This entry represents the complement component C9, which is a component of the membrane attack complex (MAC) which forms pores in the membranes of cells of invading organisms. MAC forms when C5 is cleaved into C5a and C5b, and C5b binds sequentially C6, C7, C8 andmultiple copies of the pore-forming subunit C9 []. C9 is the pore-forming subunit of the MAC [], and up to twenty subunits assemble to form a large beta barrel that forms a pore with a diameter of 100 angstroms in target membranes []. C9 is processed into a two-chain form, chains C9a and C9b, by thrombin []. The tertiary structure of C9 has been solved and shows the following domains (N- to C-terminal): TSP type-1, LDL-receptor class A, MACPF and EGF-like []. A variant of C9 is associated with macular degeneration of the eye [].
Complement component C9 is a multi-domain protein that contains anN-terminal type-1 TSP domain, an LDL-receptor class A repeat, a number ofpotential transmembrane (TM) regions and a C-terminal EGF-like domain [, , ]. Hydropathy analysis of the sequence indicates the N-terminal half of C9 to be predominantly hydrophilic in character, while the C-terminal section is more hydrophobic. The amphipathic organisation of the primary structureis consistent with the known potential of polymerised C9 to penetrate lipidbilayers, causing the formation of transmembrane channels [, ]
CD59 is a potent inhibitor of the complement membrane attack complex (MAC) action. It acts by binding to the C8 and/or C9 complements of the assembling MAC, thereby preventing incorporation of the multiple copies of C9 required for complete formation of the osmolytic pore [].
This entry represents phytoene desaturase (PDS) from plants and cyanobacteria (blue-green algae). It is an essential carotenoid biosynthetic enzyme. It converts phytoene into zeta-carotene via the intermediary of phytofluene by the symmetrical introduction of two double bonds at the C-11 and C-11' positions of phytoene with a concomitant isomerization of two neighbouring double bonds at the C9 and C9' positions from trans to cis [, ].This entry does not include plant chloroplast transit peptides and the entry does not contain zeta-carotene desaturase, which is a closely related family in the same pathway.
This domain is found in complement component proteins, complement component factor 1 and agrin. Complement components C5b, C6, C7 C8 and C9 are the constituents of the membrane attack complex (MAC) that plays a key role in the innate and adaptive immune response by forming pores in the plasma membrane of target cells. Its assembly is initiated by protelytic cleavage of C5 into C5a and C5b. C5b binds sequentially C6, C7, C8 and multiple copies of the pore-forming subunit C9. Factor I is responsible for cleaving alpha chains of C4B and C3B in the presence of the cofactors C4-binding protein and factor H respectively. Agrin is a component of the basal lamina that causes the aggregation of acetylcholine receptors and acetylcholine-esterase on the surface of muscle fibres of the neuromuscular junction.
This entry represents the alpha chain of complement component C8. C8 is a complex of three chains, alpha, beta and gamma []. C8 is a component of the membrane attack complex (MAC) which forms pores in the membranes of cells of invading organisms. MAC forms when C5 is cleaved into C5a and C5b, and C5b binds sequentially C6, C7, C8 and multiple copies of the pore-forming subunit C9 [, ]. C8 alpha is synthesized as a precursor and activation occurs by cleavage at paired basic residues by kallikrein-related peptidase 4 []. The tertiary structure of C8 alpha has been solved and shows the following domains (N- to C-terminal): first TSP type-1, LDL-receptor class A, MACPF, EGF-like, and second TSP type-1 []. This domain architecture is shared with the beta chain of C8.
This entry represents complement component C7, a subunit of the membrane attack complex (MAC) which forms pores in the membranes of cells of invading organisms. C7 anchors the MAC to the membrane. MAC forms when C5 is cleaved into C5a and C5b, and C5b binds sequentially C6, C7, C8 and multiple copies of the pore-forming subunit C9 []. The structure of C7 has been solved and C7 contains a several domains, which from N to C terminus are: TSP type-1, LDL-receptor class A, MACPF, EGF-like, another TSP type-1 and two sushi domains []. Variants of C7 are associated with immunodeficiency diseases and susceptibility to infection such as meningococcal disease caused by Neisseria meningitidis [].
This entry represents the beta chain of complement component C8. C8 is a complex of three chains, alpha, beta and gamma []. C8 is a component of the membrane attack complex (MAC) which forms pores in the membranes of cells of invading organisms. MAC forms when C5 is cleaved into C5a and C5b, and C5b binds sequentially C6, C7, C8 and multiple copies of the pore-forming subunit C9 [, ]. C8 beta is synthesized as a precursor and activation occurs by cleavage by kallikrein-related peptidase 4 []. The tertiary structure of C8 beta has been solved and shows the following domains (N- to C-terminal): first TSP type-1, LDL-receptor class A, MACPF, EGF-like, second TSP type-1 []. This domain architecture is shared with the alpha chain of C8.
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 [].
The frizzled (fz) domain is an extracellular domain of about 120 amino acids.It was first identified in the alpha-1 chain of type XVIII collagen and in members of the Frizzled family of seven transmembrane (7TM) proteins which act as receptors for secreted Wingless (Wg)/Wnt glycoproteins []. In addition to these proteins, one or two copies of the fz domain are also found [, , , , ]in:The Frzb family; secreted frizzled-like proteins.Smoothened; another 7TM receptor involved in hedgehog signaling.Carboxpeptidase Z (CPZ).Transmembrane serine protease corin (atrial natriuretic peptide-converting enzyme).Two receptor tyrosine kinases (RTKs) subfamilies, the Ror family and the muscle-specific kinase (MuSK) family.As the fz domain contains 10 cysteines which are largely conserved, it has also been called cysteine-rich domain (CRD) []. The fz domain also contains several other highly conserved residues, for example, a basic amino acid follows C6, and a conserved proline residues lies four residues C-terminal to C9 []. The crystal structure of a fz domain shows that it is predominantly α-helical with all cysteines forming disulphide bonds. In addition to helical regions, two short β-strands at the N terminus form a minimal β-sheet with the second beta sheet passing through a knot created by disulphide bonds [].Several fz domains have been shown to be both necessary and sufficient for Wg/Wnt ligand binding, strongly suggesting that the fz domain is a Wg/Wnt interacting domain [, ].
This entry represents the frizzled domain superfamily.The frizzled (fz) domain is an extracellular domain of about 120 amino acids.It was first identified in the alpha-1 chain of type XVIII collagen and in members of the Frizzled family of seven transmembrane (7TM) proteins which act as receptors for secreted Wingless (Wg)/Wnt glycoproteins []. In addition to these proteins, one or two copies of the fz domain are also found [, , , , ]in:The Frzb family; secreted frizzled-like proteins.Smoothened; another 7TM receptor involved in hedgehog signaling.Carboxpeptidase Z (CPZ).Transmembrane serine protease corin (atrial natriuretic peptide-converting enzyme).Two receptor tyrosine kinases (RTKs) subfamilies, the Ror family and the muscle-specific kinase (MuSK) family.As the fz domain contains 10 cysteines which are largely conserved, it has also been called cysteine-rich domain (CRD) []. The fz domain also contains several other highly conserved residues, for example, a basic amino acid follows C6, and a conserved proline residues lies four residues C-terminal to C9 []. The crystal structure of a fz domain shows that it is predominantly α-helical with all cysteines forming disulphide bonds. In addition to helical regions, two short β-strands at the N terminus form a minimal β-sheet with the second beta sheet passing through a knot created by disulphide bonds [].Several fz domains have been shown to be both necessary and sufficient for Wg/Wnt ligand binding, strongly suggesting that the fz domain is a Wg/Wnt interacting domain [, ].
The superfamily of alphaviruses includes 26 known members. They infect a variety of hosts including mosquitoes, birds, rodents and other mammals with worldwide distribution. Alphaviruses also pose a potential threat to human health in many areas. For example, Venezuelan Equine Encephalitis Virus (VEEV) causes encephalitis in humans as well as livestock in Central and South America, and some variants of Sinbis Virus (SIN) and Semliki Forest Virus (SFV) have been found to cause fever and arthritis in humans [].Alphaviruses possess a single-stranded RNA genome of approximately 12 kb. The genomic RNA of alphaviruses is translated into two polyproteins that, respectively, encode structural proteins and nonstructural proteins. The nonstructural proteins may be translated as one or two polyproteins, nsp123 or nsp1234, depending on the virus. These polyproteins are cleaved to generate nsp1, nsp2, nsp3 and nsp4 by a protease activity that resides within nsp2. The nsp2 protein of alphaviruses has multiple enzymatic activities. Its N-terminal domain has been shown to possess ATPase and GTPase activity, RNA helicase activity and RNA 5'-triphosphatase activity. The C-terminal nsp2pro domain of nsp2 is responsible for the regulation of 26S subgenome RNA synthesis, switching between negative- and positive-strand RNA synthesis, targeting nsp2 for nuclear transport and proteolytic processing of the nonstructural polyprotein [, ]. The nsp2pro domain is a member of peptidase family C9 of clan CA.The nsp2pro domain consists of two distinct subdomains. The nsp2pro N-terminal subdomain is largely α-helical and contains the catalytic dyad cysteine and histidine residues organised in a protein fold that differs significantly from any known cysteine protease or protein folds.The nsp2pro C-terminal subdomain displays structural similarity to S-adenosyl-L-methionine-dependent RNA methyltransferases and provides essential elements that contribute to substrate recognition and may also regulate the structure of the substrate binding cleft [].This domain covers the entire nsp2pro domain.
The family of alphaviruses includes 26 known members. They infect a variety of hosts including mosquitoes, birds, rodents and other mammals with worldwidedistribution. Alphaviruses also pose a potential threat to human health inmany area. For example, Venezuelan Equine Encephalitis Virus (VEEV) causesencephalitis in humans as well as livestock in Central and South America, andsome variants of Sinbis Virus (SIN) and Semliki Forest Virus (SFV) have beenfound to cause fever and arthritis in humans [].Alphaviruses possess a single-stranded RNA genome of approximately 12 kb. The genomic RNA of alphaviruses is translated into two polyproteins that,respectively, encode structural proteins and nonstructural proteins. Thenonstructural proteins may be translated as one or two polyproteins, nsp123 ornsp1234, depending on the virus. These polyproteins are cleaved to generatensp1, nsp2, nsp3 and nsp4 by a protease activity that resides within nsp2. Thensp2 protein of alphaviruses has multiple enzymatic acivities. Its N-terminaldomain has been shown to possess ATPase and GTPase activity, RNA helicaseactivity and RNA 5'-triphosphatase activity. The C-terminal nsp2pro domain ofnsp2 is responsible for the regulation of 26S subgenome RNA synthesis,switching between negative- and positive-strand RNA synthesis, targeting nsp2for nuclear transport and proteolytic processing of the nonstructuralpolyprotein [, ]. The nsp2pro domain is a member of peptidase family C9 of clan CA.The nsp2pro domain consists of two distinct subdomains. Thensp2pro N-terminal subdomain is largely α-helical and contains thecatalytic dyad cysteine and histidine residues organised in a protein foldthat differs significantly from any known cysteine protease or protein folds.The nsp2pro C-terminal subdomain displays structural similarity to S-adenosyl-L-methionine-dependent RNA methyltransferases and provides essential elementsthat contribute to substrate recognition and may also regulate the structureof the substrate binding cleft [].This domain covers the entire nsp2pro domain.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.
