L-amino-acid ligases are ATP-grasp superfamily enzymes that catalyze the formation of an alpha-peptide bond between two l-amino acids in an ATP-dependent manner. They share a common structural architecture that consists of three domains referred to as the A-domain, B-domain and C-domain. The C domain can be further divided into the C1-subdomain and the C2-subdomain []. This entry represents the C2 subdomain.
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.
Munc13 proteins constitute a family of three highly homologous molecules (Munc13-1, Munc13-2 and Munc13-3) with homology to Caenorhabditis elegans Unc-13. Munc13 proteins contain a phorbol ester-binding C1 domain and two C2 domains, which are Ca2+/phospholipid binding domains. Sequence analyses have uncovered two regions called Munc13 homology domains 1 (MHD1) and 2 (MHD2) that are arranged between two flanking C2 domains. MHD1 and MHD2 domains are present in a wide variety of proteins from Arabidopsis thaliana, C. elegans, Drosophila melanogaster (Fruit fly), Mus musculus (Mouse), Rattus norvegicus (Rat) and Homo sapiens (Human), some of which may function in a Munc13-like manner to regulate membrane trafficking [].The MHD1 and MHD2 domains are predicted to be α-helical []. Some proteins known to contain MHD1 and MHD2 domains are listed below:Mammalian Munc13-1. It is specifically targeted to presynaptic active zones and has a central priming function in synaptic vesicle exocytosis from glutaminergic synapses.Mammalian Munc13-2. It plays a role in vesicle maturation during exocytosis as a target of the diacylglycerol second messenger pathway.Mammalian Munc13-3. It probably plays a role in vesicle maturation during exocytosis as a target of the diacylglycerol second messenger pathway.Mammalian Munc13-4. It is predominantly expressed in lung where it is localized to goblet cells of the bronchial epithelium and to alveolar type II cells, both of which are cell types with secretory function.C. elegans Unc-13. It may form part of a signal transduction pathway, transducing the signal from diacylglycerol to effector functions.Mammalian BAI1-associated protein 3 (BAP3), which exhibits the typical Munc13-like domain structure with two C2 domains flanking the MHD1 and MHD2 domains, but which lack the long N terminuswith the C1 domain.Animal calcium-dependent activator proteins for secretion (CAPSs), regulators of large dense-core vesicle secretion. They contain only a MHD1 domain and are otherwise unrelated to Munc13 proteins.A. thaliana hypothetical proteins with MHD1 and MHD2 domains but without C1 and C2 domains.Saccharomyces cerevisiae uncharacterised protein YOR296W, where MHD1 and MHD2 enclose a central C2 domain. YOR296W is presumably involved in bud formation.Schizosaccharomyces pombe hypothetical protein C11E3.02c in chromosome I, where MHD1 and MHD2 enclose a central C2 domain.This entry represents the Munc13 homology domain 1.
Mammalian uncoordinated homology 13 (Munc13) proteins constitute a family of three highly homologous molecules (Munc13-1, Munc13-2 and Munc13-3) with homology to Caenorhabditis elegans Unc-13. Munc13 proteins contain a phorbol ester-binding C1 domain and two C2 domains, which are Ca2+/phospholipid binding domains. Sequence analyses have uncovered two regions called Munc13 homology domains 1 (MHD1) and 2 (MHD2) that are arranged between two flanking C2 domains. MHD1 and MHD2 domains are present in a wide variety of proteins from Arabidopsis thaliana, C. elegans, Drosophila melanogaster (Fruit fly), Mus musculus (Mouse), Rattus norvegicus (Rat) and Homo sapiens (Human), some of which may function in a Munc13-like manner to regulate membrane trafficking [].The MHD1 and MHD2 domains are predicted to be α-helical []. Some proteins known to contain MHD1 and MHD2 domains are listed below:Mammalian Munc13-1. It is specifically targeted to presynaptic active zones and has a central priming function in synaptic vesicle exocytosis from glutaminergic synapses.Mammalian Munc13-2. It plays a role in vesicle maturation during exocytosis as a target of the diacylglycerol second messenger pathway.Mammalian Munc13-3. It probably plays a role in vesicle maturation during exocytosis as a target of the diacylglycerol second messenger pathway.Mammalian Munc13-4. It is predominantly expressed in lung where it is localized to goblet cells of the bronchial epithelium and to alveolar type II cells, both of which are cell types with secretory function.C. elegans Unc-13. It may form part of a signal transduction pathway, transducing the signal from diacylglycerol to effector functions.Mammalian BAI1-associated protein 3 (BAP3), which exhibits the typical Munc13-like domain structure with two C2 domains flanking the MHD1 and MHD2 domains, but which lack the long N terminus with the C1 domain.Animal calcium-dependent activator proteins for secretion (CAPSs), regulators of large dense-core vesicle secretion. They contain only a MHD1 domain and are otherwise unrelated to Munc13 proteins.A. thaliana hypothetical proteins with MHD1 and MHD2 domains but without C1 and C2 domains.Saccharomyces cerevisiae uncharacterised protein YOR296W, where MHD1 and MHD2 enclose a central C2 domain. YOR296W is presumably involved in bud formation.Schizosaccharomyces pombe hypothetical protein C11E3.02c in chromosome I, where MHD1 and MHD2 enclose a central C2 domain.This entry represents the Munc13 homology domain 2.
GAP1 (GTPase-activating protein 1) family members include RASA2 (GAP1m), RASAL (RASAL1), GAP1(IP4BP or RASA3), and CAPRI (RASA4). They all display Ras GAP activity. With the exception of RASA2, they all possess an arginine finger-dependent GAP activity on Rap1 [, ]. They contain N-terminal tandem C2 domain repeats, a centrally located Ras-GAP domain, and a PH (pleckstrin homology) domain containing a Btk motif [].RASAL, like Ca2+ -promoted Ras inactivator (CAPRI, or RASAL4), is a cytosolic protein that undergoes a rapid translocation to the plasma membrane in response to receptor-mediated elevation in the concentration of intracellular free Ca2+, a translocation that activates its ability to function as a RasGAP. However, unlike RASAL4, RASAL undergoes an oscillatory translocation to the plasma membrane that occurs in synchrony with repetitive Ca2+ spikes. Its tandem C2 domains bind phospholipids upon an elevation in the intracellular free Ca2+ concentration ([Ca2+]i) [].
Synaptotagmin-13 (SYT13) belongs to the synaptotagmin family, which is a group of membrane-trafficking proteins that contain two C-terminal C2 domains (known as C2A and C2B domains). Most of the synaptotagmins have a unique N-terminal domain (transmembrane region) that is involved in membrane anchoring or specific ligand binding. Unlike most of the synaptotagmins, SYT13 does not have an N-terminal transmembrane region. Its C2 domains are lacking almost all the residues involved in Ca2+ binding []. It is highly expressed in brain and also detectable at lower levels in non-neuronal tissues []. SYT13 can suppress liver tumour cells and this function may be mediated through pathways implicated in mesenchymal to epithelial transition []. It also affects insulin secretion [].
This entry represents the novel protein kinase C (nPKC) family.The N-terminal regulatory domain of nPKC consists of a C2 domain follows by a double C1 domain (C1A and C1B). The C2 domain does not respond to calcium which makes nPKC diacylglycerol-sensitive but calcium-independent [, , ].PKC is a family of serine- and threonine-specific protein kinases that depend on lipids for activity. They can be activated by calcium but have a requirement for the second messenger diacylglycerol [, ]. Members of this family play key regulatory roles in various cellular processes. Currently, there are ten isoforms of PKC which can be classified into classical (alpha, beta I, beta II, gamma), novel (delta, epsilon, eta, theta) and atypical (zeta, iota/lambda) types based on their primary structure and biochemical characteristics [, , ]. All PKCs contain a C-terminal kinase domain and an N-terminal regulatory domain.
Protein kinase C (PKC) theta is classified as a novel PKC (nPKC). PKC theta is involved in T-cell activation and survival [, , ].The N-terminal regulatory domain of nPKC consists of a C2 domain follows by a double C1 domain (C1A and C1B). The C2 domain does not respond to calcium which makes nPKC diacylglycerol-sensitive but calcium-independent [, , ].PKC is a family of serine- and threonine-specific protein kinases that depend on lipids for activity. They can be activated by calcium but have a requirement for the second messenger diacylglycerol [, ]. Members of this family play key regulatory roles in various cellular processes. Currently, there are ten isoforms of PKC which can be classified into classical (alpha, beta I, beta II, gamma), novel (delta, epsilon, eta, theta) and atypical (zeta, iota/lambda) types based on their primary structure and biochemical characteristics [, , ]. All PKCs contain a C-terminal kinase domain and an N-terminal regulatory domain.
This entry represents the catalytic domain of PI3K-C2-alpha, which is a Class II phosphoinositide-3-kinase (PI3K) that generates phosphatidylinositol 3-phosphate (PtdIns3P) and phosphatidylinositol 3,4-bisphosphate (PtdIns(3,4)P2). It plays key roles in clathrin assembly and clathrin-mediated membrane trafficking [], insulin signaling [], and vascular smooth muscle contraction [].PI3Ks can be divided into three main classes (I, II, and III), defined by their substrate specificity, regulation, and domain structure. Class I PI3Ks are the only enzymes capable of converting PtdIns(4,5)P2 to the critical second messenger PtdIns(3,4,5)P3. Class II PI3Ks preferentially use PtdIns as a substrate to produce PtdIns(3)P, but can also phosphorylate PtdIns(4)P. They function as monomers and do not associate with any regulatory subunits. Class II enzymes contain an N-terminal Ras binding domain, a lipid binding C2 domain, a PI3K homology domain of unknown function, an ATP-binding cataytic domain, a Phox homology (PX) domain, and a second C2 domain at the C terminus [, ].
This entry represents the catalytic domain of PI3K-C2-gamma, which is a Class II phosphoinositide-3-kinase (PI3K) that generates phosphatidylinositol 3-phosphate (PtdIns3P) and phosphatidylinositol 3,4-bisphosphate (PtdIns(3,4)P2). PI3K-C2gamma is expressed in the liver, breast, and prostate []. PI3Ks can be divided into three main classes (I, II, and III), defined by their substrate specificity, regulation, and domain structure. Class I PI3Ks are the only enzymes capable of converting PtdIns(4,5)P2 to the critical second messenger PtdIns(3,4,5)P3. Class II PI3Ks preferentially use PtdIns as a substrate to produce PtdIns(3)P, but can also phosphorylate PtdIns(4)P. They function as monomers and do not associate with any regulatory subunits. Class II enzymes contain an N-terminal Ras binding domain, a lipid binding C2 domain, a PI3K homology domain of unknown function, an ATP-binding cataytic domain, a Phox homology (PX) domain, and a second C2 domain at the C terminus [, ].
This entry corresponds to the MUN domain []found in Munc13 proteins. These constitute a family of three highly homologous molecules (Munc13-1, Munc13-2 and Munc13-3) with homology to Caenorhabditis elegans unc-13p. Munc13 proteins contain a phorbol ester-binding C1 domain and two C2 domains, which are Ca2+/phospholipid binding domains. Sequence analyses have uncovered two regions called Munc13 homology domains 1 (MHD1) and 2 (MHD2) that are arranged between two flanking C2 domains. MHD1 and MHD2 domains are present in a wide variety of proteins from Arabidopsis thaliana, C. elegans, Drosophila melanogaster, mouse, rat and human, some of which may function in a Munc13-like manner to regulate membrane trafficking. Structural studies have defined MHD1 and MHD2 to be part of the larger MUN domain which forms an elongated structure composed of any pairs of alpha helices.
The MD-2-related lipid-recognition (ML) domain is implicated in lipid recognition, particularly in the recognition of pathogen related products. It has an immunoglobulin-like β-sandwich fold similar to that of E-set Ig domains. This domain is present in proteins from plants, animals and fungi, including the following proteins:Epididymal secretory protein E1 (also known as Niemann-Pick C2 protein - Npc2), which is known to bind cholesterol. Niemann-Pick disease type C2 is a fatal hereditary disease characterised by accumulation of low-density lipoprotein-derived cholesterol in lysosomes [].House-dust mite allergen proteins such as Der f 2 from Dermatophagoides farinae and Der p 2 from Dermatophagoides pteronyssinus [].This entry refers to the ML domain found in metazoan Npc2 as well and some similar proteins.
The MD-2-related lipid-recognition (ML) domain is implicated in lipid recognition, particularly in the recognition of pathogen related products. It has an immunoglobulin-like β-sandwich fold similar to that of E-set Ig domains. This domain is present in proteins from plants, animals and fungi, including the following proteins:Epididymal secretory protein E1 (also known as Niemann-Pick C2 protein - Npc2), which is known to bind cholesterol. Niemann-Pick disease type C2 is a fatal hereditary disease characterised by accumulation of low-density lipoprotein-derived cholesterol in lysosomes [].House-dust mite allergen proteins such as Der f 2 from Dermatophagoides farinae and Der p 2 from Dermatophagoides pteronyssinus [].This entry refers to the ML domain found in phosphatidylinositol/phosphatidylglycerol transfer protein (PG/PI-TP). PG/PI-TP has been shown to bind phosphatidylglycerol and phosphatidylinositol, but the biological significance of this is still obscure [].
PLC-beta (PLCbeta) is regulated by heterotrimeric G protein-coupled receptors through their C2 domain and long C-terminal extension which forms an autoinhibitory helix. There are four isoforms: PLC-beta1-4. These isoforms mediate the production of the second messenger molecules diacylglycerol (DAG) and inositol 1,4,5-trisphosphate (IP3) to propagate signals for several physiological responses [, ].PLC-beta consists of an N-terminal PH domain, a EF hand domain, a catalytic domain split into X and Y halves, a C2 domain and a C-terminal PDZ. This entry represents the PH domain of PLC-beta. The PH domain of PLC-beta2 and PLC-beta3 plays a dual role, much like PLC-delta1, by binding to the plasma membrane, as well as the interaction site for the catalytic activator [].
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 [].
The vertebrate DMRT (doublesex-and mab-3-related transcription factor) gene family encodes putative transcription factors related to the sexual regulators Doublesex (Drosophila melanogaster) and MAB-3 (Caenorhabditis elegans). They share a highly conserved DNA binding motif, the DM domain. This entry represents a domain found in the C-terminal of the DMRT C1 and C2 proteins. DMRTC1 (also known as DMRT8) is located on the X chromosome in placental mammals. It is related to DMRTC2 (DMRT7) but has lost the DM domain [].
Synaptotagmin-like protein 1 (Slp1/Jfc1) acts as a Rab27a effector and plays a role in vesicle trafficking [, ]. Through its interaction with Rab27a, Slp1 also contributes to secretory lysosome exocytosis from cytotoxic T lymphocytes. Slp1 (and Slp2) may form part of a docking complex, capturing secretory lysosomes at the immunological synapse [].Slp1 possesses two C2 domains in tandem, domain C2A showing homology with the C2B domain of synaptotagmins [].
The Antirepressor protein ant from Salmonella phage P22 prevents the prophage p22 c2 repressor protein from binding to its operators. It also inhibits the action of other prophage repressor proteins, including those of phages lambda and 434. The synthesis of antirepressor is negatively regulated by the protein products of the two other immi genes, mnt and arc [, , ]. This entry represents the N-terminal domain of this protein and similar proteins from tailed bacteriophages (Caudovirales) and bacterial prophages mostly found in Proteobacteria.
Synaptotagmin-6 (SYT6) belongs to the synaptotagmin family, which is a group of membrane-trafficking proteins that contain two C-terminal C2 domains (known as C2A and C2B domains) []. Most of the synaptotagmins have a unique N-terminal domain (transmembrane region) that is involved in membrane anchoring or specific ligand binding. SYT6 is localised to the outer acrosomal membrane of the human sperm cells and is involved in acrosomal exocytosis [].
Synaptotagmin-5 (SYT5) belongs to the synaptotagmin family, which is a group of membrane-trafficking proteins that contain two C-terminal C2 domains. Most of the synaptotagmins have a unique N-terminal domain that is involved in membrane anchoring or specific ligand binding. SYT5 is involved in the Ca2+-dependent stimulation of insulin exocytosis []. SYT5 is also known as synaptotagmin IX (SYT9) in rodents. In PC12 (phaeochromocytoma) cells, it regulates Ca2+-dependent secretion [].
This family consists of lysophospholipase / phospholipase B and cytosolic phospholipase A2 whichalso has a C2 domain . Phospholipase B enzymes catalyse the release of fatty acids from lysophsopholipids and are capable in vitroof hydrolyzing all phospholipids extractable from yeast cells []. Cytosolic phospholipase A2 associates with natural membranes in response to physiological increases in Ca2+and selectively hydrolyses arachidonyl phospholipids [], the aligned region corresponds the carboxy-terminal Ca2+-independent catalytic domain of the protein as discussed in [].
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 [].
The active breakpoint cluster region-related protein (ABR) protein contains multiple domains including a RhoGEF domain, a PH domain, a C1 domain, a C2 domain, and a C-terminal RhoGAP domain. It is related to a slightly larger protein, BCR, which is structurally similar, but has an additional N-terminal kinase domain. ABR has GAP activity for both Rac and Cdc42. It promotes the exchange of RAC or CDC42-bound GDP by GTP, thereby activating them []. This entry represents the PH domain of ABR.
Family members such as protein p6 from Bacillus subtilis phage phi29 bind double-stranded DNA, forming a large nucleoprotein complex all along the viral genome, and have been proposed to be an architectural protein with a global role in genome organization. P6 is also involved in viral transcriptional control, repressing the C2 early promoter located at the right DNA end, and together with the viral regulatory protein p4, repressing early promoters A2b/A2c and activating late promoter A3 [].
CPNA-1 is a copine domain protein required for muscle maintenance/stability in Caenorhabditis elegans []. It is localised to integrin adhesion sites in muscle tissue and might act as a linker between membrane proximal attachment proteins and those deeper within muscle cells. CPNA-1 contains a predicted transmembrane domain and is the first characterised copine domain-containing protein that lacks C2 domains. It is most similar to homologues in other nematodes, but it is also similar to mammalian copines.
Synaptotagmin-like protein 4 (SYTL4, Slp4), also known as granuphilin or exophilin-2, belongs to the synaptotagmin-like protein family (Slp), which is a group of putative membrane trafficking proteins []. The characteristic feature of the Slp family is the N-terminal Slp homology domain (SHD), which functions as a Rab27-binding domain and C-terminal tandem C2 domains (known as the C2A domain and C2B domain), putative Ca2+-binding motifs [, ]. SHD consists of two conserved regions, designated SHD1 and SHD2, which may function as protein interaction sites. The SHD1 and SHD2 of Slp4 are separated by a putative FYVE zinc finger, which resembles a FYVE-related domain that is structurally similar to the canonical FYVE domains but lacks the three signature sequences: an N-terminal WxxD motif (x for any residue), the central basic R(R/K)HHCRxCG patch, and a C-terminal RVC motif.There are several alternatively spliced isoform of Slp4. Slp4-a (granuphilin-a) has two C2 domains, whereas Slp4-b (granuphilin-b) contains only the first C2 domain. Expression of Slp4-a inhibits regulated secretion in endocrine cells. Slp4-a binds to both the GTP- and GDP-bound forms of Rab27A and inhibits a specific GTP/GDP exchange cycle required for dense-core vesicle exocytosis []. Slp4 has been detected in the pancreatic islet, in particular in insulin-positive beta cells, and in pituitary []. This entry represents the FYVE-related domain of synaptotagmin-like protein 4.
Synaptotagmin-like protein 4 (SYTL4, Slp4), also known as granuphilin or exophilin-2, belongs to the synaptotagmin-like protein family (Slp), which is a group of putative membrane trafficking proteins []. The characteristic feature of the Slp family is the N-terminal Slp homology domain (SHD), which functions as a Rab27-binding domain and C-terminal tandem C2 domains (known as the C2A domain and C2B domain), putative Ca2+-binding motifs [, ]. SHD consists of two conserved regions, designated SHD1 and SHD2, which may function as protein interaction sites. The SHD1 and SHD2 of Slp4 are separated by a putative FYVE zinc finger, which resembles a FYVE-related domain that is structurally similar to the canonical FYVE domains but lacks the three signature sequences: an N-terminal WxxD motif (x for any residue), the central basic R(R/K)HHCRxCG patch, and a C-terminal RVC motif.There are several alternatively spliced isoform of Slp4. Slp4-a (granuphilin-a) has two C2 domains, whereas Slp4-b (granuphilin-b) contains only the first C2 domain. Expression of Slp4-a inhibits regulated secretion in endocrine cells. Slp4-a binds to both the GTP- and GDP-bound forms of Rab27A and inhibits a specific GTP/GDP exchange cycle required for dense-core vesicle exocytosis []. Slp4 has been detected inthe pancreatic islet, in particular in insulin-positive beta cells, and in pituitary [].
Synaptotagmin is a membrane-trafficking protein characterised by a N-terminal transmembrane region, a linker, and 2 C-terminal C2 domains []. Synaptotagmin 7, a member of class 2 synaptotagmins, is located in presynaptic plasma membranes in neurons, dense-core vesicles in endocrine cells, and lysosomes in fibroblasts. It has been shown to play a role in regulation of Ca2+-dependent lysosomal exocytosis in fibroblasts and also functions as a vesicular Ca2+-sensor [, ]. It is distinguished from the other synaptotagmins by having over 12 splice forms [].Previously all synaptotagmins were thought to be calcium sensors in the regulation of neurotransmitter release and hormone secretion, but it has been shown that not all of them bind calcium. Of the 17 identified synaptotagmins only 8 bind calcium (1-3, 5-7, 9, 10) []. The general function of C2 domains in these is to mediate Ca2+-triggered binding of the protein to a membrane [].C2 domains fold into an 8-standed β-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. This entry represents the first C2 repeat, C2A, and has a type-I topology [].
Synaptotagmin is a membrane-trafficking protein characterized by a N-terminal transmembrane region, a linker, and 2 C-terminal C2 domains []. Synaptotagmin 7, a member of class 2 synaptotagmins, is located in presynaptic plasma membranes in neurons, dense-core vesicles in endocrine cells, and lysosomes in fibroblasts. It has been shown to play a role in regulation of Ca2+-dependent lysosomal exocytosis in fibroblasts and also functions as a vesicular Ca2+-sensor [, ]. It is distinguished from the other synaptotagmins by having over 12 splice forms [].Previously all synaptotagmins were thought to be calcium sensors in the regulation of neurotransmitter release and hormone secretion, but it has been shown that not all of them bind calcium. Of the 17 identified synaptotagmins only 8 bind calcium (1-3, 5-7, 9, 10) []. The general function of C2 domains in these is to mediate Ca2+-triggered binding of the protein to a membrane [].C2 domains fold into an 8-standed β-sandwich that can adopt 2 structural arrangements: type I and type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. This entry represents the second C2 repeat, C2B, and has a type-I topology [].
GAP1 (GTPase-activating protein 1) family members include RASA2 (GAP1m), RASAL (RASAL1), GAP1(IP4BP or RASA3), and CAPRI (RASA4). They all display Ras GAP activity. With the exception of RASA2, they all possess an arginine finger-dependent GAP activity on Rap1 [, ]. They contain N-terminal tandem C2 domain repeats, a centrally located Ras-GAP domain, and a PH (pleckstrin homology) domain containing a Btk motif [].This entry represents the RasGAP domain of RASAL. RASAL, like Ca2+ -promoted Ras inactivator (CAPRI, or RASA4), is a cytosolic protein that undergoes a rapid translocation to the plasma membrane in response to receptor-mediated elevation in the concentration of intracellular free Ca2+, a translocation that activates its ability to function as a RasGAP. Its tandem C2 domains bind phospholipids upon an elevation in the intracellular free Ca2+ concentration ([Ca2+]i). CAPRI and RASAL differ in that CAPRI is an amplitude sensor while RASAL senses calcium oscillations [, ]. This difference between them resides not in their C2 domains, but in their PH domains leading to speculation that this might reflect an association with either phosphoinositides and/or proteins [].
This entry represents the C-terminal SH2 domain (cSH2) found in the PI3K p85 subunit.Phosphoinositide 3-kinases (PI3Ks) are essential for cell growth, migration, and survival. Class IA PI3Ks are heterodimers of a p110 catalytic (C) subunit and a p85-related regulatory (R) subunit []. p110 is composed of an adaptor-binding domain, a Ras-binding domain, a C2 domain, a helical domain, and a kinase domain. p85 is composed of an SH3 domain, a RhoGap domain, a N-terminal SH2 (nSH2) domain, a inter SH2 (iSH2) domain, and C-terminal (cSH2) domain. There are two inhibitory interactions between p110alpha and p85 of P13K: 1) p85 nSH2 domain with the C2, helical, and kinase domains of p110alpha and 2) p85 iSH2 domain with C2 domain of p110alpha. There are three inhibitory interactions between p110beta and p85 of P13K: 1) p85 nSH2 domain with the C2, helical, and kinase domains of p110beta, 2) p85 iSH2 domain with C2 domain of p110beta, and 3) p85 cSH2 domain with the kinase domain of p110beta []. p110beta is oncogenic as a wild type protein while p110alpha lacks this ability. One explanation is that the regulation of p110beta by p85 is unique because of the addition of inhibitory contacts from the cSH2 domain and the loss of contacts in the iSH2 domain []. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites [].In mammals, there are multiple class IA PI3K regulatory and catalytic subunits. There are three genes that encode at least five different regulatory subunit proteins (p85alpha, p55alpha, p50alpha, p85beta, and p55gamma) and three genes encoding three catalytic subunits (p110alpha, p110beta, and p110delta) [].
This entry represents the N-terminal SH2 domain (nSH2) found in the PI3K p85 subunit.Phosphoinositide 3-kinases (PI3Ks) are essential for cell growth, migration, and survival. Class IA PI3Ks are heterodimers of a p110 catalytic (C) subunit and a p85-related regulatory (R) subunit []. p110 is composed of an adaptor-binding domain, a Ras-binding domain, a C2 domain, a helical domain, and a kinase domain. p85 is composed of an SH3 domain, a RhoGap domain, a N-terminal SH2 (nSH2) domain, a inter SH2 (iSH2) domain, and C-terminal (cSH2) domain. There are two inhibitory interactions between p110alpha and p85 of P13K: 1) p85 nSH2 domain with the C2, helical, and kinase domains of p110alpha and 2) p85 iSH2 domain with C2 domain of p110alpha. There are three inhibitory interactions between p110beta and p85 of P13K: 1) p85 nSH2 domain with the C2, helical, and kinase domains of p110beta, 2) p85 iSH2 domain with C2 domain of p110beta, and 3) p85 cSH2 domain with the kinase domain of p110beta []. p110beta is oncogenic as a wild type protein while p110alpha lacks this ability. One explanation is that the regulation of p110beta by p85 is unique because of the addition of inhibitory contacts from the cSH2 domain and the loss of contacts in the iSH2 domain []. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites [].In mammals, there are multiple class IA PI3K regulatory and catalytic subunits. There are three genes that encode at least five different regulatory subunit proteins (p85alpha, p55alpha, p50alpha, p85beta, and p55gamma) and three genes encoding three catalytic subunits (p110alpha, p110beta, and p110delta) [].
This is the inter SH2 (iSH2) domain found in phosphatidylinositol 3-kinase regulatory subunit p85alpha, p85beta and p55gamma. Phosphoinositide 3-kinases (PI3Ks) are essential for cell growth, migration, and survival. Class IA PI3Ks are heterodimers of a p110 catalytic (C) subunit and a p85-related regulatory (R) subunit []. p110 is composed of an adaptor-binding domain, a Ras-binding domain, a C2 domain, a helical domain, and a kinase domain. p85 is composed of an SH3 domain, a RhoGap domain, a N-terminal SH2 (nSH2) domain, a inter SH2 (iSH2) domain, and C-terminal (cSH2) domain. There are two inhibitory interactions between p110alpha and p85 of P13K: 1) p85 nSH2 domain with the C2, helical, and kinase domains of p110alpha and 2) p85 iSH2 domain with C2 domain of p110alpha. There are three inhibitory interactions between p110beta and p85 of P13K: 1) p85 nSH2 domain with the C2, helical, and kinase domains of p110beta, 2) p85 iSH2 domain with C2 domain of p110beta, and 3) p85 cSH2 domain with the kinase domain of p110beta []. p110beta is oncogenic as a wild type protein while p110alpha lacks this ability. One explanation is that the regulation of p110beta by p85 is unique because of the addition of inhibitory contacts from the cSH2 domain and the loss of contacts in the iSH2 domain []. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites [].In mammals, there are multiple class IA PI3K regulatory and catalytic subunits. There are three genes that encode at least five different regulatory subunit proteins (p85alpha, p55alpha, p50alpha, p85beta, and p55gamma) and three genes encoding three catalytic subunits (p110alpha, p110beta, and p110delta) [].
Cation channel sperm-associated targeting subunit tau (CTSRT, also known as Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 11 and C2 calcium-dependent domain-containing protein 6) has been identified in mice as an auxiliary component of the CatSper complex, which is involved in sperm cell hyperactivation. Sperm cell hyperactivation is required for sperm motility, essential late in the preparation of sperm for fertilization []. This protein is key for CatSper flagellar targeting and trafficking into the quadrilinear nanodomains as it links the channel-carrying vesicles and motor proteins in elongating flagella.
Synaptotagmin-14 (SYT14) belongs to the synaptotagmin family, which is a group of membrane-trafficking proteins that contain two C-terminal C2 domains (known as C2A and C2B domains). Most of the synaptotagmins have a unique N-terminal domain (transmembrane region) that is involved in membrane anchoring or specific ligand binding. In mammals, SYT14 is expressed in brain (especially in the cerebellum) []. Mutations in SYT14 gene cause spinocerebellar ataxia, autosomal recessive, 11 (SCAR11), which is a clinically and genetically heterogeneous group of cerebellar disorders []. This entry also includes synaptotagmin-14-like protein (SYT14L, also known as sytdep) from human, which is highly expressed in mature peripheral blood neutrophils [].
Tollip (Toll-interacting protein) is a component of the IL-1RI pathway which contains an N-terminal C2 domain and a C-terminal CUE domain. Tollip binds to the cytoplasmic TIR domain of IL-1Rs after IL-1 stimulation. It is sufficient for recruitment of IRAK to IL-1Rs and negatively regulates IL-1-induced signaling by inhibiting IRAK phosphorylation. In addition, Tollip directly interacts with toll-like receptors TLR2 and TLR4, and plays an inhibitory role in TLR-mediated cell activation through suppressing phosphorylation and kinase activity of IRAK. Moreover, Tollip can associate with GAT domains of Tom1 and its related proteins Tom1L1 and Tom1L2, and facilitate the recruitment of clathrin onto endosomes [, ].
Synaptotagmin-11 (SYT11) belongs to the synaptotagmin family, which is a group of membrane-trafficking proteins that contain two C-terminal C2 domains (known as C2A and C2B domains). Most of the synaptotagmins have a unique N-terminal domain (transmembrane region) that is involved in membrane anchoring or specific ligand binding. The SYT11 gene is located on a major susceptibility locus of familial schizophrenia []. The STY11 loci has also been linked to Parkinson's disease (PD) []. Parkin, a ubiquitin ligase, binds to the C2A and C2B domains of SYT11 resulting in the polyubiquitination of SYT11 [].
Synaptotagmin-3 (SYT3) belongs to the synaptotagmin family, which is a group of membrane-trafficking proteins that contain two C-terminal C2 domains. Most of the synaptotagmins have a unique N-terminal domain that is involved in membrane anchoring or specific ligand binding. SYT3 is required for the formation and delivery of cargo to the perinuclear endocytic recycling compartment (ERC) []. Among synaptotagmins 1-11, SYT3 is the only one that is expressed in T cells. It is essential for chemokine receptor CXCR4 recycling in T cells and thereby affects CXCL12 chemokine-induced migration [].
Rab effector Noc2 (also known as RPH3AL) is a Rab3 effector that mediates the regulation of secretory vesicle exocytosis in neurons and certain endocrine cells []. It also functions as a Rab27 effector and is involved in isoproterenol (IPR)-stimulated amylase release from acinar cells [, ]. Noc2 contains an N-terminal Rab3A effector domain which harbors a conserved zinc finger, but lacks tandem C2 domains. The FYVE domain of Noc2 resembles a FYVE-related domain that is structurally similar to the canonical FYVE domains but lacks the three signature sequences: an N-terminal WxxD motif (x for any residue), the central basic R(R/K)HHCRxCG patch, and a C-terminal RVC motif [].
Spondins are multi-domain extracellular matrix (ECM) protein as well as contact-repellent molecules that directs axon outgrowth and cell migration during development. Spondins are involved in patterning axonal growth trajectory through either inhibiting or promoting adhesion of embryonic nerve cells [].This superfamily represents a domain found in the N-terminal half of several Spondin proteins [], also called FS domain. It is found in F-spondins (spondin-1), mindins (spondin-2). Its homology to a common Ca2+- and lipid-binding C2 domain suggests that the F-spondin FS domain is responsible for part of the membrane targeting of F-spondin in its regulation of axon development [].
Spondins are multi-domain extracellular matrix (ECM) protein as well as contact-repellent molecules that directs axon outgrowth and cell migration during development. Spondins are involved in patterning axonal growth trajectory through either inhibiting or promoting adhesion of embryonic nerve cells [].This conserved region is found in the N-terminal half of several Spondin proteins [], also called FS domain. It is found in F-spondins (spondin-1), mindins (spondin-2). Its homology to a common Ca2+- and lipid-binding C2 domain suggests that the F-spondin FS domain is responsible for part of the membrane targeting of F-spondin in its regulation of axon development [].
This entry represents a group of plant ADP-ribosylation factor GTPase-activating proteins (ArfGAPs), such as AGD11/12/13 from Arabidopsis. ArfGAPs are a family of proteins containing an ArfGAP catalytic domain that induces the hydrolysis of GTP bound to the small guanine nucleotide-binding protein Arf, a member of the Ras superfamily of GTPases. Of all known members belonging to the ARF-GAP protein family only AGD11, 12, and 13 possess a C2 domain enabling them to bind phospholipids, phosphoinositide and proteins in a calcium-dependent manner []. The C-terminal domain of AGD12 is structurally related to ENHANCED BENDING (EHB) 1, and both of them function as calcium-dependent proteins that affect gravitropism in Arabidopsis thaliana [].
RIM proteins are scaffolding proteins at the active zone which bind to several other presynaptic proteins. The long isoforms of RIM proteins, which contain N-terminal Rab3 and Munc13 interacting domains, as well as a central PDZ domain and two C-terminal C2 domains, are encoded by two genes, Rim1 and Rim2 []. They have multiple isoforms (alpha, beta, gamma) diverging in their structural composition, which mediate overlapping and distinct functions [, ]. These isoforms are involved in determining Ca2+ channel density and vesicle docking at the presynaptic active zone []. This entry includes Rim and related proteins. In Caenorhabditis elegans Rim acts after vesicle docking likely via regulating priming [].
Synaptotagmin-15 (Syt15) belongs to the synaptotagmin family, which is a group of membrane-trafficking proteins that contain two C-terminal C2 domains (known as C2A and C2B domains). Most of the synaptotagmins have a unique N-terminal domain that is involved in membrane anchoring or specific ligand binding. Mammals contain 16 synaptotagmins; eight of these bind Ca2+ via their C2-domains (Syt1-Syt3, Syt5-7, Syt9, and Syt10), whereas the other eight, including Syt15, do not [].Unlike other synaptotagmins, the mouse and human Syt15 have an alternative splicing isoform that lacks the C-terminal portion of the C2B domain (named Syt15-b). Expression of Syt15 is mainly found in non-neuronal tissues [].
Synaptotagmin-8 (Syt8) belongs to the synaptotagmin family, which is a group of membrane-trafficking proteins that contain two C-terminal C2 domains (known as C2A and C2B domains). Most of the synaptotagmins have a unique N-terminal domain that is involved in membrane anchoring or specific ligand binding. Mammals contain 16 synaptotagmins; eight of these bind Ca2+ via their C2-domains (Syt1-Syt3, Syt5-7, Syt9, and Syt10), whereas the other eight, including Syt8, do not [].Syt8 is expressed in neurons, neuroendocrine and endocrine cells []. It is involved in insulin secretion []and may function in acrosomal exocytosis [].
This entry represents the long-chain primary alcohol dehydrogenase AdhA (ADHA) from Thermoanaerobacter ethanolicus (formerly known as Clostridium thermohydrosulfuricum). This enzyme is an alcohol dehydrogenase active against primary long-chain alcohols that catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor []. The ADH of hyperthermophilic archaeon Thermococcus hydrothermalis oxidizes a series of primary aliphatic and aromatic alcohols, preferentially from C2 to C8, but is also active towards methanol and glycerol, and is stereospecific for monoterpenes. [, , ]. Members of this protein family are mainly found in bacteria and archaea.
This entry represents mannan-binding lectin-associated serine peptidase 2 (MASP2; MEROPS identifier S01.229), a serine endopeptidase from family S1 (chymotrypsin family) which is a component in the activation of complement in the lectin pathway. MASP2 has trypsin-like specificity and it processes complement components C2 and C4 []. The fragments released, C2a and C4b, form the C3/C5 convertase. The specificity of MASP2 is identical to that of complement component C1s, but from the solved tertiary structure that enzyme-substrate interactions are different []. MASP2 is inhibited by C1 inhibitor []. MASP2 forms a homodimer, stabilized by two Ca2+ions, before it binds to mannose-binding protein C []. MASP2 autoactivates itself to a two-chain form.
This entry represents the second HR1 domain found in fungal PKC-like proteins including Pkc1p from Saccharomyces cerevisiae, and Pck1p and Pck2p from Schizosaccharomyces pombe. The yeast PKC-like proteins play a critical role in regulating cell wall biosynthesis and maintaining cell wall integrity []. They contain two HR1 domains, C2 and C1 domains, and a kinase domain. HR1 domains are anti-parallel coiled-coil (ACC) domains that bind small GTPases from the Rho family []. The HR1 domains of Pck1p and Pck2p interact with GTP-bound Rho1p and Rho2p [].
Saccharomyces cerevisiae Plc1 is a homologue of the delta isoform of mammalian phosphoinositide-specific phospholipase C (PI-PLC) []. It is required for the initial step of inositol polyphosphate (InsP) synthesis. It hydrolyzes phosphatidylinositol 4,5-biphosphate (PIP2) to generate the signaling molecules inositol 1,4,5-triphosphate (IP3) and 1,2-diacylglycerol (DAG) []. Plc1 contains an N-terminal PH domain, a EF hand domain, a catalytic domain split into X and Y halves, and a C-terminal C2 domain. This entry represents the PH domain found in Plc1 and its homologues from fungi.
Copines are a widely distributed class of Ca2+-dependent lipid-binding proteins. Most have a characteristic domain structure: two C2 domains in the N-terminal region and a von Willebrand A (VWA) domain in the C-terminal region. They are potentially involved in membrane trafficking, protein-protein interactions, and perhaps even cell division and growth [, ]. In plants, they are known as BONZAI proteins []. The copine family in plants may have effects in promoting growth and development in addition to repressing cell death [, ]. Caenorhabditis elegans copine, also known as Nra1, is Involved in nicotinic acetylcholine receptor (nAChR)-mediated sensitivity to nicotine and levamisole [].
Copines are a widely distributed class of Ca2+-dependent lipid-binding proteins. Most have a characteristic domain structure: two C2 domains in the N-terminal region and a von Willebrand A (VWA) domain in the C-terminalregion.In Arabidopsis the copine family consist of BON1 (BONZAI 1), BON2 (BONZAI 2) and BON3 (BONZAI 3). The copine family in plants may have effects in promoting growth and development in addition to repressing cell death [, ]. BON1 and BON3 negatively regulate multiple resistance (R-like) genes; these are involved in plant responses to biotic attacks but need to be repressed in the absence of biotic stresses as their effects are detrimental to plant growth and development [, , ].
Protein kinase C, delta type is a member of the novel protein kinase C (nPKC) family. PKC delta plays contrasting roles in cell death and cell survival by functioning as a pro-apoptotic protein during DNA damage-induced apoptosis [], but acting as an anti-apoptotic protein during cytokine receptor-initiated cell death []. PKC delta is also involves in tumor suppression [], required for oxygen radical production by NADPH oxidase [, ]and acts as positive or negative regulator in platelet functional responses [, ].PKC is a family of serine- and threonine-specific protein kinases that depend on lipids for activity. They can be activated by calcium but have a requirement for the second messenger diacylglycerol [, ]. Members of this family play key regulatory roles in various cellular processes. Currently, there are ten isoforms of PKC which can be classified into classical (alpha, beta I, beta II, gamma), novel (delta, epsilon, eta, theta) and atypical (zeta, iota/lambda) types based on their primary structure and biochemical characteristics [, , ]. All PKCs contain a C-terminal kinase domain and an N-terminal regulatory domain.The N-terminal regulatory domain of nPKC consists of a C2 domain follows by a double C1 domain (C1A and C1B). The C2 domain does not respond to calcium which makes nPKC diacylglycerol-sensitive but calcium-independent [, , ].
Protein kinase C, epsilon is a novel type of protein kinase C (nPKC). PKC epsilon plays essential roles in the regulation of multiple cellular processes linked to cytoskeletal proteins, such as cell adhesion [], motility, migration []and cell cycle, functions in neuron growth [, , ]and ion channel regulation [, ], and is involved in immune response [], cancer cell invasion and regulation of apoptosis [, ].The N-terminal regulatory domain of nPKC consists of a C2 domain follows by a double C1 domain (C1A and C1B). The C2 domain does not respond to calcium which makes nPKC diacylglycerol-sensitive but calcium-independent [, , ].PKC is a family of serine- and threonine-specific protein kinases that depend on lipids for activity. They can be activated by calcium but have a requirement for the second messenger diacylglycerol [, ]. Members of this family play key regulatory roles in various cellular processes. Currently, there are ten isoforms of PKC which can be classified into classical (alpha, beta I, beta II, gamma), novel (delta, epsilon, eta, theta) and atypical (zeta, iota/lambda) types based on their primary structure and biochemical characteristics [, , ]. All PKCs contain a C-terminal kinase domain and an N-terminal regulatory domain.
Protein kinase C, eta type is a member of the novel protein kinase C (nPKC) family. It is involved in the regulation of cell differentiation in keratinocytes []and pre-B cell receptor []. PKC eta also mediates regulation of epithelial tight junction integrity []and foam cell formation []. In addition, it is required for glioblastoma proliferation []and apoptosis prevention in MCF-7 cells[].PKC is a family of serine- and threonine-specific protein kinases that depend on lipids for activity. They can be activated by calcium but have a requirement for the second messenger diacylglycerol [, ]. Members of this family play key regulatory roles in various cellular processes. Currently, there are ten isoforms of PKC which can be classified into classical (alpha, beta I, beta II, gamma), novel (delta, epsilon, eta, theta) and atypical (zeta, iota/lambda) types based on their primary structure and biochemical characteristics [, , ]. All PKCs contain a C-terminal kinase domain and an N-terminal regulatory domain.The N-terminal regulatory domain of nPKC consists of a C2 domain follows by a double C1 domain (C1A and C1B). The C2 domain does not respond to calcium which makes nPKC diacylglycerol-sensitive but calcium-independent [, , ].
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.
Melanophilin, also termed SlaC2-a, or exophilin-3, is a GTP-bound form of Rab27A-, myosin Va-, and actin-binding protein present on melanosomes. It is involved in the control of transferring of melanosomes from microtubules to actin filaments. It also functions as a melanocyte type myosin Va (McM5) binding partner and directly activates the actin-activated ATPase activity of McM5 through forming a tripartite protein complex with Rab27A and an actin-based motor myosin Va [,]. SlaC2-a belongs to the Slp homologue lacking C2 domains (Slac2) family. It contains an N-terminal Slp homology domain (SHD), but lacks tandem C2 domains. The SHD consists of two conserved regions, designated SHD1 (Slp homology domain 1) and SHD2, which may function as protein interaction sites []. The SHD1 and SHD2 of SlaC2-a are separated by a putative FYVE zinc finger, which resembles a FYVE-related domain that is structurally similar to the canonical FYVE domains but lacks the three signature sequences: an N-terminal WxxD motif (x for any residue), the central basic R(R/K)HHCRxCG patch, and a C-terminal RVC motif. Moreover, Slac2-a has a middle myosin-binding domain and a C-terminal actin-binding domain [].
Rab GTPases recruit various effector proteins to organelles and vesicles. Rab11-family interacting proteins (FIPs) are involved in mediating the role of Rab11. FIPs can be divided into three classes: class I FIPs (Rip11/Rab11-FIP5, RCP/RAB11FIP1, and FIP2) which contain a C2 domain after N terminus of the protein, class II FIPs (FIP3 and FIP4) which contain two EF-hands and a proline rich region, and class III FIPs (FIP1) which exhibits no homology to known protein domains. All FIP proteins contain a highly conserved, 20-amino acid motif at the C terminus of the protein, known as Rab11/25 binding domain (RBD). Class I FIPs are thought to bind to endocytic membranes via their C2 domain, which interacts directly with phospholipids. Class II FIPs do not have any membrane binding domains leaving much to speculate about the mechanism involving FIP3 and FIP4 interactions with endocytic membranes []. Class I FIPs, but not the class II FIPs, also interact with Rab14 [].The exact function of the Rab11 and FIP interaction is unknown, but there is speculation that it involves the role of forming a targeting complex that recruits a group of proteins involved in membrane transport to organelles. Recent studies have identified several Rab11-FIP complex-binding proteins that regulate distinct membrane traffic pathways [].This family consist of class I FIPs.
RPGR-interacting protein 1 (RPGRIP1) is mutated in the eye disease Leber congenital amaurosis (LCA) and its structural homologue, RPGRIP1-like (RPGRIP1L, also called NPHP8 or fantom), is mutated in many different ciliopathies [, ]. Both are multidomain proteins that are predicted to interact with retinitis pigmentosa G-protein regulator (RPGR) []. Both consist of an N-terminal coiled coil domain, two C2 domains (C2N and C2C), and a C-terminal RPGR-interacting domain (RID). RID is a C2 domain with a canonical beta sandwich structure that does not bind Ca2+ and/or phospholipids and thus constitutes a unique type of protein-protein interaction module [].Both RPGRIP1 and RPGRIP1L interact with the ciliary transition zone protein nephrocystin 4 (NPHP4) via their C2C domain [, ]. An hypothesis is that RPGRIP1 and RPGRIP1L function as cilium-specific scaffolds that recruit a Nek4 signaling network which regulates cilium stability []. The expression of RPGRIP1 seems to be limited to photoreceptors and amacrine cells in the retina [], whereas RPGRIP1L is found in other tissues as well.
Phosphoinositide 3-kinases (PI3Ks) are essential for cell growth, migration, and survival. Class IA PI3Ks are heterodimers of a p110 catalytic (C) subunit and a p85-related regulatory (R) subunit []. p110 is composed of an adaptor-binding domain, a Ras-binding domain, a C2 domain, a helical domain, and a kinase domain. p85 is composed of an SH3 domain, a RhoGap domain, a N-terminal SH2 (nSH2) domain, a inter SH2 (iSH2) domain, and C-terminal (cSH2) domain. There are two inhibitory interactions between p110alpha and p85 of P13K: 1) p85 nSH2 domain with the C2, helical, and kinase domains of p110alpha and 2) p85 iSH2 domain with C2 domain of p110alpha. There are three inhibitory interactions between p110beta and p85 of P13K: 1) p85 nSH2 domain with the C2, helical, and kinase domains of p110beta, 2) p85 iSH2 domain with C2 domain of p110beta, and 3) p85 cSH2 domain with the kinase domain of p110beta []. p110beta is oncogenic as a wild type protein while p110alpha lacks this ability. One explanation is that the regulation of p110beta by p85 is unique because of the addition of inhibitory contacts from the cSH2 domain and the loss of contacts in the iSH2 domain []. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites [].In mammals, there are multiple class IA PI3K regulatory and catalytic subunits. There are three genes that encode at least five different regulatory subunit proteins (p85alpha, p55alpha, p50alpha, p85beta, and p55gamma) and three genes encoding three catalytic subunits (p110alpha, p110beta, and p110delta) [].Among all the class IA PI3K combinations, p85alpha/p110alpha heterodimer has been the most intensely investigated. p110alpha has been shown to be stabilized and inhibited by dimerization with p85alpha []. Moreover, p85alpha (also called PIK3R1) has functions independent of its PI3K regulatory role. It can independently stimulate signalling pathways involved in cytoskeletal rearrangements []. PIK3R1 has been shown to play an important role in insulin signalling [].This entry represents the iSH2 domain found in PIK3R1.
SMP is a proposed lipid-binding module, ie a synaptotagmin-like mitochondrial-lipid-binding domain found in eukaryotes. The SMP domain has a β-barrel structure like protein modules in the tubular-lipid-binding (TULIP) superfamily. It dimerises to form an approximately 90-Angstrom-long cylinder traversed by a channel lined entirely with hydrophobic residues. The following two C2 domains then form arched structures flexibly linked to the SMP domain. The SMP domain is a lipid-binding domain that links the ER with other lipid bilayer-membranes within the cell [].This entry represents the SMP domain found in plant synaptotagmins []and extended synaptotagmins from metazoa. The extended synaptotagmins transport glycerolipids between the two bilayers via their lipid-harboring SMP domains and Ca2 + regulates their membrane tethering and lipid transport function [].
Synaptotagmin-like protein 5 (SYTL5 or Slp5) is a novel Rab27A-specific effector that is highly expressed in placenta and liver. Slp5 specifically interacted with the GTP-bound form of Rab27A and is involved in Rab27A-dependent membrane trafficking in specific tissues. Slp5 contains an N-terminal Slp homology domain (SHD) and C-terminal tandem C2 domains. The Slp homology domain (SHD) consists of two conserved regions, designated SHD1 (Slp homology domain 1) and SHD2, which may function as protein interaction sites. The SHD1 and SHD2 of Slp5 are separated by a putative FYVE zinc finger, which resembles a FYVE-related domain that is structurally similar to the canonical FYVE domains but lacks the three signature sequences: an N-terminal WxxD motif (x for any residue), the central basic R(R/K)HHCRxCG patch, and a C-terminal RVC motif [].This entry represents the FYVE-related domain found in SYTL5.
Ras GTPase-activating protein 1 (also known as p120-RasGAP) is an inhibitory regulator of the Ras-cyclic AMP pathway [, ]. Its C-terminal catalytic domain promotes GTP hydrolysis and plays a key role in the regulation of Ras-GTP bound []. Its N-terminal part contains two SH2, SH3, PH (pleckstrin homology) and CaLB/C2 (calcium-dependent phospholipid-binding domain) domains, which allow various functions such as anti-/pro-apoptosis, proliferation and cell migration [].Alternative splicing results in two isoforms. The shorter isoform which lacks the N-terminal hydrophobic region, has the same activity, and is expressed in placental tissues. In general the longer isoform contains two SH2 domains, an SH3 domain, a pleckstrin homology (PH) domain, and a calcium-dependent phospholipid-binding C2 domain. The C terminus contains the catalytic domain of RasGap which catalyzes the activation of Ras by hydrolyzing GTP-bound active Ras into an inactive GDP-bound form of Ras [].
Synaptotagmin-4 (SYT4) belongs to the synaptotagmin family, which is a group of membrane-trafficking proteins that contain two C-terminal C2 domains. Most of the synaptotagmins have a unique N-terminal domain that is involved in membrane anchoring or specific ligand binding. This entry represents SYT4 from chordates. SYT4 is a Ca2+-sensor in the fly but not in the rat []. Like all synaptotagmins, SYT4 contains the highly conserved C2A and C2B calcium-binding domains, but an amino acid substitution found in the C2A domain decreases SYT4's affinity for calcium under some conditions [, ]. In adult hypothalamic oxytocin neurons, SYT4 is specifically induced by high-fat diet, and this negatively regulates oxytocin exocytosis, which is associated with obesity []. In humans the SYT4 gene is localised to a locus linked to schizophrenia and bipolar disorder [].
The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis, such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome [].One of the subunits of the APC that is required for its ubiquitination activity is Doc1/Apc10, a protein composed of a Doc1 homology domain that has been identified in a number of diverse putative E3 ubiquitin ligases []. The Doc1 homology domain forms a β-sandwich structure that is related in architecture to the galactose-binding domain of galactose oxidase, the coagulation factor C2 domain and a domain of XRCC1. This group represents a subgroup of subunit 10.
Synaptotagmin-17 (SYT17) belongs to the synaptotagmin family, which is a group of membrane-trafficking proteins that contain two C-terminal C2 domains. Although synaptotagmins have been found to have a unique N-terminal domain that is involved in membrane anchoring (e.g., synaptotagmin) or specific ligand binding (e.g., rabphilin-3A and Doc2, ), SYT17 does not contain this domain. SYT17 is highly expressed in brain and kidney (B/K) []. However, despite the lack of a transmembrane domain, it is tightly bound to the membrane fraction after treatment with high concentration of salt or high pH. Deletion and mutation analyses indicate that the cysteine cluster at the N terminus is essential for membrane localisation of SYT17. When wild-type SYT17 is expressed in PC12 cells, SYT17 proteins are localised mainly to the perinuclear region (trans-Golgi network), whereas mutant SYT17 carrying Cys-to-Ala substitutions are cytosolic [].
Ras GTPase-activating protein 1 (also known as p120-RasGAP) is an inhibitory regulator of the Ras-cyclic AMP pathway [, ]. Its C-terminal catalytic domain promotes GTP hydrolysis and plays a key role in the regulation of Ras-GTP bound []. Its N-terminal part contains two SH2, SH3, PH (pleckstrin homology) and CaLB/C2 (calcium-dependent phospholipid-binding domain) domains, which allow various functions such as anti-/pro-apoptosis, proliferation and cell migration [].Alternative splicing results in two isoforms. The shorter isoform which lacks the N-terminal hydrophobic region, has the same activity, and is expressed in placental tissues. In general the longer isoform contains two SH2 domains, an SH3 domain, a pleckstrin homology (PH) domain, and a calcium-dependent phospholipid-binding C2 domain. The C terminus contains the catalytic domain of RasGap which catalyzes the activation of Ras by hydrolyzing GTP-bound active Ras into an inactive GDP-bound form of Ras [].This entry represents the N-terminal SH2 domain.
Ras GTPase-activating protein 1 (also known as p120-RasGAP) is an inhibitory regulator of the Ras-cyclic AMP pathway [, ]. Its C-terminal catalytic domain promotes GTP hydrolysis and plays a key role in the regulation of Ras-GTP bound []. Its N-terminal part contains two SH2, SH3, PH (pleckstrin homology) and CaLB/C2 (calcium-dependent phospholipid-binding domain) domains, which allow various functions such as anti-/pro-apoptosis, proliferation and cell migration [].Alternative splicing results in two isoforms. The shorter isoform which lacksthe N-terminal hydrophobic region, has the same activity, and is expressed in placental tissues. In general the longer isoform contains two SH2 domains, an SH3 domain, a pleckstrin homology (PH) domain, and a calcium-dependent phospholipid-binding C2 domain. The C terminus contains the catalytic domain of RasGap which catalyzes the activation of Ras by hydrolyzing GTP-bound active Ras into an inactive GDP-bound form of Ras [].This entry represents the C-terminal SH2 domain.
NADH:ubiquinone oxidoreductase (complex I) () is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondria, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins [].This family consists of several NADH dehydrogenase [ubiquinone]1 subunit C2 (NDUC2 or NDUFC2, also known as NADH-ubiquinone oxidoreductase subunit b14.5b) proteins. It is an accessory protein, not involved in catalysis [, ].
This entry represents a conserved region within a number of eukaryotic dedicator of cytokinesis proteins (DOCK), which are guanine nucleotide exchange factors (GEFs) [, , ], that activate some small GTPases by exchanging bound GDP for free GTP such as Rac. DOCK proteins are required during several cellular processes, such as cell motility and phagocytosis []. These proteins have a DOCK-homology region 1 (DHR-1, also known as DOCK-type C2 domain) at the N-terminal and a DHR-2 (also known as DOCKER domain) at the C-terminal. The DOCKER domain () is a GEF catalytic domain organised into three lobes, A, B and C, with the Rho-family binding site and catalytic centre generated entirely from lobes B and C. This entry represents Lobe C, which form an antiparallel four α-helical bundle and contains a loop known as the nucleotide sensor characterised by a conserved valine residue essential for catalytic activity [, ].
This entry represents a conserved region within a number of eukaryotic dedicator of cytokinesis proteins (DOCK), which are guanine nucleotide exchange factors (GEFs) [, , ], that activate some small GTPases by exchanging bound GDP for free GTP such as Rac. DOCK proteins are required during several cellular processes, such as cell motility and phagocytosis []. These proteins have a DOCK-homology region 1 (DHR-1, also known as DOCK-type C2 domain) at the N-terminal and a DHR-2 (also known as DOCKER domain) at the C-terminal. The DOCKER domain () is a GEF catalytic domain organised into three lobes, A, B and C, with the Rho-family binding site and catalytic centre generated entirely from lobes B and C. This entry represents Lobe A, formed from an antiparallel array of α-helices that adopts a tetratricopeptide repeat-like fold, which through extensive contacts with lobe B, stabilises DHR-2 domain [, ].
Protein kinases C (PKCs) constitute a family of Ser/Thr kinases. PKCs are classified into three groups (classical, atypical, and novel) depending on their mode of activation and the structural characteristics of their regulatory domain [, ]. Novel PKCs (nPKCs) comprise delta, epsilon, eta, and theta isoforms, which have tandem C1 domains and a C2 domain that does not bind calcium []. nPKCs are calcium-independent, but require DAG (1,2-diacylglycerol) and phosphatidylserine (PS) for activity. PKC-delta plays a role in cell cycle regulation and programmed cell death in many cell types [, , ]. It slows down cell proliferation, inducing cell cycle arrest and enhancing cell differentiation. PKC-delta is also involved in the regulation of transcription as well as immune and inflammatory responses [, ]. It plays a central role in the genotoxic stress response that leads to DNA damaged-induced apoptosis [].
Protein kinases C (PKCs) constitute a family ofSer/Thr kinases. PKCs are classified into three groups (classical, atypical, and novel) depending on their mode of activation and the structural characteristics of their regulatory domain [, ]. Conventional PKCs (cPKCs) have functional C1A and C1B domains, and a C2 domain. PKCs undergo three phosphorylations in order to take mature forms [, ]. In addition, cPKCs depend on calcium, DAG (1,2-diacylglycerol), and in most cases, phosphatidylserine for activation. There are three conventional PKC isoenzymes (alpha, beta, and gamma).PKC-alpha is expressed in many tissues and is associated with cell proliferation, apoptosis, and cell motility [, ]. It plays a role in the signalling of the growth factors PDGF, VEGF, EGF, and FGF. Abnormal levels of PKC-alpha have been detected in many transformed cell lines and several human tumours [, , , ]. In addition, PKC-alpha is required for HER2 dependent breast cancer invasion [].
Protein kinases C (PKCs) constitute a family of Ser/Thr kinases. PKCs are classified into three groups (classical, atypical, and novel) depending on their mode of activation and the structural characteristics of their regulatory domain [, ]. Conventional PKCs (cPKCs) have functional C1A and C1B domains, and a C2 domain. PKCs undergo three phosphorylations in order to take mature forms [, ]. In addition, cPKCs depend on calcium, DAG (1,2-diacylglycerol), and in most cases, phosphatidylserine for activation. There are three conventional PKC isoenzymes (alpha, beta, and gamma).The PKC beta isoforms (I and II), generated by alternative splicing of a single gene, are preferentially activated by hyperglycemia-induced DAG (1,2-diacylglycerol) in retinal tissues. This is implicated in diabetic microangiopathy such as ischemia, neovascularization, and abnormal vasodilator function [, , , ]. PKC-beta is also being explored as a therapeutic target in cancer [, ]. It contributes to tumour formation and is involved in the tumour host mechanisms of inflammation and angiogenesis [].
Protein kinases C (PKCs) constitute a family of Ser/Thr kinases. PKCs are classified into three groups (classical, atypical, and novel) depending on their mode of activation and the structural characteristics of their regulatory domain [, ]. Novel PKCs (nPKCs) comprise delta, epsilon, eta, and theta isoforms, which have tandem C1 domains and a C2 domain that does not bind calcium []. nPKCs are calcium-independent, but require DAG (1,2-diacylglycerol) and phosphatidylserine (PS) for activity. PKC-eta is predominantly expressed in squamous epithelia, where it plays a crucial role in the signaling of cell-type specific differentiation []. It is also expressed in pro-B cells and early-stage thymocytes, and acts as a key regulator in early B-cell development []. PKC-eta increases glioblastoma multiforme (GBM) proliferation and resistance to radiation, and is being developed as a therapeutic target for the management of GBM [].
This represents a conserved region approximately 180 residues long within eukaryotic copines. Copines are Ca2+-dependent phospholipid-binding proteins that are thought to be involved in membrane-trafficking, and may also be involved in cell division and growth []. They were originally identified in paramecium. They are found in human and orthologues have been found in C. elegans and Arabidopsis Thaliana. None have been found in D. Melanogaster or S. Cereviciae. Phylogenetic distribution suggests that copines have been lost in some eukaryotes []. No functional properties have been assigned to the VWA domains present in copines. The members of this subgroup contain a functional MIDAS motif based on their preferential binding to magnesium and manganese. However, the MIDAS motif is not totally conserved, in most cases the MIDAS consists of the sequence DxTxS instead of the motif DxSxS that is found in most cases. The C2 domains present in copines mediate phospholipid binding [, ].
The active zone is the presynaptic region in the nerve terminals that mediates neurotransmitter release and is composed a dense collection of proteins called the cytomatrix at the active zone (CAZ). The CAZ proteins are thought to mediate synapse formation and regulate neurotransmitter release [, ].RIM proteins are scaffolding proteins at the active zone which bind to several other presynaptic proteins. The long isoforms of RIM proteins, which contain N-terminal Rab3 and Munc13 interacting domains, as well as a central PDZ domain and two C-terminal C2 domains, are encoded by two genes, Rim1 and Rim2 []. They have multiple isoforms (alpha, beta, gamma) diverging in their structural composition, which mediate overlapping and distinct functions [, ]. These isoforms are involved in determining Ca2+ channel density and vesicle docking at the presynaptic active zone []. This entry represents regulating synaptic membrane exocytosis protein 2 (RIM2). RIM2alpha plays a critical role in insulin granule exocytosis [].
Synaptotagmin-12 (Syt12) belongs to the synaptotagmin family, which is a group of membrane-trafficking proteins that contain two C-terminal C2 domains (known as C2A and C2B domains). Most of the synaptotagmins have a unique N-terminal domain that is involved in membrane anchoring or specific ligand binding. Mammals contain 16 synaptotagmins; eight of these bind Ca2+ via their C2-domains (Syt1-Syt3, Syt5-7, Syt9, and Syt10), whereas the other eight, including Syt12, do not [].Syt12 colocalises with and binds Syt1 on synaptic vesicles, but regulates spontaneous release independently from Syt1. Syt12 is phosphorylated by cAMP-dependent protein kinase A (PKA) at a single site, and mutation of this site blocks the effect of Syt12 on spontaneous release []. Syt12 is not essential for basal synaptic transmission, but is required for cAMP-dependent mossy fibre long-term potentiation (LTP), a presynaptic form of long-term plasticity that is induced by PKA activation [].
Protein piccolo, also known as aczonin, is a neuron-specific presynaptic active zone scaffolding protein that mainly interacts with a detergent-resistant cytoskeletal-like subcellular fraction and is involved in the organization of the interplay between neurotransmitter vesicles, the cytoskeleton, and the plasma membrane at synaptic active zones []. It binds profilin, an actin-binding protein implicated in actin cytoskeletal dynamics []. It also functions as a presynaptic low-affinity Ca2 sensor and has been implicated in Ca2 regulation of neurotransmitter release []. Piccolo is a multi-domain protein containing two N-terminal FYVE zinc fingers, a polyproline tract, and a PDZ domain and two C-terminal C2 domains. This entry represents the first FYVE domain, which resembles a FYVE-related domain that is structurally similar to the canonical FYVE domains but lacks the three signature sequences: an N-terminal WxxD motif (x for any residue), the central basic R(R/K)HHCRxCG patch, and a C-terminal RVC motif.
Synaptotagmins are synaptic vesicle membrane proteins found in abundance in nerve cells and some endocrine cells [, ]. The amino acid sequence of synaptotagmin comprises a single transmembrane region with a short vesicular N-terminal region, and a cytoplasmic C-terminal region containing 2 internal repeats similar to the C2 regulatory domain of protein kinase C. The protein is believed to be important in the docking and fusion of synaptic vesicles with the plasma membrane, i.e. with neurotransmitter release [, ].Synaptotagmin 7, a member of class 2 synaptotagmins, is located in presynaptic plasma membranes in neurons, dense-core vesicles in endocrine cells, and lysosomes in fibroblasts. It has been shown to play a role in regulation of Ca2+-dependent lysosomal exocytosis in fibroblasts and also functions as a vesicular Ca2+-sensor [, ]. It is distinguished from the other synaptotagmins by having over 12 splice forms [].
Proteins in this family contain an MD-2-related lipid-recognition (ML) domain, which is implicated in lipid recognition, particularly in the recognition of pathogen related products. It has an immunoglobulin-like β-sandwich fold similar to that of E-set Ig domains. This domain is present in proteins from plants, animals and fungi, including the following proteins:NPC intracellular cholesterol transporter 2 (NPC2), which is known to bind cholesterol. Niemann-Pick disease type C2 is a fatal hereditary disease characterised by accumulation of low-density lipoprotein-derived cholesterol in lysosomes [].Phosphatidylglycerol/phosphatidylinositol transfer protein (Npc2) from yeasts, which catalyzes the intermembrane transfer of phosphatidylglycerol and phosphatidylinositol [].House-dust mite allergen proteins such as Der f 2 from Dermatophagoides farinae and Der p 2 from Dermatophagoides pteronyssinus [].
This entry represents the EF-hand domain found in 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase delta-3 (PLC-delta3).PLC-delta-3 is essential for trophoblast and placental development []. It locates at the cleavage furrow where it may participate in cytokinesis []. PI-PLC-delta3 contains a core set of domains, including an N-terminal pleckstrin homology (PH) domain, four atypical EF-hand motifs, a PLC catalytic core, and a single C-terminal C2 domain. The PLC catalytic core domain is a TIM barrel with two highly conserved regions (X and Y) split by a highly degenerate linker sequence. In addition, PI-PLC-delta3 possesses a classical leucine-rich nuclear export sequence (NES) located in the EF hand motifs, which may be responsible transporting PI-PLC-delta3 from the cell nucleus [].
PLCgamma2 (phospholipase C-gamma-2 or 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-2) is primarily expressed in haematopoietic cells, specifically in B cells []. It is activated by tyrosine phosphorylation by B cell receptor (BCR) kinases and is recruited to the plasma membrane where its substrate is located. It is required in pre-BCR signaling and in the maturation of B cells []. PLCs catalyze the hydrolysis of phosphatidylinositol (4,5)-bisphosphate [PtdIns(4,5)P2]to produce Ins(1,4,5)P3 and diacylglycerol (DAG). Ins(1,4,5)P3 initiates the calcium signaling cascade while DAG functions as an activator of PKC [, ]. PLCgamma2 contains a Pleckstrin homology (PH) domain followed by an elongation factor (EF) domain, two catalytic regions of PLC domains that flank two tandem SH2 domains, followed by an SH3 domain and C2 domain.
PLCgamma1 (phospholipase C-II or 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1) is widely expressed and is essential in growth and development []. It is activated by the TrkA receptor tyrosine kinase and functions as a key regulator of cell differentiation []. PLCs catalyze the hydrolysis of phosphatidylinositol (4,5)-bisphosphate [PtdIns(4,5)P2]to produce Ins(1,4,5)P3 and diacylglycerol (DAG). Ins(1,4,5)P3 initiates the calcium signaling cascade while DAG functions as an activator of PKC []. PLCgamma contains a pleckstrin homology (PH) domain followed by an elongation factor (EF) domain, two catalytic regions of PLC domains that flank two tandem SH2 domains, followed by a SH3 domain and C2 domain. The SH3 domain of PLCgamma1 directly interacts with dynamin-1 and can serve as a guanine nucleotide exchange factor (GEF) [, ]. It also interacts with Cbl, inhibiting its phosphorylation and activity.This entry represents the SH3 domain of PLCgamma1.
Intersectin-2 (ITSN2) is an adaptor protein that functions in exo- and endocytosis, actin cytoskeletal reorganization, and signal transduction []. It plays a role in clathrin-coated pit (CCP) formation []. It binds to many proteins through its multidomain structure and facilitates the assembly of multimeric complexes. ITSN2 also functions as a specific GEF for Cdc42 activation in epithelial morphogenesis, and is required in mitotic spindle orientation []. It exists in alternatively spliced short and long isoforms. The short isoform contains two Eps15 homology domains (EH1 and EH2), a coiled-coil region and five SH3 domains (SH3A-E), while the long isoform, in addition, contains RhoGEF (also called Dbl-homologous or DH), Pleckstrin homology (PH) and C2 domains. This entry represents the first SH3 domain of ITSN2.
Intersectin-2 (ITSN2) is an adaptor protein that functions in exo- and endocytosis, actin cytoskeletal reorganization, and signal transduction []. It plays a role in clathrin-coated pit(CCP) formation []. It binds to many proteins through its multidomain structure and facilitates the assembly of multimeric complexes. ITSN2 also functions as a specific GEF for Cdc42 activation in epithelial morphogenesis, and is required in mitotic spindle orientation []. It exists in alternatively spliced short and long isoforms. The short isoform contains two Eps15 homology domains (EH1 and EH2), a coiled-coil region and five SH3 domains (SH3A-E), while the long isoform, in addition, contains RhoGEF (also called Dbl-homologous or DH), Pleckstrin homology (PH) and C2 domains. This entry represents the second SH3 domain of ITSN2.
Intersectin-2 (ITSN2) is an adaptor protein that functions in exo- and endocytosis, actin cytoskeletal reorganization, and signal transduction []. It plays a role in clathrin-coated pit (CCP) formation []. It binds to many proteins through its multidomain structure and facilitates the assembly of multimeric complexes. ITSN2 also functions as a specific GEF for Cdc42 activation in epithelial morphogenesis, and is required in mitotic spindle orientation []. It exists in alternatively spliced short and long isoforms. The short isoform contains two Eps15 homology domains (EH1 and EH2), a coiled-coil region and five SH3 domains (SH3A-E), while the long isoform, in addition, contains RhoGEF (also called Dbl-homologous or DH), Pleckstrin homology (PH) and C2 domains. This entry represents the third SH3 domain of ITSN2.
Intersectin-2 (ITSN2) is an adaptor protein that functions in exo- and endocytosis, actin cytoskeletal reorganization, and signal transduction []. It plays a role in clathrin-coated pit (CCP) formation []. It binds to many proteins through its multidomain structure and facilitates the assembly of multimeric complexes. ITSN2 also functions as a specific GEF for Cdc42 activation in epithelial morphogenesis, and is required in mitotic spindle orientation []. It exists in alternatively spliced short and long isoforms. The short isoform contains two Eps15 homology domains (EH1 and EH2), a coiled-coil region and five SH3 domains (SH3A-E), while the long isoform, in addition, contains RhoGEF (also called Dbl-homologous or DH), Pleckstrin homology (PH) and C2 domains. This entry represents the fourth SH3 domain of ITSN2.
Intersectin-2 (ITSN2) is an adaptor protein that functions in exo- and endocytosis, actin cytoskeletal reorganization, and signal transduction []. It plays a role in clathrin-coated pit (CCP) formation []. It binds to many proteins through its multidomain structure and facilitates the assembly of multimeric complexes. ITSN2 also functions as a specific GEF for Cdc42 activation in epithelial morphogenesis, and is required in mitotic spindle orientation []. It exists in alternatively spliced short and long isoforms. The short isoform contains two Eps15 homology domains (EH1 and EH2), a coiled-coil region and five SH3 domains (SH3A-E), while the long isoform, in addition, contains RhoGEF (also called Dbl-homologous or DH), Pleckstrin homology (PH) and C2 domains. This entry represents the fifth SH3 domain of ITSN2.
PKN1 is a serine/threonine protein kinase activated by the Rho family of small GTPases, and by fatty acids such as arachidonic and linoleic acids [, ]. It is expressed ubiquitously and is the most abundant PKN isoform in neurons []. PKN1 is implicated in a variety of functions including cytoskeletal reorganization, cardiac cell survival, cell adhesion, and glucose transport, among others [, ]. PKN1 contains three HR1 domains, a C2 domain, and a kinase domain.This entry represents the second HR1 domain of PKN1. HR1 domains are anti-parallel coiled-coil (ACC) domains that bind small GTPases from the Rho family; PKN1 binds the GTPases RhoA, RhoB, and RhoC, and can also interact weakly with Rac [].
PKN, also called Protein-kinase C-related kinase (PRK), is a serine/threonine protein kinase that can be activated by the small GTPase Rho, and by fatty acids such as arachidonic and linoleic acids. It is involved in many biological processes including cytoskeletal regulation, cell adhesion, vesicle transport, glucose transport, regulation of meiotic maturation and embryonic cell cycles, signaling to the nucleus, and tumorigenesis []. In some vertebrates, there are three PKN isoforms from different genes (designated PKN1, PKN2, and PKN3), which show different enzymatic properties, tissue distribution, and varied functions [, ]. PKN proteins contain three HR1 domains, a C2 domain, and a kinase domain. This entry represents the first HR1 domain of PKN. HR1 domains are anti-parallel coiled-coil (ACC) domains that bind small GTPases from the Rho family [].
Mannose-binding protein C (MBL2) is a calcium-dependent lectin involved in innate immune defence. It binds to oligosaccharides (mannose, fucose and N-acetylglucosamine) on the surface of micro-organisms and initiates complement activation of the lectin pathway []. It also binds to late apoptotic cells, enabling their uptake by macrophages []. MBL2 forms a homotrimer []which then binds to mannan-binding lectin-associated serine peptidases, leading to their activation and cleavage of complement components C2 and C4 to form the C3/C5 convertase [, ]. MBL2 expressed on the brush border epithelial cells of kidney-proximal tubules interacts with meprin precursors, preventing activation []. The tertiary structure of MBL2 has been solved, and the protein contains a collagen-like and a C-typelectin domain [].
RasSynGAP family members include SynGAP, DOC-2/DAB2-interacting protein (DAB2IP) and neuronal growth-associated protein (nGAP/RASAL2). They contain the PH domain, C2 domain and the RasGAP domain.SynGAP (also known as SYNGAP1) is a negative regulator of Ras and Rap GTPases [, ]. It is s primarily expressed in the excitatory neurons in the brain. It has several isoforms, SYNGAP A, B and C, differing in their N-termini. A and B isoforms contain unique peptide sequence and a complete PH domain, whereas isoform C is a shorter, truncated protein with no unique peptide sequence and no PH domain []. Mutations in the SynGAP gene cause mental retardation, autosomal dominant 5 [].This entry represents the PH domain of SynGAP.
Abr (active breakpoint cluster region-related protein) and Bcr (breakpoint cluster region protein) are homologous proteins containing a C-terminal domain with GTPase-activating protein (GAP) activity specific for Rac. They control multiple cellular functions of murine macrophages []. They contain several domains, including tandem DH-PH, C2 and GAP domains. Bcr has an extra N-terminal oligomerization domain []. Bcr has been shown to fused to Abl tyrosine kinase in leukemia. The fusion of Bcr to Abl deregulates the tyrosine kinase activity of Abl []. The N-terminal oligomerization domain is thought to be the most critical component that allows the formation of homo-tetramer Bcr/Abl complexes and deregulates the Abl tyrosine kinase [, ]. The GTPase-activating activity of Bcr has been shown to be regulated by transglutaminase 2 (TG2), a multifunctional protein that has been implicated in numerous pathologies including that of neurodegeneration and celiac disease [, ].Abr is a critical regulator of Rho and Cdc42 during the single cell wound healing [].
This entry represents a group of plant synaptotagmins and related proteins. In Arabodopsis, there are five members, SYT1-5. Structurally, they have a short uncleaved N-terminal signal peptide that overlaps a transmembrane (TM) domain, followed by a cytosolic variable region and two C-terminal C2 domains, C2A and C2B. Whereas C2A and C2B each bind phospholipids in a Ca2+-dependent manner, fold independently and act synergistically, C2B is essential for activity []. Arabidopsis SYT1, also known as SYTA, plays an important role in maintaining plasma membrane integrity during freezing and osmotic stresses [, ]. It also serves as a virus movement protein that transports its cargos to plasmodesmata for cell-to-cell spread via an endocytic recycling pathway [].
This entry represents a domain found at the C terminus of some GTPase-activating proteins (also known as GAP) found in animals, including Disabled homologue 2-interacting protein (DAB2P) and Ras/Rap GTPase-activating protein SynGAP (SYGP1). DAB2P functions as a tumour suppressor that is also involved in several processes such as innate immune response and inflammation and plays a key role in brain development and function [, , ]. SYGP1 is essential for postsynaptic signalling and has been related to brain injury, leading to long-term learning and memory deficits [, ].This domain, which is found associated with the RasGAP domain () and the C2 domain (), includes a coiled-coil domain that forms a parallel trimer in solution [].
This entry represents phosphoinositol-specific phospholipase C (PLC) from eukaryotes. Proteins in this entry include PLC-beta, gamma, delta, epsilon, eta, zeta and inactive phospholipase C-like protein 2 (PLC-L2). Phosphoinositol-specific phospholipase C (PLC; () plays an important role in signal transduction processes [], mediating the cellular actions of a variety of hormones, neurotransmitters and growth factors. Upon agonist-dependent activation, PLC catalyses the hydrolysis of membrane phosphatidylinositol 4,5-bisphosphate (PIP2), generating the second messengers inositol 1,4,5-trisphosphate (IP3) and diacylglycerol (DAG). IP3 binds specific intracellular receptors to trigger Ca2+mobilisation, while DAG mediates activation of a family of protein kinase C isozymes. This catalytic process is tightly regulated by reversible phosphorylation and binding of regulatory proteins [, , ]. Based on molecular size, immunoreactivity and amino acid sequence, several subtypes have been classified. Overall, sequence identity between sub-types is low, yet all isoforms share a split TIM barrel containing two conserved domains, designated X and Y []. The core eukaryotic PLC enzyme is composed of a pleckstrin homology (PH) domain, four tandem EF hand domains, a split TIM barrel, and a C2 domain []. The presence of an insert in the TIM barrel led to the naming of the N- and C-terminal halves of the TIM barrel as 'X-box' and 'Y-box'. The order of these two regions is always the same (NH2-X-Y-COOH), but the spacing is variable. In most isoforms, the distance between these two regions is only 50-100 residues, for example, in PLC-beta subtypes, X and Y domains are separated by a stretch of 70-120 amino acids rich in Ser, Thr and acidic residues (their C terminus is rich in basic residues). However, in PLC-gammas, there is an insert of more than 400 residues containing a PH domain, two SH2 domains, and one SH3 domain. The two conserved X and Y domains have been shown to be important for the catalytic activity. C-terminal to the Y-box, there is a C2 domain, possibly involved in Ca-dependent membrane attachment.
These proteins belong to MEROPS peptidase family S1 (chymotrypsin family, clan PA(S)), subfamily S1A.This family contains two mammalian proteins, complement C2 and complement factor B, which, respectively, have analogous roles in the classical and alternative pathways of complement activation. These proteins are composed of three regions, an N-terminal three-module complement control protein domain, a von Willebrand factor A domain, and a C-terminal serine protease domain. Briefly, they are activated by cleavage and function as the serine protease components of the C3/C5 convertases, which play similar roles in these pathways although composed of different proteins. Homologs in non-mammalian species are often more or less equally related to mammalian C2 and B and may be designated as complement B/C2. Strongylocentrotus purpuratus (Purple sea urchin) has an atypical factor B with a five-module complement control protein domain.The structures of the von Willebrand factor A and serine protease domains from human complement factor B () have been analysed [, ]. The A domain forms the classical vWF A domain fold, which consists of a central β-sheet flanked on both sides by amphipathic alpha helices. It contains an integrin-like MIDAS (metal ion-dependent adhesion site) motif that adopts the open conformation typical of integrin-ligand complexes, with an acidic residue from another A domain (provided by a fortuitous crystal contact) completing the coordination of the metal ion. Although a closed conformation was not observed, modelling studies suggest that the A domain could adopt this conformation, implying that as with integrins, ligand-binding may induce conformational changes which transduce a signal to other domains in the protein []. The serine protease domain forms a chymotrypsin fold with several novel features []. Like other serine proteases it forms two β-sheets, composed of six β-strands each, surrounded by surface helices and loops. However, several novel deletions and insertions occur within these surface helices and loops, and differences in active site conformation also exist.
Metallothioneins (MT) are small proteins that bind heavy metals, such as zinc, copper, cadmium, nickel, etc. They have a high content of cysteine residues that bind the metal ions through clusters of thiolate bonds [, ]. An empirical classification into three classes has been proposed by Fowler and coworkers []and Kojima []. Members of class I are defined to include polypeptides related in the positions of their cysteines to equine MT-1B, and include mammalian MTs as well as from crustaceans and molluscs. Class II groups MTs from a variety of species, including sea urchins,fungi, insects and cyanobacteria. Class III MTs are atypical polypeptides composed of gamma-glutamylcysteinyl units [].This original classification system has been found to be limited, in the sense that it does not allow clear differentiation of patterns of structural similarities, either between or within classes. Subsequently, a new classification was proposed on the basis of sequence similarity derived from phylogenetic relationships, which basically proposes an MT family for each main taxonomic group of organisms []. Crustacean MTs belong to family 3. They are small proteins, with 18 totally conserved cysteines. The members of this family are recognised by the sequence pattern P-[GD]-P-C-C-x(3,4)-C-x-C located at the Nterm. The taxonomic range of the members extends to crustaceans. Known characteristics of this family are: 58 to 60 AAs; variants exist with and without the N-terminal Met. Protein sequence is divided into two structural domains, containing each 9 Cys binding 3 bivalent metal ions. Family 3 includes subfamilies: c1, c2, c. All sequences are very similar. c1 and c2 are forming two distinct monophyletic groups in the AA phylogenetic tree. c are crustacean MTs different from c1 and c2 based on phylogenetic analyses.
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 sulfhydryl 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 IB includes the eukaryotic mitochondrial cyt C and prokaryotic 'short' cyt C2 exemplified by Rhodopila globiformis cyt C2; Class IA includes 'long' cyt C2, such as Rhodospirillum rubrum cyt C2 and Aquaspirillum itersonii cyt C-550, which have several extra loops by comparison with Class IB cyt C.Class I cytC has a characterised fold which comprises 5 α-helices arranged in a unique tertiary structure and a conserved N-terminal sequence -Cys-Xxx-Xxx-Cys-His- where the cysteines mediate the covalent cross-linking of the heme to the protein and the His [].The 3D structures of a considerable number of class IA and IB cytC have been determined. The proteins consist of 3-6 α-helices; the three most conserved 'core' helices form a 'basket' around the haem group, with one haem edge exposed to the solvent. Most class I cytC have conserved aromatic residues clustered around the haem and axial ligands.
Rho guanosine triphosphatases (GTPases) are critical regulators of cell motility, polarity, adhesion, cytoskeletal organisation, proliferation, geneexpression, and apoptosis. Conversion of these biomolecular switches to the activated GTP-bound state is controlled by two families of guanine nucleotide exchanges factors (GEFs). DH-PH proteins are a large group of Rho GEFs comprising a catalytic Dbl homology (DH) domain with anadjacent pleckstrin homology (PH) domain within the context of functionally diverse signalling modules. The evolutionarily distinct and smaller family of DOCK (dedicator of cytokinesis) or CDM (CED-5, DOCK1180, Myoblast city) proteins activate either Rac or Cdc42 to control cell migration, morphogenesis, and phagocytosis. DOCK proteins share the DOCK-type C2 domain (also termed the DOCK-homology region (DHR)-1 or CDM-zizimin homology 1 (CZH1) domain and the DOCKER domain (also termed the DHR-2 or CZH2 domain) [, , , , , , ].The DOCK-type C2 domain is located toward the N terminus []. The DOCKER domain is a GEF catalytic domain of ~400 residues situated within the C terminus. The structure of the DOCKER domain differs from that of other GEF catalytic domains. It is organised into three lobes of roughly equal size (lobes A, B, and C), with the Rho-family binding site and catalytic centre generated entirely from lobes B and C. Lobe A is formed from an antiparallel array of alpha helices. Through extensive contacts with lobe B, lobe A stabilises the DHR2 domain. Lobe B adopts an unusual architecture of two antiparallel beta sheets disposed in a loosely packed orthogonal arrangement, whereas lobe C comprises a four-helix bundle [, ].This entry represents the DOCKER domain.
