Fe-Se hydrogenases []. Hydrogen oxidation is coupled to the reduction of electron acceptors (such as oxygen, nitrate, sulphate, carbon dioxide and fumarate), whereas proton reduction (hydrogen evolution) is essential in pyruvate fermentation or in the disposal of excess electrons.The Ni-Fe hydrogenases,when isolated, are found to catalyse both hydrogen evolution and uptake, with low-potential multihaem cytochromes, such as cytochrome c3, acting as either electron donors or acceptors, depending on their oxidation state. Both periplasmic (soluble) and membrane-bound hydrogenases are known.The Ni-Fe hydrogenases are heterodimeric proteins consisting of small (S) and large (L) subunits. The small subunit contains three iron-sulphur clusters (two [4Fe-4S]and one [3Fe-4S]); the large subunit contains a nickel ion []. Small subunits of membrane-bound Ni-Fe hydrogenases contain a C-terminal domain of about 40 residues that is absent in periplasmic forms.The 3D structure of the Ni-Fe hydrogenase from Desulfovibrio gigas has been determined at 2.85A resolution []. The small subunit consists of two domains, I(S) and II(S). The alpha/beta twisted open sheet structure of the N-terminal I(S) domain is similar to that of flavodoxin; the C-terminal II(S) domain contains two α-helices and has no β-structure. The Fe-S clusters are distributed almost along a straight line, with the [3Fe-4S]cluster located half-way between the two [4Fe-4S]clusters. The two [4Fe-4S]clusters have been termed proximal (prox) and distal (dist), based on their distance to the Ni atom. Domain I(S) binds the [4Fe-4S]prox cluster, while domain II(S) binds the [4Fe-4S]dist and [3Fe-4S]clusters. The [4Fe-4S]prox cluster is coordinated by Cys-17, Cys-20, Cys-112 and Cys-148; [4Fe-4S]dist is coordinated by His-185, Cys-188, Cys-213 and Cys-219; and [3Fe-4S]is coordinated by Cys-228, Cys-246 and Cys-249 [4Fe-4S]dist is the first known example of a [4Fe-4S]cluster in protein structure ligated by a His side chain. A crown of acidic residues surrounds the partially-exposed His-185 and this might provide a recognition site for the redox partner (cytochrome c3) []. A mechanism of electron transfer from the Ni active site through the Fe-S clusters to the cytochrome c3 has been suggested []. The role of the [3Fe-4S]cluster is not clear: its high redox potential and its absence from some homologous hydrogenases put its involvement in electron transfer in doubt [].
This domain defines cysteine peptidases belong to MEROPS peptidase family C3 (picornain, clan PA(C)), subfamilies 3CA and 3CB. The protein fold of this peptidase domain for members of this family resembles that of the serine peptidase, chymotrypsin [], the type example for clan PA.Picornaviral proteins are expressed as a single polyproteinwhich is cleaved by the viral 3C cysteine protease []. The poliovirus polyprotein is selectively cleaved between the Gln-|-Gly bond. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly.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.
