Cytoplasmic proteins Nck are non-enzymatic adaptor proteins composed of three SH3 (Src homology 3) domains and a C-terminal SH2 domain []. They regulate actin cytoskeleton dynamics by linking proline-rich effector molecules to protein tyrosine kinases and phosphorylated signaling intermediates []. They function downstream of the PDGFbeta receptor and are involved in Rho GTPase signaling and actin dynamics []. They associate with tyrosine-phosphorylated growth factor receptors or their cellular substrates [, ]. There are two vertebrate Nck proteins, Nck1 and Nck2. This entry represents the SH2 domain of Nck2.
The arfaptin homology (AH) domain is a protein domain found in a range of proteins, including arfaptins, protein kinase C-binding protein PICK1 []and mammalian 69kDa islet cell autoantigen (ICA69) []. The AH domain of arfaptin has been shown to dimerise and to bind Arf and Rho family GTPases [, ], including ARF1, a small GTPase involved in vesicle budding at the Golgi complex and immature secretory granules.The AH domain consists of three α-helices arranged as an extended antiparallel α-helical bundle. Two arfaptin AH domains associate to form a highly elongated, crescent-shaped dimer [, ].
The Rac1-binding domain is the C-terminal portion of YpkA from Yersinia. It is an all-helical molecule consisting of two distinct subdomains connected by a linker. The N-terminal end of this domain (residues 434-615) consists of six helices organised into two three-helix bundles packed against each other. This region is involved with binding to GTPases. The C-terminal end (residues 705-732) is a novel and elongated fold consisting of four helices clustered into two pairs, and this fold carries the helix implicated in actin activation. The Rac1-binding domain mimics host guanidine nucleotide dissociation inhibitors (GDIs) of the Rho GTPases, thereby inhibiting nucleotide exchange in Rac1 and causing cytoskeletal disruption in the host [].
Protein diaphanous homologue 3 (DIAPH3) belongs to the formin homology family, Diaphanous subfamily (also known as the Diaphanous-related formins, Drfs). In addition to the FH1 and FH2 domains, Drfs contain an N-terminal GTPase-binding domain (mDiaN) and a C-terminal Diaphanous-autoregulatory domain (DAD).DIAPH3 (also known as mDia2, which can be confusing) acts in a Rho-dependent manner to recruit profilin to the membrane, where it promotes actin polymerisation. It is required for cytokinesis, stress fibre formation, and transcriptional activation of the serum response factor []. It couples Rho and Src tyrosine kinase during signaling and the regulation of actin dynamics [].
This entry represents the SH3 domain of DBS.DBS, also called MCF2L or OST, functions as a Rho GTPase guanine nucleotide exchange factor (RhoGEF), facilitating the exchange of GDP and GTP. It was originally isolated from a cDNA screen for sequences that cause malignant growth. It plays roles in regulating clathrin-mediated endocytosis and cell migration through its activation of Rac1 and Cdc42 [, ]. Depending on cell type, DBS can also activate RhoA and RhoG [, ]. DBS contains a Sec14-like domain [], spectrin-like repeats, a RhoGEF or Dbl homology (DH) domain, a Pleckstrin homology (PH) domain [], and an SH3 domain.
ARHGEF37 contains a RhoGEF (or Dbl homology, DH) domain followed by a Bin/Amphiphysin/Rvs (BAR) domain, and two C-terminal SH3 domains. Its specific function is unknown. Its domain architecture is similar to the C-terminal half of DNMBP or Tuba, a cdc42-specific GEF that provides a functional link between dynamin, Rho GTPase signaling, and actin dynamics, and plays an important role in regulating cell junction configuration. GEFsactivate small GTPases by exchanging bound GDP for free GTP [].This entry represents the firs C-terminal SH3 domain of ARHGEF37.
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 [].
In general, FGDs (including FGD1, FGD2, FGD3 and FGD4/Frabin) have a RhoGEF (DH) domain, followed by an N-terminal PH domain, a FYVE domain and a C-terminal PH domain. All FGDs are guanine nucleotide exchange factors that activates the Rho GTPase Cdc42, an important regulator of membrane trafficking. The RhoGEF domain is responsible for GEF catalytic activity, while the N-terminal PH domain is involved in intracellular targeting of the DH domain []. FGD2 is expressed by antigen-presenting cells where it may be involved in leukocyte signaling and vesicle trafficking [].This entry represents the N-terminal PH domain of FGD2.
The Rnd proteins, which form a distinct sub-group of the Rho family of small GTP-binding proteins, have been shown to regulate the organization of the actin cytoskeleton in several tissues []. RhoN (also known as Rnd2 or Rho7) is a member of the novel Rho subfamily Rnd, together with Rnd1/Rho6 and Rnd3/RhoE/Rho8. Unlike other small G proteins, Rnd2/RhoN, Rnd3/RhoE, and Rnd1/Rho6 and do not hydrolyze GTP []. This is due to changes in key amino acids involved in catalysing GTP hydrolysis [].Rnd2/RhoN is transiently expressed in radially migrating cells in the brain while they are within the subventricular zone of the hippocampus and cerebral cortex. These migrating cells typically develop into pyramidal neurons. Cells that exogenously expressed Rnd2/RhoN failed to migrate to upper layers of the brain, suggesting that Rnd2/RhoN plays a role in the radial migration and morphological changes of developing pyramidal neurons, and that Rnd2/RhoN degradation is necessary for proper cellular migration. The Rnd2/RhoN GEF Rapostlin is found primarily in the brain and together with Rnd2/RhoN induces dendrite branching [, ]. Unlike Rnd1/Rho6 and Rnd3/RhoE/Rho8, which are RhoA antagonists, Rnd2/RhoN binds the GEF Pragmin and significantly stimulates RhoA activity and Rho-A mediated cell contraction []. Rnd2/RhoN is also found to be expressed in spermatocytes and early spermatids, with male-germ-cell Rac GTPase-activating protein (MgcRacGAP), where it localizes to the Golgi-derived pro-acrosomal vesicle [].
Formins participate in the assembly of the actin and microtubule cytoskeletons in processes like cell division, migration, and development. Diaphanous-related formins (DRF) contain an N-terminal GTPase-binding domain (GBD) and a C-terminal diaphanous autoregulatory domain (DAD). DRFs are regulated by an autoinhibitory interaction of the C-terminal DAD with the DRF N-terminal armadillo repeat-like region (see ) in the DID or GBD/FH3 domain [, , ]. This autoinhibition is released upon competitive binding of an activated Rho GTPase to the GBD. The release of DAD allows the catalytical formin homology 2 (FH2) domain to then nucleate and elongate nonbranched actin filaments.The DAD domain is a ~32 amino acid autoinhibitory domain, which facilitates intramolecular binding. The DAD core forms an α-helical structure and the C-terminal part of the domain contains several basic residues that form a basic region [, , , ].Proteins known to contain a DAD domain include:Fruit fly protein diaphanous, which plays an important role during cytokinesis.Mammalian diaphanous-related formins (DRF) 1-3, which act as Rho GTPase effectors during cytoskeletal remodelling.Saccharomyces cerevisiae (Baker's yeast) proteins BNI1 and BNI1-related protein 1 (BNR1).Emericella nidulans (Aspergillus nidulans) cytokinesis protein sepA, which participates in two actin-mediated processes, septum formation and polarized growth.Mammalian disheveled-associated activator of morphogenesis (DAAM) proteins.Mammalian formin-like 1 protein (Fmnl1) or formin-related protein gene in leukocytes (FRL).
There are two forms of Pix proteins: alpha Pix (also called Rho guanine nucleotide exchange factor (GEF) 6, 90Cool-2 or ARHGEF6) and beta Pix (GEF7, p85Cool-1 or ARHGEF7), which activate small GTPases by exchanging bound GDP for free GTP. betaPix contains an N-terminal SH3 domain, a RhoGEF/DH domain, a PH domain, a GIT1 binding domain (GBD), and a C-terminal coiled-coil (CC) domain []. It acts as a GEF for both Cdc42 and Rac1 [], and plays important roles in regulating neuroendocrine exocytosis, focal adhesion maturation, cell migration, synaptic vesicle localization, and insulin secretion [, , , ]. alphaPix differs in that it contains a calponin homology (CH) domain, which interacts with beta-parvin, N-terminal to the SH3 domain. alphaPix is an exchange factor for Rac1 and Cdc42 and mediates Pak activation on cell adhesion to fibronectin. Mutations in alphaPix can cause X-linked mental retardation. alphaPix also interacts with Huntington's disease protein (htt), and enhances the aggregation of mutant htt (muthtt) by facilitating SDS-soluble muthtt-muthtt interactions. The DH-PH domain of a Pix was required for its binding to htt. In the majority of Rho GEF proteins, the DH-PH domain is responsible for the exchange activity [, , , , ].This entry represents the PH domain of ARHGEF6 and ARHGEF7.
RhoG is a GTPase with high sequence similarity to members of the Rac subfamily, including the regions involved in effector recognition and binding. However, RhoG does not bind to known Rac1 and Cdc42 effectors, including proteins containing a Cdc42/Rac interacting binding (CRIB) motif. Instead, RhoG interacts directly with Elmo, an upstream regulator of Rac1, in a GTP-dependent manner and forms a ternary complex with Dock180 to induce activation of Rac1 []. The RhoG-Elmo-Dock180 pathway is required for activation of Rac1 and cell spreading mediated by integrin, as well as for neurite outgrowth induced by nerve growth factor. Thus RhoG activates Rac1 through Elmo and Dock180 to control cell morphology []. RhoG has also been shown to play a role in caveolar trafficking []and has a novel role in signaling the neutrophil respiratory burst stimulated by G protein-coupled receptor (GPCR) agonists []. Most Rho proteins contain a lipid modification site at the C terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins.
RasGRF2 belongs to the RasGRF family. It is a dual Ras/Rac guanine nucleotide exchange factor (GEF) that has been shown to be necessary for long-term potentiation in situ [, ]. It is also involved in T-cell signalling responses through Ras GTPases []. RasGRF2 has been linked to alcoholism [].RasGRF is a Ras family guanine nucleotide exchange factor sharing homology with Saccharomyces cerevisiae Cdc25 that stimulates nucleotide exchange on S. cerevisiae RAS []. RasGRF N-terminal region contains a Dbl homology (DH) domain which is generally present in GEFs for the Rho family of small G proteins, whereas the C-terminal Cdc25-related domain is linked to Ras GTPase signalling []. The presence of regulatory domains for Rho and Ras GTPases implicates the role of RasGRF in the control of the both pathways []. Two RasGRF, RasGRF1 and 2, have been identified in mammals []. Their function can be inhibited by its interaction with Cdc42 in its inactive GDP bound form. Reciprocally, the effects of Cdc42 on cytoskeletal dynamics can be inhibited by RasGRF1/2 [].
Based on sequence similarities a domain of homology has been identified in the following proteins [, ]:Citron and Citron kinase. These two proteins interact with the GTP-bound forms of the small GTPases Rho and Rac but not with Cdc42.Myotonic dystrophy kinase-related Cdc42-binding kinase (MRCKalpha). This serine/threonine kinase interacts with the GTP-bound form of the small GTPase Cdc42 and to a lesser extent with that of Rac.NCK Interacting Kinase (NIK), a serine/threonine protein kinase.ROM-1 and ROM-2, from yeast. These proteins are GDP/GTP exchange proteins (GEPs) for the small GTP binding protein Rho1.This domain, called the citron homology domain (CNH), is often found after cysteine rich and pleckstrin homology (PH) domains at the C-terminal end of a group of eukaryotic proteins. It is thought to act as a regulatory domain and could be involved in macromolecular interactions [, , , ]. Its structure has been solved in Rho guanyl nucleotide exchange factor (Rom2) from Neosartorya fumigata (Aspergillus fumigatus, ), where it shows a canonical β-propeller fold containing seven blades connected by small loops and arranged in a circular fashion [].
T-lymphoma invasion and metastasis-inducing protein 1 (Tiam1) is a guanine exchange factor (GEF) for CDC42 and the Rho-family GTPase Rac1, which plays an important role in cell-matrix adhesion and in cell migration [, ]. Tiam1 is involved in multiple steps of tumorigenesis [].Tiam2 has been shown to localise to the nuclear envelope and to regulate Rac1 activity at the nuclear envelope which regulates the perinuclear actin cap []. It has been shown to promote invasion and motility of non-small cell lung cancer cells []. It has also been shown to promote epithelial-to-mesenchymal transition and results in proliferation and invasion in liver cancer cells []. This entry includes a group of guanine nucleotide exchange factors, including Tiam1/2 from humans and Sif from Drosophila [, , ]. Tiam1/2 are activators of the Rho GTPase Rac1 and critical for cell morphology, adhesion, migration, and polarity [].
WAS/WASL-interacting protein family member 1 (WIPF1, also known as WIP) is involved in a wide variety of cellular functions,including cellular signalling, endocytosis and actin cytoskeletonremodelling []. It binds to and stabilises N-WASP and WASP []. WIP and WASP can form a complex, which plays an important role in Arp2/3-mediated actin polymerisation and is regulated by Cdc42 (a small GTPase of the Rho family) [, ]. WIP can also participates in the reorganisation of the actin-based cytoskeleton and stabilises actin filaments in a WASP-independent manner []. In blood cells, WIP participates in conveying WASP to areas of active actin assembly following antigen-receptor and chemokinereceptor signalling [, , , ]. WIP deficiency is linked to Wiskott-Aldrich syndrome 2, which is an immunodeficiency disorder characterised by eczema, thrombocytopenia, recurrent infections, defective T-cell proliferation, and impaired natural killer cell function [].
In plants, the small GTP-binding proteins called Rops work as signalling switches that control growth, development and plant responses to various environmental stimuli. Rop (Rho of plants) proteins, Rac-like, and atRac in Arabidopsis thaliana belong to the Rho family of Ras-related GTP-binding proteins that turn on signalling pathways by switching from a GDP-bound inactive to a GTP-bound active conformation. Activation depends on guanine nucleotide exchange factors (GEFs) that catalyse the otherwise slow GDP dissociation for subsequent GTP binding. The plant-specific RopGEFs represent a unique family of exchange factors that display no homology to any known RhoGEFs from animals and fungi. They comprise a highly conserved catalytic domain termed PRONE (plant-specific Rop nucleotide exchanger) with exclusive substrate specificity for members of the Rop family. The PRONE domain has been shown to be necessary and sufficient to promote nucleotide release from Rop [, , ].
Epithelial Cell Transforming Sequence 2 (Ect2) is a guanine nucleotide exchange factor (GEF) that catalyses the exchange of GDP for GTP. Like other GEFs, Ect2 serves as molecular switches in diverse signaling pathways, including cell polarity, mitotic spindle assembly, cytokinesis, etc [, , ]. Ect2 interacts with several members of the Rho GTPase family including, RhoA, RhoB, RhoC, RhoG, Rac1 and Cdc42 [, , , , ]. Ect2 regulates the formation of the actomyosin contractile ring at mitotic exit through activation of RhoA and functions in metaphase for the process of spindle assembly through activation of Cdc42 []. Ect2 is regulated through a number of mechanisms including phosphorylation, intracellular localization and intra- and inter-molecular interactions []. Ect2 is established as a human oncogene []. It is highly expressed in a variety of human tumors including brain lung, bladder, esophageal, pancreatic and ovarian tumors [, , , , ]. Ect2 is also suggested to play a role in neuronal differentiation and brain development [].
HR1 was first described as a three times repeated homology region of the N-terminal non-catalytic part of protein kinase PRK1(PKN) []. The first two of these repeats were later shown to bind the small G protein rho [, ]known to activate PKN in its GTP-bound form. Similar rho-binding domains also occur in a number of other protein kinases and in the rho-binding proteins rhophilin and rhotekin. Recently, the structure of the N-terminal HR1 repeat complexed with RhoA has been determined by X-ray crystallography. This domain contains two long alpha helices forming a left-handed antiparallel coiled-coil fold termed the antiparallel coiled- coil (ACC) finger domain. The two long helices encompass the basic region and the leucine repeat region, which are identified as the Rho-binding region [, , ].
This entry represents the catalytic domain of serine/threonine kinase p21-activated kinase (PAK) 3.PAK3 is highly expressed in the brain. It is implicated in neuronal plasticity, synapse formation, dendritic spine morphogenesis, cell cycle progression, neuronal migration, and apoptosis [, ]. Inactivating mutations in the PAK3 gene cause X-linked non-syndromic mental retardation, the severity of which depends on the site of the mutation [, ]. PAK3 belongs to the group I PAKs.Group I PAKs contain a PBD (p21-binding domain) overlapping with an AID (autoinhibitory domain), a C-terminal catalytic domain, SH3 binding sites and a non-classical SH3 binding site for PIX (PAK-interacting exchange factor). PAKs are Rho family GTPase-regulated kinases that serve as important mediators in the function of Cdc42 (cell division cycle 42) and Rac [].
PAK2 plays a role in pro-apoptotic signaling. It is cleaved and activated by caspases leading to morphological changes during apoptosis []. PAK2 is also activated in response to a variety of stresses including DNA damage, hyperosmolarity, serum starvation, and contact inhibition, and may play a role in coordinating the stress response []. PAK2 also contributes to cancer cell invasion through a mechanism distinct fromthat of PAK1 []. PAK2 belongs to the group I PAKs.Group I PAKs contain a PBD (p21-binding domain) overlapping with an AID (autoinhibitory domain), a C-terminal catalytic domain, SH3 binding sites and a non-classical SH3 binding site for PIX (PAK-interacting exchange factor). PAKs are Rho family GTPase-regulated kinases that serve as important mediators in the function of Cdc42 (cell division cycle 42) and Rac [].This entry corresponds to the PAK2 C-terminal catalytic domain.
Toxins A (TcdA) and B (TcdB) of Clostridium difficile belong to the family of clostridial glucosylating toxins. These toxins glucosylate small GTPases of Rho and Ras families, inhibiting the signalling and regulatory functions of these switch proteins. After receptor-binding, the toxins are endocytosed to reach acidic endosomal compartments from where the toxins are translocated into the cytosol []. TcdB has been shown to consist of a N-terminal glucosyltransferase domain (GTD), responsible for the biological effects of the toxin, a cysteine protease domain (CPD), responsible for autocatalytic cleavage, a hydrophobic region (HR), which has been suggested to be involved in toxin translocation, and a C-terminal repetitive domain involved in receptor binding. The pore-forming region of toxin B has been described to be in a region in the middle of the protein, within amino acid residues 830 and 990 [].This entry represents the pore forming domain of TcdA and TcdB. It is also found in other toxins.
This entry defines the apparent leader peptides of tryptophanase operons in Escherichia coli, Vibrio cholerae, Photobacterium profundum, Haemophilus influenzae, and related species. It has been suggested that these peptides act in cis to alter the behaviour of the translating ribosome [].The tryptophanese (tna) operon leader peptide catalyses the degradation of L-tryptophan to indole, pyruvate and ammonia, enabling the bacteria to utilise tryptophan as a source of carbon, nitrogen and energy. The tna operon of Escherichia coli contains two major structural genes, tnaA and tnaB. Preceding tnaA in the tna operon is a 319 -nucleotide transcribed regulatory region that contains the coding region for a 24-residue leader peptide, TnaC. The RNA sequence in the vicinity of the tnaC stop codon is rich in Cytidylate residues which is required for efficient Rho -dependent termination in the leader region of the tna operon [].
Cytoplasmic proteins Nck are non-enzymatic adaptor proteins composed of three SH3 (Src homology 3) domains and a C-terminal SH2 domain []. They regulate actin cytoskeleton dynamics by linking proline-rich effector molecules to protein tyrosine kinases and phosphorylated signaling intermediates []. They function downstream of the PDGFbeta receptor and are involved in Rho GTPase signaling and actin dynamics []. They associate with tyrosine-phosphorylated growth factor receptors or their cellular substrates [, ]. There are two vertebrate Nck proteins, Nck1 and Nck2. Nck1 (also called Nck-alpha) plays a crucial role in connecting signaling pathways of tyrosine kinase receptors and important effectors in actin dynamics and cytoskeletal remodeling []. It binds and activates RasGAP, resulting in the downregulation of Ras []. It is also involved in the signaling of endothilin-mediated inhibition of cell migration [].This entry represents the SH2 domain of Nck1.
Vav proteins are involved in several processes that require cytoskeletal reorganization, such as the formation of the immunological synapse (IS), phagocytosis, platelet aggregation, spreading, and transformation. Vavs function as guanine nucleotide exchange factors (GEFs) for the Rho/Rac family of GTPases []. Vav family members have several conserved motifs/domains including: a leucine-rich region, a leucine-zipper, a calponin homology (CH) domain, an acidic domain, a Dbl-homology (DH) domain, a pleckstrin homology (PH) domain, a cysteine-rich domain, two SH3 domains, a proline-rich region, and a SH2 domain. Vavs are the only known Rho GEFs that have both the DH/PH motifs and SH2/SH3 domains in the same protein. This entry represents the SH2 domain which mediates a high affinity interaction with tyrosine phosphorylated proteins []. 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 [].
The aldo-keto reductase family includes a number of related monomeric NADPH-dependent oxidoreductases, such as aldehyde reductase, aldose reductase, prostaglandin F synthase, xylose reductase, rho crystallin, and many others []. All possess a similar structure, with a beta-α-β fold characteristic of nucleotide binding proteins []. The fold comprises a parallel beta-8/alpha-8-barrel, which contains a novel NADP-binding motif. The binding site is located in a large, deep, elliptical pocket in the C-terminal end of the beta sheet, the substrate being bound in an extended conformation. The hydrophobic nature of the pocket favours aromatic and apolar substrates over highly polar ones [].Binding of the NADPH coenzyme causes a massive conformational change, reorienting a loop, effectively locking the coenzyme in place. This binding is more similar to FAD- than to NAD(P)-binding oxidoreductases [].Some proteins of this entry contain a K+ ion channel beta chain regulatory domain; these are reported to have oxidoreductase activity []. This entry represents the NADP-dependent oxidoreductase domain superfamily.
Arl2 (Arf-like 2) GTPases are members of the Arf family that bind GDP and GTP with very low affinity. Unlike most Arf family proteins, Arl2 is not myristoylated at its N-terminal helix. The protein PDE-delta, first identified in photoreceptor rod cells, binds specifically to Arl2 and is structurally very similar to RhoGDI. Despite the high structural similarity between Arl2 and Rho proteins and between PDE-delta and RhoGDI, the interactions between the GTPases and their effectors are very different. In its GTP bound form, Arl2 interacts with the protein Binder of Arl2 (BART), and thecomplex is believed to play a role in mitochondrial adenine nucleotide transport []. In its GDP bound form, Arl2 interacts with tubulin- folding Cofactor D; this interaction is believed to play a role in regulation of microtubule dynamics that impact the cytoskeleton, cell division, and cytokinesis [].This entry also includes Alp41 from fission yeasts which is essential for the cofactor-dependent biogenesis of microtubules [].
Mitochondrial Rho (Miro) proteins are aberrant members of the small GTPase superfamily found in most eukaryotes. Miro contains a transmembrane region located at the C terminus anchors the protein to the outer membrane of mitochondria, the GTPase domains and EF-hands located in the cytoplasm. Miro and its cytoplasmic binding partner Milton/TRAK link mitochondria to kinesin and dynein molecular motors in various cell types []. Mammals have two Miro orthologs , Miro1 and Miro2. They mediate mitochondrial trafficking in neurons by linking mitochondria to kinesin and dynein motor proteins for their transport in axons and dendrites [, ]. Yeasts have one Miro homologue, known as Gem1, which is part of the ERMES complex that links the ER to mitochondria []. Interestingly, ERMES is absent in metazoa []. This entry represents the tandemly repeated GTPase domain from these proteins.
Eukaryotic protein kinases [, , , ]are enzymes that belong to a very extensive family of proteins which share a conserved catalytic core common with both serine/threonine and tyrosine protein kinases.Rho kinases are serine/threonine kinases that are important in cell migration, cell proliferation and cell survival. Disorders of the central nervous system including stroke, inflammatory and demyelinating diseases, Alzheimer's disease and neuropathic pain may be linked to abnormal activation of Rho kinases [].This entry represents a set of Rho-associated, coiled-coil-containing, protein kinases. They phosphorylate a large number of important signalling proteins and help regulate the assembly of the actin cytoskeleton. Proteins in this entry have been shown to play a role in smooth muscle formation, and promote the formation of stress fibres and of focal adhesion complexes [, ].
Citron Rho-interacting kinase (CRIK) is a dual specificity protein kinase, which catalyses the autophosphorylation and phosphorylation of exogenous substrates on both serine/threonine and tyrosine residues []. It plays an important role in the regulation of cytokinesis and the development of the central nervous system. It is required for KIF14 localization to the central spindle and mid-body. It is also a putative RHO/RAC effector that binds to the GTP-bound forms of RHO and RAC1. This protein occurs in at least two different isoforms: CRIK (about 240kDa), in which the kinase domain is followed by the sequence of Citron (a Rho/Rac binding protein); and CRIK-short kinase (CRIK-SK, about 54kDa), which consists mostly of the kinase domain. CRIK may fulfil more specialised functions in specific cell types [].
The RGS (Regulator of G-protein Signaling) domain is an essential part of the p115RhoGEF protein, a member of the RhoGEF (Rho guanine nucleotide exchange factor) subfamily of the RGS protein family. The RhoGEFs are peripheral membrane proteins that regulate essential cellular processes, including cell shape, cell migration, cell cycle progression of cells, and gene transcription by linking signals from heterotrimeric G-alpha12/13 protein-coupled receptors to Rho GTPase activation, leading to various cellular responses, such as actin reorganization and gene expression [, ].The RhoGEF subfamily includes p115RhoGEF, LARG, PDZ-RhoGEF and its rat specific splice variant GTRAP48. The RGS domain of RhoGEFs has very little sequence similarity with the canonical RGS domain of the RGS proteins and is often refered to as RH (RGS Homology) domain. In addition to being a G-alpha13/12 effector, the p115RhoGEF protein also functions as a GTPase-activating protein (GAP) for G-alpha13 []. This entry represents the RGS domain of p115RhoGEF.
Protein diaphanous homologue 1 (Dia1) belongs to the formin homology family, Diaphanous subfamily (also known as the Diaphanous-related formins, Drfs). In addition to the FH1 and FH2 domains, Drfs contain an N-terminal GTPase-binding domain (mDiaN) and a C-terminal Diaphanous-autoregulatory domain (DAD).Dia1 contains the N-terminal RhoA-binding domain (RBD) followed by a four armadillo-repeats containing Diaphanous inhibitory domain (DID) that binds the C-terminal Diaphanous autoregulatory domain (DAD) [, ]. Dia1 nucleates actin filaments and regulate actin polymerisation and depolymerisation. The activities of Dia1 is regulated by an autoinhibitory interaction between DAD domain and the GBD/FH3 domain. This autoinhibition is released upon competitive binding of an activated GTPase. The release of DAD allows the FH2 domain to then nucleate and elongate nonbranched actin filaments []. Dia1 couples Rho and Src tyrosine kinase during signaling and the regulation of actin dynamics [].
This domain superfamily is found in several bacterial cytotoxic necrotizing factor proteins as well as related dermonecrotic toxin (DNT) from Bordetella species [].Cytotoxic necrotizing factor 1 (CNF1) is a toxin whose structure from Escherichia coli revealed a 4-layer alpha/beta/beta/alpha structure containing mixed β-sheets []. CNF1 is expressed in strains of E. coli causing uropathogenic and neonatal meningitis. CNF1 alters host cell actin cytoskeleton and promotes bacterial invasion of the blood-brain barrier endothelial cells []. CNF1 belongs to a unique group of large cytotoxins that cause constitutive activation of Rho guanosine triphosphatases (GTPases), which are key regulators of the actin cytoskeleton [].Bordetella dermonecrotic toxin (DNT) stimulates the assembly of actin stress fibres and focal adhesions by deamidating or polyaminating Gln63 of the small GTPase Rho. DNT is an A-B toxin composed of an N-terminal receptor-binding (B) domain and a C-terminal enzymatically active (A) domain [].
Cdc42 is an essential GTPase that belongs to the Rho family of Ras-like GTPases. These proteins act as molecular switches by responding to exogenous and/or endogenous signals and relaying those signals to activate downstream components of a biological pathway. Cdc42 transduces signals to the actin cytoskeleton to initiate and maintain polarized growth and to mitogen-activated protein morphogenesis. In Saccharomyces cerevisiae, Cdc42 plays an important role in multiple actin-dependent morphogenetic events such as bud emergence, mating-projection formation, and pseudohyphal growth []. In mammalian cells, Cdc42 regulates a variety of actin-dependent events and induces the JNK/SAPK protein kinase cascade, which leads to the activation of transcription factors within the nucleus []. Cdc42 mediates these processes through interactions with a myriad of downstream effectors, whose number and regulation we are just starting to understand. In addition, Cdc42 has been implicated in a number of human diseases through interactions with its regulators and downstream effectors [].
This entry represent the first SH3 domain of Nck2. It binds the PxxDY sequence in the CD3e cytoplasmic tail; this binding inhibits phosphorylation by Src kinases, resulting in the downregulation of TCR surface expression []. Nck2 (also known as Grb4) is a member of the Nck family. It plays a crucial role in connecting signaling pathways of tyrosine kinase receptors and important effectors in actin dynamics and cytoskeletal remodeling []. It binds neuronal signaling proteins such as ephrinB []. Cytoplasmic proteins Nck are non-enzymatic adaptor proteins composed of three SH3 (Src homology 3) domains and a C-terminal SH2 domain []. They regulate actin cytoskeleton dynamics by linking proline-rich effector molecules to protein tyrosine kinases and phosphorylated signaling intermediates []. They function downstream of the PDGFbeta receptor and are involved in Rho GTPase signaling and actin dynamics []. They associate with tyrosine-phosphorylated growth factor receptors or their cellular substrates [, ]. There are two vertebrate Nck proteins, Nck1 and Nck2.
This entry represent the second SH3 domain of Nck2. The second SH3 domain of Nck appears to prefer ligands containing the APxxPxR motif []. Nck2 (also known as Grb4) is a member of the Nck family. It plays a crucial role in connecting signaling pathways of tyrosine kinase receptors and important effectors in actin dynamics and cytoskeletal remodeling []. It binds neuronal signaling proteins such as ephrinB []. Cytoplasmic proteins Nck are non-enzymatic adaptor proteins composed of three SH3 (Src homology 3) domains and a C-terminal SH2 domain []. They regulate actin cytoskeleton dynamics by linking proline-rich effector molecules to protein tyrosine kinases and phosphorylated signaling intermediates []. They function downstream of the PDGFbeta receptor and are involved in Rho GTPase signaling and actin dynamics []. They associate with tyrosine-phosphorylated growth factor receptors or their cellular substrates [, ]. There are two vertebrate Nck proteins, Nck1 and Nck2.
This entry represent the third SH3 domain of Nck2. The third SH3 domain of Nck appears to prefer ligands with a PxAPxR motif [].Nck2 (also known as Grb4) is a member of the Nck family. It plays a crucial role in connecting signaling pathways of tyrosine kinase receptors and important effectors in actin dynamics and cytoskeletal remodeling []. It binds neuronal signaling proteins such as ephrinB []. Cytoplasmic proteins Nck are non-enzymatic adaptor proteins composed of three SH3 (Src homology 3) domains and a C-terminal SH2 domain []. They regulate actin cytoskeleton dynamics by linking proline-rich effector molecules to protein tyrosine kinases and phosphorylated signaling intermediates []. They function downstream of the PDGFbeta receptor and are involved in Rho GTPase signaling and actin dynamics []. They associate with tyrosine-phosphorylated growth factor receptors or their cellular substrates [, ]. There are two vertebrate Nck proteins, Nck1 and Nck2.
This entry represent the second SH3 domain of Nck1. The second SH3 domain of Nck appears to prefer ligands containing the APxxPxR motif [].Nck1 (also called Nck-alpha) plays a crucial role in connecting signaling pathways of tyrosine kinase receptors and important effectors in actin dynamics and cytoskeletal remodeling []. It binds and activates RasGAP, resulting in the downregulation of Ras []. It is also involved in the signaling of endothilin-mediated inhibition of cell migration [].Cytoplasmic proteins Nck are non-enzymatic adaptor proteins composed of three SH3 (Src homology 3) domains and a C-terminal SH2 domain []. They regulate actin cytoskeleton dynamics by linking proline-rich effector molecules to protein tyrosine kinases and phosphorylated signaling intermediates []. They function downstream of the PDGFbeta receptor and are involved in Rho GTPase signaling and actin dynamics []. They associate with tyrosine-phosphorylated growth factor receptors or their cellular substrates [, ]. There are two vertebrate Nck proteins, Nck1 and Nck2.
This entry represent the third SH3 domain of Nck1. The third SH3 domain of Nck appears to prefer ligands with a PxAPxR motif [].Nck1 (also called Nck-alpha) plays a crucial role in connecting signaling pathways of tyrosine kinase receptors and important effectors in actin dynamics and cytoskeletal remodeling []. It binds and activates RasGAP, resulting in the downregulation of Ras []. It is also involved in the signaling of endothilin-mediated inhibition of cell migration [].Cytoplasmic proteins Nck are non-enzymatic adaptor proteins composed of three SH3 (Src homology 3) domains and a C-terminal SH2 domain []. They regulate actin cytoskeleton dynamics by linking proline-rich effector molecules to protein tyrosine kinases and phosphorylated signaling intermediates []. They function downstream of the PDGFbeta receptor and are involved in Rho GTPase signaling and actin dynamics []. They associate with tyrosine-phosphorylated growth factor receptors or their cellular substrates [, ]. There are two vertebrate Nck proteins, Nck1 and Nck2.
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 [].
PAK2 plays a role in pro-apoptotic signaling. It is cleaved and activated by caspases leading to morphological changes during apoptosis []. PAK2 is also activated in response to a variety of stresses including DNA damage, hyperosmolarity, serum starvation, and contact inhibition, and may play a role in coordinating the stress response []. PAK2 also contributes to cancer cell invasion through a mechanism distinct from that of PAK1 []. PAK2 belongs to the group I PAKs.Group I PAKs contain a PBD (p21-binding domain) overlapping with an AID (autoinhibitory domain), a C-terminal catalytic domain, SH3 binding sites and a non-classical SH3 binding site for PIX (PAK-interacting exchange factor). PAKs are Rho family GTPase-regulated kinases that serve as important mediators in the function of Cdc42 (cell division cycle 42) and Rac [].
PAK6 may play a role in stress responses through its activation by the mitogen-activated protein kinase (MAPK) p38 and MAPK kinase 6 (MKK6) pathway []. PAK6 is highly expressed in the brain. It is not required for viability, but together with PAK5, it is required for normal levels of locomotion and activity, and for learning and memory []. Increased expression of PAK6 is found in primary and metastatic prostate cancer [].PAK6 belongs to the group II PAKs, which contain a PBD (p21-binding domain) and a C-terminal catalytic domain, but do not harbor an AID (autoinhibitory domain) or SH3 binding sites []. PAKs are Rho family GTPase-regulated kinases that serve as important mediators in the function of Cdc42 (cell division cycle 42) and Rac [].
ARHGEF12 (also called LARG) is a Rho guanine-nucleotide exchange factor that are RhoA-selective and directly activated by the Galpha12/13 family of heterotrimeric G proteins. LARG contains a regulator of G protein signaling (RGS) homology (RH) domain, the catalytic Dbl homology (DH) domain and the pleckstrin homology (PH) domain. The DH and PH domains bind RhoA and catalyze the exchange of GDP for GTP on RhoA. The active site of RhoA adopts two distinct GDP-excluding conformations among the four unique complexes in the asymmetric unit. The LARG PH domain also contains a potential protein-docking site. LARG forms a homotetramer via its DH domains []. This entry represents the PH domain of ARHGEF12. It has an exposed hydrophobic patch that could interface with other domains of LARG or other regulatory proteins [].
This entry represents the PH domain of guanine nucleotide exchange factor DBS. The DBS PH domain participates in binding to both the Cdc42 and RhoA GTPases []. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner [].DBS, also called MCF2L or OST, functions as a Rho GTPase guanine nucleotide exchange factor (RhoGEF), facilitating the exchange of GDP and GTP. It was originally isolated from a cDNA screen for sequences that cause malignant growth. It plays roles in regulating clathrin-mediated endocytosis and cell migration through its activation of Rac1 and Cdc42 [, ]. Depending on cell type, DBS can also activate RhoA and RhoG [, ]. DBS contains a Sec14-like domain [], spectrin-like repeats, a RhoGEF or Dbl homology (DH) domain, a Pleckstrin homology (PH) domain [], and an SH3 domain.
The aldo-keto reductase family includes a number of related monomeric NADPH-dependent oxidoreductases, such as aldehyde reductase, aldose reductase, prostaglandin F synthase, xylose reductase, rho crystallin, and many others []. All possess a similar structure, with a beta-α-β fold characteristic of nucleotide binding proteins []. The fold comprises a parallel beta-8/alpha-8-barrel, which contains a novel NADP-binding motif. The binding site is located in a large,deep, elliptical pocket in the C-terminal end of the beta sheet, the substrate being bound in an extended conformation. The hydrophobicnature of the pocket favours aromatic and apolar substrates over highly polar ones [].Binding of the NADPH coenzyme causes a massive conformational change, reorienting a loop, effectively locking thecoenzyme in place. This binding is more similar to FAD- than to NAD(P)-binding oxidoreductases [].Some proteins of this entry contain a K+ ion channel beta chain regulatory domain; these are reported to have oxidoreductase activity []. This entry represents the NADP-dependent oxidoreductase domain found in these proteins.
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 domain is found in several bacterial cytotoxic necrotizing factor proteins as well as related dermonecrotic toxin (DNT) from Bordetella species [].Cytotoxic necrotizing factor 1 (CNF1) is a toxin whose structure from Escherichia coli revealed a 4-layer alpha/beta/beta/alpha structure containing mixed β-sheets []. CNF1 is expressed in strains of E. coli causing uropathogenic and neonatal meningitis. CNF1 alters host cell actin cytoskeleton and promotes bacterial invasion of the blood-brain barrier endothelial cells []. CNF1 belongs to a unique group of large cytotoxins that cause constitutive activation of Rho guanosine triphosphatases (GTPases), which are key regulators of the actin cytoskeleton [].Bordetella dermonecrotic toxin (DNT) stimulates the assembly of actin stress fibres and focal adhesions by deamidating or polyaminating Gln63 of the small GTPase Rho. DNT is an A-B toxin composed of an N-terminal receptor-binding (B) domain and a C-terminal enzymatically active (A) domain [].
The aldo-keto reductase family includes a number of related monomeric NADPH-dependent oxidoreductases, such as aldehyde reductase, aldosereductase, prostaglandin F synthase, xylose reductase, rho crystallin, andmany others []. All possess a similar structure, with a beta-α-β fold characteristic of nucleotide binding proteins [].The fold comprises a parallel beta-8/alpha-8-barrel, which contains a novel NADP-binding motif. The binding site is located in a large,deep, elliptical pocket in the C-terminal end of the beta sheet, the substrate being bound in an extended conformation. The hydrophobicnature of the pocket favours aromatic and apolar substrates over highlypolar ones [].Binding of the NADPH coenzyme causes a massiveconformational change, reorienting a loop, effectively locking thecoenzyme in place. This binding is more similar to FAD- than toNAD(P)-binding oxidoreductases [].Some proteins of this entry contain a K+ ion channel beta chain regulatory domain; these are reported to have oxidoreductase activity [].
The Rac1-binding domain is the C-terminal portion of YpkA from Yersinia. It is an all-helical molecule consisting of two distinct subdomains connected by a linker. The N-terminal end of this domain (residues 434-615) consists of six helices organised into two three-helix bundles packed against each other. This region is involved with binding to GTPases. The C-terminal end (residues 705-732) is a novel and elongated fold consisting of four helices clustered into two pairs, and this fold carries the helix implicated in actin activation. The Rac1-binding domain mimics host guanidine nucleotide dissociation inhibitors (GDIs) of the Rho GTPases, thereby inhibiting nucleotide exchange in Rac1 and causing cytoskeletal disruption in the host [].This superfamily represents the N-terminal GTPase binding subdomain of the Rac1-binding domain.
The Rac1-binding domain is the C-terminal portion of YpkA from Yersinia. It is an all-helical molecule consisting of two distinct subdomains connected by a linker. The N-terminal end of this domain (residues 434-615) consists of six helices organised into two three-helix bundles packed against each other. This region is involved with binding to GTPases. The C-terminal end (residues 705-732) is a novel and elongated fold consisting of four helices clustered into two pairs, and this fold carries the helix implicated in actin activation. The Rac1-binding domain mimics host guanidine nucleotide dissociation inhibitors (GDIs) of the Rho GTPases, thereby inhibiting nucleotide exchange in Rac1 and causing cytoskeletal disruption in the host [].This superfamily represents the C-terminal subdomain of the Rac1-binding domain. This domain is made up of one long, kinked helix and three smaller helices. The long helix has 2 points of contact which allow the domain to bind Rac1 at regions called Switch I and Switch II on the Rac1 protein.
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.
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 an adjacent pleckstrin homology (PH) domain within the context of functionally diverse signalling modules. The evolutionarily distinct andsmaller 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 DHR-2 domain (also termed the CZH2 or DOCKER domain), [, , , , , ].The ~200 residue DOCK-type C2 domain is located toward the N terminus. It adopts a C2-like architecture and interacts with phosphatidylinositol3,4,5-trisphosphate []to mediate signalling and membrane localization. The central core of the DOCK-type C2 domain domain adopts an antiparallel β-sandwich with the "type II"C2 domain fold (a circular permutation of the more common "type I"topology), in which two 4-stranded sheets with strand order 6-5-2-3 and 7-8-1-4 create convex- and concave-exposed faces, respectively [].Some DOCK proteins are listed below:Mammalian Mammalian dedicator of cytokinesis 180 (DOCK180 or DOCK1),important for cell migration.Mammalian DOCK2, important for lymphocyte development, homong, activation,adhesion, polarization and migration processes.Mammalian DOCK3 (also known as MOCA), is expressed predominantly in neuronsand resides in growth cones and membrane ruffles.Mammalian DOCK4, possesses tumor suppressor properties.Mammalian DOCK9 (zizimin1), plays an important role in dendrite growth inhippocampal neurons through activation of Cdc42.Drosophila melanogaster Myoblast city.Caenorhabditis elegans CED-5.
Bacterial transcription antitermination protein, NusG, is a component of the transcription complex and interacts with the termination factor Rho and RNA polymerase [, ]. NusG is a bacterial transcriptional elongation factor involved in transcription termination and antitermination [, ].RfaH is a transcription antitermination protein that enhances distal genes transcription elongation in a specialized subset of operons that encode extracytoplasmic components []. It is most closely related to the transcriptional termination/antitermination protein NusG and contains the KOW motif []. This protein appears to be limited to the proteobacteria.RfaH is recruited into a multi-component RNA polymerase complex by the ops element, which is a short conserved DNA sequence located downstream of the main promoter of these operons. Once bound, RfaH suppresses pausing and inhibits Rho-dependent and intrinsic termination at a subset of sites. Termination signals are bypassed, which allows complete synthesis of long RNA chains. Enhances expression of several operons involved in synthesis of lipopolysaccharides, exopolysaccharides, hemolysin, and sex factor. Also negatively controls expression and surface presentation of AG43 and possibly another AG43-independent factor that mediates cell-cell interactions and biofilm formation [, , ].This entry includes NusG and its paralogue RfaH [].
PLEKHG1 (also called ARHGEF41), PLEKHG2 (also called ARHGEF42 or CLG/common-site lymphoma/leukemia guanine nucleotide exchange factor2), and PLEKHG3 (also called ARHGEF43) have RhoGEF DH/double-homology domains in tandem with a PH domain which is involved in phospholipid binding. They function as a guanine nucleotide exchange factor (GEF) and are involved in the regulation of Rho protein signal transduction []. Mutations in PLEKHG1 have been associated panic disorder (PD), an anxiety disorder characterized by panic attacks and anticipatory anxiety [].PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane []. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.
This entry represents a domain consisting of twelve helices that fold into a compact structure that contains the overall structural scaffold observed in other regulator of G protein signalling (RGS) proteins and three additional helical elements that pack closely to it. Helices 1-9 comprise the RGS fold, in which helices 4-7 form a classic antiparallel bundle adjacent to the other helices. Like other RGS structures, helices 7 and 8 span the length of the folded domain and form essentially one continuous helix with a kink in the middle. Helices 10-12 form an apparently stable C-terminal extension of the structural domain, and although other RGS proteins lack this structure, these elements are intimately associated with the rest of the structural framework by hydrophobic interactions. This domain binds to active G-alpha proteins, promoting GTP hydrolysis by the alpha subunit of heterotrimeric G proteins, thereby inactivating the G protein and rapidly switching off G protein-coupled receptor signalling pathways []. This RGS-like domain is found in Rho guanine nucleotide exchange factors (RhoGEF) such as Pdz-RhoGEF []and p115RhoGEF [].
This entry represents the ELMO (EnguLfment and Cell MOtility) domain, which is found in a number of eukaryotic proteins involved in the cytoskeletal rearrangements required for phagocytosis of apoptotic cells and cell motility, including CED-12, ELMO-1 and ELMO-2. ELMO-1 and ELMO-2 are components of signalling pathways that regulate phagocytosis and cell migration and are mammalian orthologues of the Caenorhabditis elegans gene, ced-12 that is required for the engulfment of dying cells and cell migration. ELMO-1/2 act in association with DOCK1 and CRK. ELMO-1/2 interact with the SH3-domain of DOCK1 via an SH3-binding site to enhance the guanine nucleotide exchange factor (GEF) activity of DOCK1. ELMO-1/2 could be part of a complex with DOCK1 and Rac1 that could be required to activate Rac Rho small GTPases. Regulatory GTPases in the Ras superfamily employ a cycle of alternating GTP binding and hydrolysis, controlled by guanine nucleotide exchange factors and GTPase-activating proteins (GAPs), as essential features of their actions in cells. Within the Ras superfamily, the Arf family is composed of 30 members, including 22 Arf-like (Arl) proteins. The ELMO domain has been proposed to be a GAP domain for ARL2 and other members of the Arf family [].
The Rnd proteins, which form a distinct sub-group of the Rho family of small GTP-binding proteins, have been shown to regulate the organization of the actin cytoskeleton in several tissues []. This entry represents RhoE (also known as Rnd3 or Rho8), which is a member of the Rnd subfamily. Unlike other small G proteins, RhoE, along with two other proteins Rnd1/Rho6 and Rnd2/RhoN, does not hydrolyze GTP []. This is due to changes in key amino acids involved in catalysing GTP hydrolysis []. RhoE is known to bind the serine-threonine kinase ROCK I. Unphosphorylated RhoE associates primarily with membranes, but ROCK I-phosphorylated RhoE localizes in the cytosol []. Phosphorylation of RhoE correlates with its activity in disrupting RhoA-induced stress fibres and inhibiting Ras-induced fibroblast transformation []. In mammary epithelial tumor cells, RhoE regulates the assembly of the apical junction complex and tight junction formation []. In cells that lack stress fibres, such as macrophages and monocytes, RhoE induces a redistribution of actin, causing morphological changes in the cell []. In addition, RhoE has been shown to inhibit cell cycle progression in G1 phase at a point upstream of the pRb family pocket protein checkpoint []. RhoE has also been shown to inhibit Ras- and Raf-induced fibroblast transformation. RhoE is underexpressed in prostate cancer cells both in vitro and in vivo; re-expression of RhoE suppresses cell cycle progression and increases apoptosis, suggesting it may play a role in tumor suppression [].
Rsr1 is a member of the Rap subfamily of the Ras family that is found in fungi. In budding yeasts, Rsr1 is involved in selecting a site for bud growth on the cell cortex, which directs the establishment of cell polarization. The Rho family GTPase cdc42 and its GEF, cdc24, then establish an axis of polarized growth by organizing the actin cytoskeleton and secretory apparatus at the bud site. It is believed that cdc42 interacts directly with Rsr1 in vivo [, ]. In filamentous fungi, polar growth occurs at the tips of hypha and at novel growth sites along the extending hypha. In Ashbya gossypii, Rsr1 is a key regulator of hyphal growth, localizing at the tip region and regulating in apical polarization of the actin cytoskeleton [].Most Ras proteins contain a lipid modification site at the C terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins [].
Arf6 (ADP ribosylation factor 6) proteins localize to the plasma membrane, where they perform a wide variety of functions. In its active, GTP-bound form, Arf6 is involved in cell spreading, Rac-induced formation of plasma membrane ruffles, cell migration, wound healing, and Fc-mediated phagocytosis. Arf6 appears to change the actin structure at the plasma membrane by activating Rac, a Rho family protein involved in membrane ruffling. Arf6 is required for and enhances Rac formation of ruffles. Arf6 can regulate dendritic branching in hippocampal neurons, and in yeast it localizes to the growing bud, where it plays a role in polarized growth and bud site selection. In leukocytes, Arf6 is required for chemokine-stimulated migration across endothelial cells. Arf6 also plays a role in down-regulation of beta2-adrenergic receptors and luteinizing hormone receptors by facilitating the release of sequestered arrestin to allow endocytosis. Arf6 is believed to function at multiple sites on the plasma membrane through interaction with a specific set of GEFs, GAPs, and effectors []. Arf6 has been implicated in breast cancer and melanoma cell invasion [, ], and in actin remodelling at the invasion site of Chlamydia infection [].It's worth noting that the Arf6 homologue in Saccharomyces cerevisiae is known as Arf3 [].
Secretion of virulence factors in Gram-negative bacteria involves transportation of the protein across two membranes to reach the cell exterior. There have been four secretion systems described in animal enteropathogens, such as Salmonella and Yersinia, with further sequence similarities in plant pathogens like Ralstonia and Erwinia [].The type III secretion system is of great interest, as it is used to transport virulence factors from the pathogen directly into the host cell and is only triggered when the bacterium comes into close contact with the host. The protein subunits of the system are very similar to those of bacterial flagellar biosynthesis. However, while the latter forms a ring structure to allow secretion of flagellin and is an integral part of the flagellum itself [], type III subunits in the outer membrane translocate secreted proteins through a channel-like structure.Exotoxins secreted by the type III system do not possess a secretion signal, and are considered unique for this reason []. Yersinia secrete a Rho GTPase-activating protein, YopE [, ], that disrupts the host cell actin cytoskeleton. YopE is regulated by another bacterial gene, SycE [], that enables the exotoxin to remain soluble in the bacterial cytoplasm. A similar protein, exoenzyme S (ExoS) from Pseudomonas aeruginosa, has both ADP-ribosylation and GTPase activity [, ].This entry refers to the GTPase-activating protein (GAP) domain found in YopE, ExoS, and also SptP (Secreted effector protein) [].
OCRL1 hydrolyzes phosphatidylinositol 4,5-bisphosphate (PtIns(4,5)P2) and the signaling molecule phosphatidylinositol 1,4,5-trisphosphate (PtIns(1,4,5)P3), and thereby modulates cellular signaling events []. OCRL1 resides on vesicular structures throughout the endosomal system and the Golgi complex, and is also present at the plasma membrane in membrane ruffles and at late-stage endocytic clathrin-coated pits. It binds clathrin, clathrin adaptors, several GTPases, and the endocytic proteins APPL1 and Ses1/2 []. Mutations in the OCRL1 gene cause Lowe Syndrome, leading to cataracts, mental retardation and renal failure []. Mutations in OCRL can also give rise to a milder pathology, Dent disease 2, which is characterised by renal Fanconi syndrome in the absence of extrarenal pathologies [].OCRL1 shares ~45% sequence identity with INPP5B and has the same domain organization. However, a loop in the Rho GAP domain contains a second clathrin box which is absent in INPP5B. INPP5B shares most interacting partners with OCRL, except for clathrin and the endocytic clathrin adaptor AP-2 []. OCRL1 contains a PH domain, a 5-phosphatase domain, an ASH domain and a Rho-GAP domain. The RhoGAP domain lacks the catalytic arginine and is catalytically inactive. However, the RhoGAP domain of OCRL interacts with Rac and Cdc42, but only the Cdc42 interaction is GTP-dependent. The RhoGAP domain also interacts with three endocytic proteins containing the F&H motif: APPL1, Ses1 and Ses2. OCRL1 interacts with Rab GTPase (Rab8) through its ASH domain []. This entry represents the inositol polyphosphate 5-phosphatase (INPP5c) domain of OCRL1/INPP5B.
Toxins A (TcdA) and B (TcdB) of Clostridium difficile belong to the family of clostridial glucosylating toxins. These toxins glucosylate small GTPases of Rho and Ras families, inhibiting the signalling and regulatory functions of these switch proteins. After receptor-binding, the toxins are endocytosed to reach acidic endosomal compartments from where the toxins are translocated into the cytosol []. TcdB has been shown to consist of a N-terminal glucosyltransferase domain (GTD), responsible for the biological effects of the toxin, a cysteine protease domain (CPD), responsible for autocatalytic cleavage, a hydrophobic region (HR), which has been suggested to be involved in toxin translocation, and a C-terminal repetitive domain involved in receptor binding. The pore-forming region of toxin B has been described to be in a region in the middle of the protein, within amino acid residues 830 and 990 [].This entry represents a short helical bundle domain found associated with the catalytic domain of TcdA and TcdB []. It is also found in some other toxins. The function of this domain is unknown, but it may be involved in substrate recognition.
Toxins A (TcdA) and B (TcdB) of Clostridium difficile belong to the family of clostridial glucosylating toxins. These toxins glucosylate small GTPases of Rho and Ras families, inhibiting the signalling and regulatory functions of these switch proteins. After receptor-binding, the toxins are endocytosed to reach acidic endosomal compartments from where the toxins are translocated into the cytosol []. TcdB has been shown to consist of a N-terminal glucosyltransferase domain (GTD), responsible for the biological effects of the toxin, a cysteine protease domain (CPD), responsible for autocatalytic cleavage, a hydrophobic region (HR), which has been suggested to be involved in toxin translocation, and a C-terminal repetitive domain involved in receptor binding. The pore-forming region of toxin B has been described to be in a region in the middle of the protein, within amino acid residues 830 and 990 [].This entry represents the N-terminal glucosyltransferase domain from TcdA and TcdB. It is also found in other toxins. The GTD of TcdB has been shown to glycosylate the host's RhoA protein [].
This entry represents the SH2 domain of VAV1 from vertebrates.VAV1 (also known as proto-oncogene vav) is expressed predominantly in the hematopoietic system and it plays an important role in the development and activation of B and T cells [, , ]. It is activated by tyrosine phosphorylation to function as a guanine nucleotide exchange factor (GEF) for Rho GTPases following cell surface receptor activation, triggering various effects such as cytoskeletal reorganization, transcription regulation, cell cycle progression, and calcium mobilization [, ]. It also serves as a scaffold protein and has been shown to interact with Ku70, Socs1, Janus kinase 2, SIAH2, S100B, Abl gene, ZAP-70, SLP76, and Syk, among others []. The VAV protein family members are multiple domain proteins, including Vav from flies and VAV1/2/3 from mammals. VAV1 predominates in hematopoietic cells, whereas VAV2 and VAV3 are more broadly expressed. They have a calponin homology (CH) domain, an acidic domain (AC), a Dbl homology (DH) domain, a pleckstrin homology (PH) domain, a cysteine-rich (CR) domain containing a zinc finger, and a complex region with SH2 and SH3 domains. Therefore they may participate in the activity of several pathways [, ]. They are signal transducer proteins that couple tyrosine kinase signals with the activation of the Rho/Rac GTPases, [, , ].
STAT3 is a member of the STAT protein family. STAT3 mediates the expression of a variety of genes in response to cell stimuli, and plays a key role in many cellular processes such as cell growth and apoptosis. STAT3 has been shown to interact with Rho GTPases []Three alternatively spliced transcript variants encoding distinct isoforms have been described. STAT3 activation is required for self-renewal of embryonic stem cells (ESCs) []and is essential for the differentiation of the TH17 helper T cells []. Mutations in the STAT3 gene result in hyperimmunoglobulin E syndrome and human cancers []. This entry represents the SH2 domain of STAT3.STAT proteins have a dual function: signal transduction and activation of transcription. When cytokines are bound to cell surface receptors, the associated Janus kinases (JAKs) are activated, leading to tyrosine phosphorylation of the given STAT proteins []. Phosphorylated STATs form dimers, translocate to the nucleus, and bind specific response elements to activate transcription of target genes []. STAT proteins contain an N-terminal domain (NTD), a coiled-coil domain (CCD), a DNA-binding domain (DBD), an α-helical linker domain (LD), an SH2 domain, and a transactivation domain (TAD). The SH2 domain is necessary for receptor association and tyrosine phosphodimer formation. There are seven mammalian STAT family members which have been identified: STAT1, STAT2, STAT3, STAT4, STAT5 (STAT5A and STAT5B), and STAT6 [].
The type III secretion system of Gram-negative bacteria is used to transport virulence factors from the pathogen directly into the host cell []and is only triggered when the bacterium comes into close contact with the host. Effector proteins secreted by the type III system do not possess a secretion signal, and are considered unique because of this. Yersinia spp. secrete an effector protein called YopE through the type III needle []. This acts as a Rho GTPase-activating protein that disrupts the host cell actin cytoskeleton, and is regulated by a chaperone protein called SycE/YerA []. In the absence of the SycE chaperone, YopE is not transported through the needle and remains in the bacterial cytoplasm, so suggesting a crucial role for this moiety []. Both the YopE regulator and SycE/YerA proteins share similarity with the exoenzyme S (ExoS) gene product of Pseudomonas aeruginosa []. ExoS has both ADP-ribosylating and GTPase activity, and is implicated as a virulence factor. As type III secretion in Pseudomonas is often associated with systemic and even fatal infections in susceptible patients [], the proteins involved are of interest as vaccine and drug targets.
Formin homology (FH) proteins play a crucial role in the reorganisation of the actin cytoskeleton, which mediates various functions of the cell cortex including motility, adhesion, and cytokinesis []. Formins are multidomain proteins that interact with diverse signalling molecules and cytoskeletal proteins, although some formins have been assigned functions within the nucleus. Formins are characterised by the presence of three FH domains (FH1, FH2 and FH3), although members of the formin family do not necessarily contain all three domains []. The proline-rich FH1 domain mediates interactions with a variety of proteins, including the actin-binding protein profilin, SH3 (Src homology 3) domain proteins, and WW domain proteins. The FH2 domain () is required to inhibit actin polymerisation. The FH3 domain is less well conserved and is required for directing formins to the correct intracellular location, such the mitotic spindle [], or the projection tip during conjugation []. In addition, some formins can contain a GTPase-binding domain (GBD) () required for binding to Rho small GTPases, and a C-terminal conserved Dia-autoregulatory domain (DAD).This entry represents the FH3 domain.
This entry represents a group of plant CRIB domain-containing proteins including RIC2 and RIC4 from Arabidopsis. They belong to the RIC (ROP-interactive CRIB motif-containing protein) family. It has been shown that overexpression of RIC2 in tobacco germinating pollen reduces pollen tube elongation [].ROP1 and ROP6 have been shown to interact with RIC4, which promotes F-actin assembly. Together, they are involved in various processes of F-actin dynamics, cell growth, and plant/microbe interactions [].The RIC (ROP-interactive CRIB motif-containing protein) family members act as Rho GTPase (Rop) targets that function in distinct Rop signaling pathways []. RICs interact with multiple ROP GTPases via their conserved CRIB motif, and link ROP proteins to diverse target molecules that bind to their variable domains []. RICs share several consensus amino acid residues upstream of the CRIB motif and a consensus PSWMXDFK block downstream of the CRIB motif. Unlike other group members, members of group V, consisting of RIC4 and RIC2, lack the PSWMXDFK block and contain a relatively long N terminus in front of the CRIB motif and a short C terminus [].
Protein phosphatase 1(PP-1) is a major protein serine/threonine phosphatase that regulates a vast array of cellular processes. PP-1 action is controlled through regulatory subunits that not only dictate substrate specificity and subcellular localisation, but often regulate PP-1 activity []. The myosin phosphatase targeting protein (MYPT) family consists of regulatory subunits MYPT1, MYPT2, MBS85, MYPT3 and TIMAP. MYPT family members share several conserved domains, including an RVxF motif for PP1c binding, and several ankyrin repeats that mediate protein-protein interactions [].This entry consists of protein phosphatase 1 regulatory subunits 16A (MYPT3) and 16B (TIMAP). MYPT3 and TIMAP contain a C-terminal CaaX box (a prenylation motif where 'a' indicates an aliphatic amino acid: CLLM in MYPT3 and CRIS in TIMAP), similar to that identified in the Rho family of small GTPases, which targets the proteins to the cell membrane []. MYPT3 binding to PP1c inhibits its catalytic activity towards LC20, contrary to other MYPT family members []. TIMAP (TGF-beta-inhibited membrane-associated protein) is primarily localised to the plasma membrane of endothelial cells [, ]. TIMAP-PP1c substrates identified include the non-integrin laminin receptor 1 (LAMR1), which is involved in regulation of cell motility and angiogenesis [], and ERM (ezrin-radixin-moesin) proteins, which crosslink actin filaments with plasma membranes [].
Formin homology (FH) proteins play a crucial role in the reorganisation of the actin cytoskeleton, which mediates various functions of the cell cortex including motility, adhesion, and cytokinesis []. Formins are multidomain proteins that interact with diverse signalling molecules and cytoskeletal proteins, although some formins have been assigned functions within the nucleus. Formins are characterised by the presence of three FH domains (FH1, FH2 and FH3), although members of the formin family do not necessarily contain all three domains []. The proline-rich FH1 domain mediates interactions with a variety of proteins, including the actin-binding protein profilin, SH3 (Src homology 3) domain proteins, and WW domain proteins. The FH2 domain is required for the self-association of formin proteins through the ability of FH2 domains to directly bind each other [], and may also act to inhibit actin polymerisation []. The FH3 domain () is less well conserved and may be important for determining intracellular localisation of formin family proteins. In addition, some formins can contain a GTPase-binding domain (GBD) () required for binding to Rho small GTPases, and a C-terminal conserved Dia-autoregulatory domain (DAD).This superfamily represents the FH2 domain, which was shown by X-ray crystallography to have an elongated, crescent shape containing three helical subdomains [].
In plants, the small GTP-binding proteins called Rops work as signalling switches that control growth, development and plant responses to various environmental stimuli. Rop proteins (Rho of plants, Rac-like and atRac in Arabidopsis thaliana belong to the Rho family of Ras-related GTP-binding proteins that turn on signalling pathways by switching from a GDP-bound inactive to a GTP-bound active conformation. Activation depends on guanine nucleotide exchange factors (GEFs) that catalyse the otherwise slow GDP dissociation for subsequent GTP binding. The plant-specific RopGEFs represent a unique family of exchange factor that display no homology to any known RhoGEFs from animals and fungi. They comprise a highly conserved catalytic domain termed PRONE (plant-specific Rop nucleotide exchanger) with exclusive substrate specificity for members of the Rop family. The PRONE domain has been shown to be necessary and sufficient to promote nucleotide release from Rop [, , ].The PRONE domain can be divided into three highly conserved subdomains separated by two short stretches of variable amino acid residues [, ]. It is approximately 370 residues in length and displays an almost all α-helical structure except for a β-turn that protrudes from the main body of the molecule. The overall structure of the PRONE domain can be divided into two subdomains, the first one including helices alpha1-5 and alpha13, the second alpha6-12 [, ].
This superfamily represents a structural domain which consists of three α-helices, including the arfaptin homology (AH) domain and the BAR (Bin-Amphiphysin-Rvs) domain.The arfaptin homology (AH) domain is a protein domain found in a range of proteins, including arfaptins, protein kinase C-binding protein PICK1 []and mammalian 69kDa islet cell autoantigen (ICA69) []. The AH domain of arfaptin has been shown to dimerise and to bind Arf and Rho family GTPases [, ], including ARF1, a small GTPase involved in vesicle budding at the Golgi complex and immature secretory granules. The AH domain consists of three α-helices arranged as an extended antiparallel α-helical bundle. Two arfaptin AH domains associate to form a highly elongated, crescent-shaped dimer [, ].Members of the Amphiphysin protein family are key regulators in the early steps of endocytosis, involved in the formation of clathrin-coated vesicles by promoting the assembly of a protein complex at the plasma membrane and directly assist in the induction of the high curvature of the membrane at the neck of the vesicle. Amphiphysins contain a characteristic domain, known as the BAR (Bin-Amphiphysin-Rvs) domain, which is required for their in vivofunction and their ability to tubulate membranes []. The crystal structure of these proteins suggest the domain forms a crescent-shaped dimer of a three-helix coiled coil with a characteristic set of conserved hydrophobic, aromatic and hydrophilic amino acids. Proteins containing this domain have been shown to homodimerise, heterodimerise or, in a few cases, interact with small GTPases.
This entry represents engulfment and cell motility protein 2 (ELMO2) from vertebrates. ELMO2 is a scaffolding component of the Elmo-DOCK complex. Elmo2 and DOCK1 are essential for the rapid recruitment and spreading of E-cadherin, actin reorganisation, localised Rac and Rho GTPase activities, and the development of strong cell-cell adhesion []. ELMO2 interacts with Axl, a receptor tyrosine kinase, and this interaction contributes to cancer cell invasion and proliferation [].ELMO 1-3 are orthologues of the Caenorhabditis elegans ced-12, which is required for the engulfment of dying cells and cell migration []. They are cytoplasmic adaptor proteins that interact with DOCK family guanine nucleotide exchange factors (GEFs) to promote activation of the small GTPase Rac []. ELMO proteins interact with the SH3-domain of DOCKs via an SH3-binding site to enhance the GEF activity of DOCKs. Regulatory GTPases in the Ras superfamily employ a cycle of alternating GTP binding and hydrolysis, controlled by GEFs and GTPase-activating proteins (GAPs), as essential features of their actions in cells [, ].
Formin homology (FH) proteins play a crucial role in the reorganisation of the actin cytoskeleton, which mediates various functions of thecell cortex including motility, adhesion, and cytokinesis []. Formins are multidomain proteins that interact with diverse signalling molecules and cytoskeletal proteins, although some formins have been assigned functions within the nucleus. Formins are characterised by the presence of three FH domains (FH1, FH2 and FH3), although members of the formin family do not necessarily contain all three domains []. The proline-rich FH1 domain mediates interactions with a variety of proteins, including the actin-binding protein profilin, SH3 (Src homology 3) domain proteins, and WW domain proteins. The FH2 domain is required for the self-association of formin proteins through the ability of FH2 domains to directly bind each other [], and may also act to inhibit actin polymerisation []. The FH3 domain () is less well conserved and may be important for determining intracellular localisation of formin family proteins. In addition, some formins can contain a GTPase-binding domain (GBD) () required for binding to Rho small GTPases, and a C-terminal conserved Dia-autoregulatory domain (DAD).This entry represents the FH2 domain, which was shown by X-ray crystallography to have an elongated, crescent shape containing three helical subdomains [].
FCH domain is a short conserved region of around 60 amino acids first described as a region of homology between FER and CIP4 proteins []. In the CIP4 protein the FCH domain binds to microtubules []. The FCH domain is always found N-terminally and is followed by a coiled-coil region. The FCH and coiled-coil domains are structurally similar to Bin/amphiphysin/RVS (BAR) domains []. They are α-helical membrane-binding modules that function in endocytosis, regulation of the actin cytoskeleton and signalling []. Proteins containing an FCH domain can be divided in 3 classes []:A subfamily of protein kinases usually associated with an SH2 domain:Fps/fes (Fujimani poultry sarcoma/feline sarcoma) proto-oncogenes. They are non-receptor protein-tyrosine kinases preferentially expressed in myeloid lineage. The viral oncogene has an unregulated kinase activity which abrogates the need for cytokines and influences differentiation of haematopoietic progenitor cells.Fes related protein (fer). It is an ubiquitously expressed homologue of Fes.Adaptor proteins usually associated with a C-terminal SH3 domain:Schizosaccharomyces pombe CDC15 protein. It mediates cytoskeletal rearrangements required for cytokinesis. It is essential for viability.CD2 cytoplasmic domain binding protein.Mammalian Cdc42-interacting protein 4 (CIP4). It may act as a link between Cdc42 signaling and regulation of the actin cytoskeleton.Mammalian PACSIN proteins. A family of cytoplasmic phosphoproteins playing a role in vesicle formation and transport.A subfamily of Rho-GAP proteins:Mammalian RhoGAP4 proteins. They may down-regulate Rho-like GTPases in hematopoietic cells.Yeast RHO GTPase-activating protein RGD1 (also known as YBR260C).Caenorhabditis elegans hypothetical protein ZK669.1.
Formins (formin homology proteins) proteins play a crucial role in the reorganisation of the actin cytoskeleton and associate with the fast-growing end (barbed end) of actin filaments [, ]. This entry represents the formin homologues from animals (and some fungi), including protein cappuccino from Drosophila melanogaster and formins from human and mouse. Protein cappuccino acts as an actin nucleation factor and promotes assembly of actin filaments together with spir. It may play a role in intracellular vesicle transport along actin fibres, providing a novel link between actin cytoskeleton dynamics and intracellular transport []. Formins are characterised by the presence of three FH domains (FH1, FH2 and FH3), although members of the formin family do not necessarily contain all three domains []. The proline-rich FH1 domain mediates interactions with a variety of proteins, including the actin-binding protein profilin, SH3 (Src homology 3) domain proteins, and WW domain proteins. The FH2 domain is required for the self-association of formin proteins through the ability of FH2 domains to directly bind each other [], and may also act to inhibit actin polymerisation []. The FH3 domain () is less well conserved and may be important for determining intracellular localisation of formin family proteins. In addition, some formins can contain a GTPase-binding domain (GBD) () required for binding to Rho small GTPases, and a C-terminal conserved Dia-autoregulatory domain (DAD).
Secretion of virulence factors in Gram-negative bacteria involves transportation of the protein across two membranes to reach the cell exterior. There have been four secretion systems described in animal enteropathogens, such as Salmonella and Yersinia, with further sequence similarities in plant pathogens like Ralstonia and Erwinia [].The type III secretion system is of great interest, as it is used to transport virulence factors from the pathogen directly into the host cell and is only triggered when the bacterium comes into close contact with the host. The protein subunits of the system are very similar to those of bacterial flagellar biosynthesis. However, while the latter forms a ring structure to allow secretion of flagellin and is an integral part of the flagellum itself [], type III subunits in the outer membrane translocate secreted proteins through a channel-like structure.Exotoxins secreted by the type III system do not possess a secretion signal, and are considered unique for this reason []. Yersinia secrete a Rho GTPase-activating protein, YopE [, ], that disrupts the host cell actin cytoskeleton. YopE is regulated by another bacterial gene, SycE [], that enables the exotoxin to remain soluble in the bacterial cytoplasm. A similar protein, exoenzyme S (ExoS) from Pseudomonas aeruginosa, has both ADP-ribosylation and GTPase activity [, ].This entry represents the bacterial GAP (GTPase-activating protein) domain found in YopE, ExoS, and also SptP (Secreted effector protein) [].
This entry represent the first SH3 domain of Nck1. The first SH3 domain of Nck binds the PxxDY sequence in the CD3e cytoplasmic tail; this binding inhibits phosphorylation by Src kinases, resulting in the downregulation of TCR surface expression [].Nck1 (also called Nck-alpha) plays a crucial role in connecting signaling pathways of tyrosine kinase receptors and important effectors in actin dynamics and cytoskeletal remodeling []. It binds and activates RasGAP, resulting in the downregulation of Ras []. It is also involved in the signaling of endothilin-mediated inhibition of cell migration [].Cytoplasmic proteins Nck are non-enzymatic adaptor proteins composed of three SH3 (Src homology 3) domains and a C-terminal SH2 domain []. They regulate actin cytoskeleton dynamics by linking proline-rich effector molecules to protein tyrosine kinases and phosphorylated signaling intermediates []. They function downstream of the PDGFbeta receptor and are involved in Rho GTPase signaling and actin dynamics []. They associate with tyrosine-phosphorylated growth factor receptors or their cellular substrates [, ]. There are two vertebrate Nck proteins, Nck1 and Nck2.
VAV1 (also known as proto-oncogene vav) is expressed predominantly in the hematopoietic system and it plays an important role in the development and activation of B and T cells [, , ]. It is activated by tyrosine phosphorylation to function as a guanine nucleotide exchange factor (GEF) for Rho GTPases following cell surface receptor activation, triggering various effects such as cytoskeletal reorganization, transcription regulation, cell cycle progression, and calcium mobilization [, ]. It also serves as a scaffold protein and has been shown to interact with Ku70, Socs1, Janus kinase 2, SIAH2, S100B, Abl gene, ZAP-70, SLP76, and Syk, among others []. The VAV protein family members are multiple domain proteins, including Vav from flies and VAV1/2/3 from mammals. VAV1 predominates in hematopoietic cells, whereas VAV2 and VAV3 are more broadly expressed. They have a calponin homology (CH) domain, an acidic domain (AC), a Dbl homology (DH) domain, a pleckstrin homology (PH) domain, a cysteine-rich (CR) domain containing a zinc finger, and a complex region with SH2 and SH3 domains. Therefore they may participate in the activity of several pathways [, ]. They are signal transducer proteins that couple tyrosine kinase signals with the activation of the Rho/Rac GTPases, [, , ]. This entry represents the second SH3 domain of VAV1. This domain interacts with a wide variety of proteins including cytoskeletal regulators (zyxin), RNA-binding proteins (Sam68), transcriptional regulators, viral proteins, and dynamin 2 [].
FGD6 is a member ofthe FGD family. It has been found to coordinate cell polarity and endosomal membrane recycling in osteoclasts []. This entry represent the N-terminal PH domain of FGD6.FGDs have a RhoGEF (DH) domain, followed by an N-terminal PH domain, a FYVE domain and a C-terminal PH domain. All FGDs are guanine nucleotide exchange factors that activates the Rho GTPase Cdc42, an important regulator of membrane trafficking. The RhoGEF domain is responsible for GEF catalytic activity, while the N-terminal PH domain is involved in intracellular targeting of the DH domain []. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner []. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity []. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane []. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes [].
This entry represents the catalytic domain from several bacterial cytotoxic necrotizing factor proteins and the related dermonecrotic toxin (DNT) from Bordetella species. Cytotoxic necrotizing factor 1 (CNF1) is a toxin which in Escherichia coli forms a 4-layer alpha/beta/beta/alpha structure containing mixed β-sheets []. CNF1 is expressed in strains of E. coli causing uropathogenic and neonatal meningitis. It alters the host cell actin cytoskeleton and promotes bacterial invasion of the blood-brain barrier endothelial cells []. CNF1 belongs to a unique group of large cytotoxins that cause constitutive activation of Rho guanosine triphosphatases (GTPases), which are key regulators of the actin cytoskeleton [].Bordetella dermonecrotic toxin (DNT) stimulates the assembly of actin stress fibres and focal adhesions by deamidating or polyaminating Gln63 of the small GTPase Rho. DNT is an A-B toxin composed of an N-terminal receptor-binding (B) domain and a C-terminal enzymatically active (A) domain [].A similar structural motif can be found in several hypothetical proteins, including YfiH from Shigella flexneri [], YlmD from Bacillus stearothermophilus, NMB0706 from Neisseria meningitidis serogroup B and CC0490 from Caulobacter crescentus.
VAV1 (also known as proto-oncogene vav) is expressed predominantly in the hematopoietic system and it plays an important role in the development and activation of B and T cells [, , ]. It is activated by tyrosine phosphorylation to function as a guanine nucleotide exchange factor (GEF) for Rho GTPases following cell surface receptor activation, triggering various effects such as cytoskeletal reorganization, transcription regulation, cell cycle progression, and calcium mobilization [, ]. It also serves as a scaffold protein and has been shown to interact with Ku70, Socs1, Janus kinase 2, SIAH2, S100B, Abl gene, ZAP-70, SLP76, and Syk, among others []. The VAV protein family members are multiple domain proteins, including Vav from flies and VAV1/2/3 from mammals. VAV1 predominates in hematopoietic cells, whereas VAV2 and VAV3 are more broadly expressed. They have a calponin homology (CH) domain, an acidic domain (AC), a Dbl homology (DH) domain, a pleckstrin homology (PH) domain, a cysteine-rich (CR) domain containing a zinc finger, and a complex region with SH2 and SH3 domains. Therefore they may participate in the activity of several pathways [, ]. They are signal transducer proteins that couple tyrosine kinase signals with the activation of the Rho/Rac GTPases, [, , ]. This entry represents the first SH3 domain of VAV1.
The FERM domain (F for 4.1 protein, E for ezrin, R for radixin and M for moesin) is a widespread protein module involved in localising proteins to the plasma membrane []. FERM domains are found in a number of cytoskeletal-associated proteins that associate with various proteins at the interface between the plasma membrane and the cytoskeleton. The FERM domain is located at the N terminus of the majority of FERM-containing proteins [, ], which includes: Band 4.1, which links the spectrin-actin cytoskeleton of erythrocytes to the plasma membrane.Ezrin, a component of the undercoat of the microvilli plasma membrane.Moesin, which is probably involved in binding major cytoskeletal structures to the plasma membrane.Radixin, which is involved in the binding of the barbed end of actin filaments to the plasma membrane in the undercoat of the cell- to-cell adherens junction.Talin, a cytoskeletal protein concentrated in regions of cell-substratum contact and, in lymphocytes, of cell-cell contacts.Filopodin, a slime mold protein that binds actin and which is involved in the control of cell motility and chemotaxis.Merlin (or schwannomin).Protein NBL4.Unconventional myosins X, VIIa and XV, which are mutated in congenital deafness.Focal-adhesion kinases (FAKs), cytoplasmic protein tyrosine kinases involved in signalling through integrins.Janus tyrosine kinases (JAKs), cytoplasmic tyrosine kinases that are non-covalently associated with the cytoplasmic tails of receptors for cytokines or polypeptidic hormones.Non-receptor tyrosine-protein kinase TYK2.Protein-tyrosine phosphatases PTPN3 and PTPN4, enzyme that appear to act at junctions between the membrane and the cytoskeleton.Protein-tyrosine phosphatases PTPN14 and PTP-D1, PTP-RL10 and PTP2E.Caenorhabditis elegans protein phosphatase ptp-1.Ezrin, moesin, and radixin are highly related proteins (ERM protein family), but the other proteins in which the FERM domain is found do not share any region of similarity outside of this domain. ERM proteins are made of three domains, the FERM domain, a central helical domain and a C-terminal tail domain, which binds F-actin. The amino-acid sequence of the FERM domain is highly conserved among ERM proteins and is responsible for membrane association by direct binding to the cytoplasmic domain or tail of integral membrane proteins. ERM proteins are regulated by an intramolecular association of the FERM and C-terminal tail domains that masks their binding sites for other molecules. For cytoskeleton-membrane cross-linking, the dormant molecules becomes activated and the FERM domain attaches to the membrane by binding specific membrane proteins, while the last 34 residues of the tail bind actin filaments. Aside from binding to membranes, the activated FERM domain of ERM proteins can also bind the guanine nucleotide dissociation inhibitor of Rho GTPase (RhoDGI), which suggests that in addition to functioning as a cross-linker, ERM proteins may influence Rho signalling pathways. The crystal structure of the FERM domain reveals that it is composed of three structural modules (F1, F2, and F3) that together form a compact clover-shaped structure [].The FERM domain has also been called the amino-terminal domain, the 30kDa domain, 4.1N30, the membrane-cytoskeletal-linking domain, the ERM-like domain, the ezrin-like domain of the band 4.1 superfamily, the conserved N-terminal region, and the membrane attachment domain [].This domain is the N-terminal ubiquitin-like structural domain of the FERM domain.
The FERM domain (F for 4.1 protein, E for ezrin, R for radixin and M for moesin) is a widespread protein module involved in localising proteins to the plasma membrane []. FERM domains are found in a number of cytoskeletal-associated proteins that associate with various proteins at the interface between the plasma membrane and the cytoskeleton. The FERM domain is located at the N terminus of the majority of FERM-containing proteins [, ], which includes: Band 4.1, which links the spectrin-actin cytoskeleton of erythrocytes to the plasma membrane.Ezrin, a component of the undercoat of the microvilli plasma membrane.Moesin, which is probably involved in binding major cytoskeletal structures to the plasma membrane.Radixin, which is involved in the binding of the barbed end of actin filaments to the plasma membrane in the undercoat of the cell- to-cell adherens junction.Talin, a cytoskeletal protein concentrated in regions of cell-substratum contact and, in lymphocytes, of cell-cell contacts.Filopodin, a slime mold protein that binds actin and which is involved in the control of cell motility and chemotaxis.Merlin (or schwannomin).Protein NBL4.Unconventional myosins X, VIIa and XV, which are mutated in congenital deafness.Focal-adhesion kinases (FAKs), cytoplasmic protein tyrosine kinases involved in signalling through integrins.Janus tyrosine kinases (JAKs), cytoplasmic tyrosine kinases that are non-covalently associated with the cytoplasmic tails of receptors for cytokines or polypeptidic hormones.Non-receptor tyrosine-protein kinase TYK2.Protein-tyrosine phosphatases PTPN3 and PTPN4, enzyme that appear to act at junctions between the membrane and the cytoskeleton.Protein-tyrosine phosphatases PTPN14 and PTP-D1, PTP-RL10 and PTP2E.Caenorhabditis elegans protein phosphatase ptp-1.Ezrin, moesin, and radixin are highly related proteins (ERM protein family), but the other proteins in which the FERM domain is found do not share any region of similarity outside of this domain. ERM proteins are made of three domains, the FERM domain, a central helical domain and a C-terminal tail domain, which binds F-actin. The amino-acid sequence of the FERM domain is highly conserved among ERM proteins and is responsible for membrane association by direct binding to the cytoplasmic domain or tail of integral membrane proteins. ERM proteins are regulated by an intramolecular association of the FERM and C-terminal tail domains that masks their binding sites for other molecules. For cytoskeleton-membrane cross-linking, the dormant molecules becomes activated and the FERM domain attaches to the membrane by binding specific membrane proteins, while the last 34 residues of the tail bind actin filaments. Aside from binding to membranes, the activated FERM domain of ERM proteins can also bind the guanine nucleotide dissociation inhibitor of Rho GTPase (RhoDGI), which suggests that in addition to functioning as a cross-linker, ERM proteins may influence Rho signalling pathways. The crystal structure of the FERM domain reveals that it is composed of three structural modules (F1, F2, and F3) that together form a compact clover-shaped structure [].The FERM domain has also been called the amino-terminal domain, the 30kDa domain, 4.1N30, the membrane-cytoskeletal-linking domain, the ERM-like domain, the ezrin-like domain of the band 4.1 superfamily, the conserved N-terminal region, and the membrane attachment domain [].This entry represents the PH-like domain found at the C terminus of the FERM domain.
The FERM domain (F for 4.1 protein, E for ezrin, R for radixin and M for moesin) is a widespread protein module involved in localising proteins to the plasma membrane []. FERM domains are found in a number of cytoskeletal-associated proteins that associate with various proteins at the interface between the plasma membrane and the cytoskeleton. The FERM domain is located at the N terminus of the majority of FERM-containing proteins [, ], which includes: Band 4.1, which links the spectrin-actin cytoskeleton of erythrocytes to the plasma membrane.Ezrin, a component of the undercoat of the microvilli plasma membrane.Moesin, which is probably involved in binding major cytoskeletal structures to the plasma membrane.Radixin, which is involved in the binding of the barbed end of actin filaments to the plasma membrane in the undercoat of the cell- to-cell adherens junction.Talin, a cytoskeletal protein concentrated in regions of cell-substratum contact and, in lymphocytes, of cell-cell contacts.Filopodin, a slime mold protein that binds actin and which is involved in the control of cell motility and chemotaxis.Merlin (or schwannomin).Protein NBL4.Unconventional myosins X, VIIa and XV, which are mutated in congenital deafness.Focal-adhesion kinases (FAKs), cytoplasmic protein tyrosine kinases involved in signalling through integrins.Janus tyrosine kinases (JAKs), cytoplasmic tyrosine kinases that are non-covalently associated with the cytoplasmic tails of receptors for cytokines or polypeptidic hormones.Non-receptor tyrosine-protein kinase TYK2.Protein-tyrosine phosphatases PTPN3 and PTPN4, enzyme that appear to act at junctions between the membrane and the cytoskeleton.Protein-tyrosine phosphatases PTPN14 and PTP-D1, PTP-RL10 and PTP2E.Caenorhabditis elegans protein phosphatase ptp-1.Ezrin, moesin, and radixin are highly related proteins (ERM protein family), but the other proteins in which the FERM domain is found do not share any region of similarity outside of this domain. ERM proteins are made of three domains, the FERM domain, a central helical domain and a C-terminal tail domain, which binds F-actin. The amino-acid sequence of the FERM domain is highly conserved among ERM proteins and is responsible for membrane association by direct binding to the cytoplasmic domain or tail of integral membrane proteins. ERM proteins are regulated by an intramolecular association of the FERM and C-terminal tail domains that masks their binding sites for other molecules. For cytoskeleton-membrane cross-linking, the dormant molecules becomes activated and the FERM domain attaches to the membrane by binding specific membrane proteins, while the last 34 residues of the tail bind actin filaments. Aside from binding to membranes, the activated FERM domain of ERM proteins can also bind the guanine nucleotide dissociation inhibitor of Rho GTPase (RhoDGI), which suggests that in addition to functioning as a cross-linker, ERM proteins may influence Rho signalling pathways. The crystal structure of the FERM domain reveals that it is composed of three structural modules (F1, F2, and F3) that together form a compact clover-shaped structure [].The FERM domain has also been called the amino-terminal domain, the 30kDa domain, 4.1N30, the membrane-cytoskeletal-linking domain, the ERM-like domain, the ezrin-like domain of the band 4.1 superfamily, the conserved N-terminal region, and the membrane attachment domain [].
The FERM domain (F for 4.1 protein, E for ezrin, R for radixin and M for moesin) is a widespread protein module involved in localising proteins to the plasma membrane []. FERM domains are found in a number of cytoskeletal-associated proteins that associate with various proteins at the interface between the plasma membrane and the cytoskeleton. The FERM domain is located at the N terminus of the majority of FERM-containing proteins [, ], which includes: Band 4.1, which links the spectrin-actin cytoskeleton of erythrocytes to the plasma membrane.Ezrin, a component of the undercoat of the microvilli plasma membrane.Moesin, which is probably involved in binding major cytoskeletal structures to the plasma membrane.Radixin, which is involved in the binding of the barbed end of actin filaments to the plasma membrane in the undercoat of the cell- to-cell adherens junction.Talin, a cytoskeletal protein concentrated in regions of cell-substratum contact and, in lymphocytes, of cell-cell contacts.Filopodin, a slime mold protein that binds actin and which is involved in the control of cell motility and chemotaxis.Merlin (or schwannomin).Protein NBL4.Unconventional myosins X, VIIa and XV, which are mutated in congenital deafness.Focal-adhesion kinases (FAKs), cytoplasmic protein tyrosine kinases involved in signalling through integrins.Janus tyrosine kinases (JAKs), cytoplasmic tyrosine kinases that are non-covalently associated with the cytoplasmic tails of receptors for cytokines or polypeptidic hormones.Non-receptor tyrosine-protein kinase TYK2.Protein-tyrosine phosphatases PTPN3 and PTPN4, enzyme that appear to act at junctions between the membrane and the cytoskeleton.Protein-tyrosine phosphatases PTPN14 and PTP-D1, PTP-RL10 and PTP2E.Caenorhabditis elegans protein phosphatase ptp-1.Ezrin, moesin, and radixin are highly related proteins (ERM protein family), but the other proteins in which the FERM domain is found do not share any region of similarity outside of this domain. ERM proteins are made of three domains, the FERM domain, a central helical domain and a C-terminal tail domain, which binds F-actin. The amino-acid sequence of the FERM domain is highly conserved among ERM proteins and is responsible for membrane association by direct binding to the cytoplasmic domain or tail of integral membrane proteins. ERM proteins are regulated by an intramolecular association of the FERM and C-terminal tail domains that masks their binding sites for other molecules. For cytoskeleton-membrane cross-linking, the dormant molecules becomes activated and the FERM domain attaches to the membrane by binding specific membrane proteins, while the last 34 residues of the tail bind actin filaments. Aside from binding to membranes, the activated FERM domain of ERM proteins can also bind the guanine nucleotide dissociation inhibitor of Rho GTPase (RhoDGI), which suggests that in addition to functioning as a cross-linker, ERM proteins may influence Rho signalling pathways. The crystal structure of the FERM domain reveals that it is composed of three structural modules (F1, F2, and F3) that together form a compact clover-shaped structure [].The FERM domain has also been called the amino-terminal domain, the 30kDa domain, 4.1N30, the membrane-cytoskeletal-linking domain, the ERM-like domain, the ezrin-like domain of the band 4.1 superfamily, the conserved N-terminal region, and the membrane attachment domain [].
The FERM domain (F for 4.1 protein, E for ezrin, R for radixin and M for moesin) is a widespread protein module involved in localising proteins to the plasma membrane []. FERM domains are found in a number of cytoskeletal-associated proteins that associate with various proteins at the interface between the plasma membrane and the cytoskeleton. The FERM domain is located at the N terminus of the majority of FERM-containing proteins [, ], which includes: Band 4.1, which links the spectrin-actin cytoskeleton of erythrocytes to the plasma membrane.Ezrin, a component of the undercoat of the microvilli plasma membrane.Moesin, which is probably involved in binding major cytoskeletal structures to the plasma membrane.Radixin, which is involved in the binding of the barbed end of actin filaments to the plasma membrane in the undercoat of the cell- to-cell adherens junction.Talin, a cytoskeletal protein concentrated in regions of cell-substratum contact and, in lymphocytes, of cell-cell contacts.Filopodin, a slime mold protein that binds actin and which is involved in the control of cell motility and chemotaxis.Merlin (or schwannomin).Protein NBL4.Unconventional myosins X, VIIa and XV, which are mutated in congenital deafness.Focal-adhesion kinases (FAKs), cytoplasmic protein tyrosine kinases involved in signalling through integrins.Janus tyrosine kinases (JAKs), cytoplasmic tyrosine kinases that are non-covalently associated with the cytoplasmic tails of receptors for cytokines or polypeptidic hormones.Non-receptor tyrosine-protein kinase TYK2.Protein-tyrosine phosphatases PTPN3 and PTPN4, enzyme that appear to act at junctions between the membrane and the cytoskeleton.Protein-tyrosine phosphatases PTPN14 and PTP-D1, PTP-RL10 and PTP2E.Caenorhabditis elegans protein phosphatase ptp-1.Ezrin, moesin, and radixin are highly related proteins (ERM protein family), but the other proteins in which the FERM domain is found do not share any region of similarity outside of this domain. ERM proteins are made of three domains, the FERM domain, a central helical domain and a C-terminal tail domain, which binds F-actin. The amino-acid sequence of the FERM domain is highly conserved among ERM proteins and is responsible for membrane association by direct binding to the cytoplasmic domain or tail of integral membrane proteins. ERM proteins are regulated by an intramolecular association of the FERM and C-terminal tail domains that masks their binding sites for other molecules. For cytoskeleton-membrane cross-linking, the dormant molecules becomes activated and the FERM domain attaches to the membrane by binding specific membrane proteins, while the last 34 residues of the tail bind actin filaments. Aside from binding to membranes, the activated FERM domain of ERM proteins can also bind the guanine nucleotide dissociation inhibitor of Rho GTPase (RhoDGI), which suggests that in addition to functioning as a cross-linker, ERM proteins may influence Rho signalling pathways. The crystal structure of the FERM domain reveals that it is composed of three structural modules (F1, F2, and F3) that together form a compact clover-shaped structure [].The FERM domain has also been called the amino-terminal domain, the 30kDa domain, 4.1N30, the membrane-cytoskeletal-linking domain, the ERM-like domain, the ezrin-like domain of the band 4.1 superfamily, the conserved N-terminal region, and the membrane attachment domain [].
The FERM domain (F for 4.1 protein, E for ezrin, R for radixin and M for moesin) is a widespread protein module involved in localising proteins to the plasma membrane []. FERM domains are found in a number of cytoskeletal-associated proteins that associate with various proteins at the interface between the plasma membrane and the cytoskeleton. The FERM domain is located at the N terminus of the majority of FERM-containing proteins [, ], which includes: Band 4.1, which links the spectrin-actin cytoskeleton of erythrocytes to the plasma membrane.Ezrin, a component of the undercoat of the microvilli plasma membrane.Moesin, which is probably involved in binding major cytoskeletal structures to the plasma membrane.Radixin, which is involved in the binding of the barbed end of actin filaments to the plasma membrane in the undercoat of the cell- to-cell adherens junction.Talin, a cytoskeletal protein concentrated in regions of cell-substratum contact and, in lymphocytes, of cell-cell contacts.Filopodin, a slime mold protein that binds actin and which is involved in the control of cell motility and chemotaxis.Merlin (or schwannomin).Protein NBL4.Unconventional myosins X, VIIa and XV, which are mutated in congenital deafness.Focal-adhesion kinases (FAKs), cytoplasmic protein tyrosine kinases involved in signalling through integrins.Janus tyrosine kinases (JAKs), cytoplasmic tyrosine kinases that are non-covalently associated with the cytoplasmic tails of receptorsfor cytokines or polypeptidic hormones.Non-receptor tyrosine-protein kinase TYK2.Protein-tyrosine phosphatases PTPN3 and PTPN4, enzyme that appear to act at junctions between the membrane and the cytoskeleton.Protein-tyrosine phosphatases PTPN14 and PTP-D1, PTP-RL10 and PTP2E.Caenorhabditis elegans protein phosphatase ptp-1.Ezrin, moesin, and radixin are highly related proteins (ERM protein family), but the other proteins in which the FERM domain is found do not share any region of similarity outside of this domain. ERM proteins are made of three domains, the FERM domain, a central helical domain and a C-terminal tail domain, which binds F-actin. The amino-acid sequence of the FERM domain is highly conserved among ERM proteins and is responsible for membrane association by direct binding to the cytoplasmic domain or tail of integral membrane proteins. ERM proteins are regulated by an intramolecular association of the FERM and C-terminal tail domains that masks their binding sites for other molecules. For cytoskeleton-membrane cross-linking, the dormant molecules becomes activated and the FERM domain attaches to the membrane by binding specific membrane proteins, while the last 34 residues of the tail bind actin filaments. Aside from binding to membranes, the activated FERM domain of ERM proteins can also bind the guanine nucleotide dissociation inhibitor of Rho GTPase (RhoDGI), which suggests that in addition to functioning as a cross-linker, ERM proteins may influence Rho signalling pathways. The crystal structure of the FERM domain reveals that it is composed of three structural modules (F1, F2, and F3) that together form a compact clover-shaped structure [].The FERM domain has also been called the amino-terminal domain, the 30kDa domain, 4.1N30, the membrane-cytoskeletal-linking domain, the ERM-like domain, the ezrin-like domain of the band 4.1 superfamily, the conserved N-terminal region, and the membrane attachment domain [].This entry represents the conserved sites of the FERM domain.
The FERM domain (F for 4.1 protein, E for ezrin, R for radixin and M for moesin) is a widespread protein module involved in localising proteins to the plasma membrane []. FERM domains are found in a number of cytoskeletal-associated proteins that associate with various proteins at the interface between the plasma membrane and the cytoskeleton. The FERM domain is located at the N terminus of the majority of FERM-containing proteins [, ], which includes: Band 4.1, which links the spectrin-actin cytoskeleton of erythrocytes to the plasma membrane.Ezrin, a component of the undercoat of the microvilli plasma membrane.Moesin, which is probably involved in binding major cytoskeletal structures to the plasma membrane.Radixin, which is involved in the binding of the barbed end of actin filaments to the plasma membrane in the undercoat of the cell- to-cell adherens junction.Talin, a cytoskeletal protein concentrated in regions of cell-substratum contact and, in lymphocytes, of cell-cell contacts.Filopodin, a slime mold protein that binds actin and which is involved in the control of cell motility and chemotaxis.Merlin (or schwannomin).Protein NBL4.Unconventional myosins X, VIIa and XV, which are mutated in congenital deafness.Focal-adhesion kinases (FAKs), cytoplasmic protein tyrosine kinases involved in signalling through integrins.Janus tyrosine kinases (JAKs), cytoplasmic tyrosine kinases that are non-covalently associated with the cytoplasmic tails of receptors for cytokines or polypeptidic hormones.Non-receptor tyrosine-protein kinase TYK2.Protein-tyrosine phosphatases PTPN3 and PTPN4, enzyme that appear to act at junctions between the membrane and the cytoskeleton.Protein-tyrosine phosphatases PTPN14 and PTP-D1, PTP-RL10 and PTP2E.Caenorhabditis elegans protein phosphatase ptp-1.Ezrin, moesin, and radixin are highly related proteins (ERM protein family), but the other proteins in which the FERM domain is found do not share any region of similarity outside of this domain. ERM proteins are made of three domains, the FERM domain, a central helical domain and a C-terminal tail domain, which binds F-actin. The amino-acid sequence of the FERM domain is highly conserved among ERM proteins and is responsible for membrane association by direct binding to the cytoplasmic domain or tail of integral membrane proteins. ERM proteins are regulated by an intramolecular association of the FERM and C-terminal tail domains that masks their binding sites for other molecules. For cytoskeleton-membrane cross-linking, the dormant molecules becomes activated and the FERM domain attaches to the membrane by binding specific membrane proteins, while the last 34 residues of the tail bind actin filaments. Aside from binding to membranes, the activated FERM domain of ERM proteins can also bind the guanine nucleotide dissociation inhibitor of Rho GTPase (RhoDGI), which suggests that in addition to functioning as a cross-linker, ERM proteins may influence Rho signallingpathways. The crystal structure of the FERM domain reveals that it is composed of three structural modules (F1, F2, and F3) that together form a compact clover-shaped structure [].The FERM domain has also been called the amino-terminal domain, the 30kDa domain, 4.1N30, the membrane-cytoskeletal-linking domain, the ERM-like domain, the ezrin-like domain of the band 4.1 superfamily, the conserved N-terminal region, and the membrane attachment domain [].
Proteins containing this domain include FARP1, FARP2 and FRMD7. FARP1 and FARP2 are members of the Dbl family guanine nucleotide exchange factors (GEFs) which are upstream positive regulators of Rho GTPases []. FARP1 has increased expression in differentiated chondrocytes. FARP2 is thought to regulate neurite remodeling by mediating the signaling pathways from membrane proteins to Rac. It is found in brain, lung, and testis, as well as embryonic hippocampal and cortical neurons []. They are composed of a N-terminal FERM domain, a proline-rich (PR) domain, Dbl-homology (DH), and two C-terminal PH domains.FRMD7 (FERM domain-containing protein 7) and Caenorhabditis elegans CFRM3 have a FERM domain that is closely related to that in FARP1 and FARP2. Both have unknown functions. They contain an N-terminal FERM domain, a PH domain, followed by a FA (FERM adjacent) domain []. FRMD7 has been linked to Idiopathic congenital nystagmus , an infant-onset disease with the typical features of bilateral ocular oscillations, visual impairment, and abnormal head movement []. The FERM domain has a cloverleaf tripart structure composed of: (1) FERM_N (A-lobe or F1); (2) FERM_M (B-lobe, or F2); and (3) FERM_C (C-lobe or F3). The C-lobe/F3 within the FERM domain is part of the PH domain family. Like most other ERM members they have a phosphoinositide-binding site in their FERM domain. The FERM C domain is the third structural domain within the FERM domain. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM domain is also found in protein tyrosine phosphatases (PTPs) , the tyrosine kinases FAK and JAK, in addition to other proteins involved in signaling. This domain is structurally similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites [, ].
OCRL1 hydrolyzes phosphatidylinositol 4,5-bisphosphate (PtIns(4,5)P2) and the signaling molecule phosphatidylinositol 1,4,5-trisphosphate (PtIns(1,4,5)P3), and thereby modulates cellular signaling events []. OCRL1 resides on vesicular structures throughout the endosomal system and the Golgi complex, and is also present at the plasma membrane in membrane ruffles and at late-stage endocytic clathrin-coated pits. It binds clathrin, clathrin adaptors, several GTPases, and the endocytic proteins APPL1 and Ses1/2 []. Mutations in the OCRL1 gene cause Lowe Syndrome, leading to cataracts, mental retardation and renal failure []. Mutations in OCRL can also give rise to a milder pathology, Dent disease 2, which is characterised by renal Fanconi syndrome in the absence of extrarenal pathologies [].OCRL1 shares ~45% sequence identity with INPP5B (not included in this entry) and has the same domain organization. However, a loop in the Rho GAP domain contains a second clathrin box which is absent in INPP5B. INPP5B shares most interacting partners with OCRL, except for clathrin and the endocytic clathrin adaptor AP-2 []. OCRL1 contains a PH domain, a 5-phosphatase domain, an ASH domain and a Rho-GAP domain. The RhoGAP domain lacks the catalytic arginine and is catalytically inactive. However, the RhoGAP domain of OCRL interacts with Rac and Cdc42, but only the Cdc42 interaction is GTP-dependent. The RhoGAP domain also interacts with three endocytic proteins containing the F&H motif: APPL1, Ses1 and Ses2. OCRL1 interacts with Rab GTPase (Rab8) through its ASH domain []. This entry represents the PH domain of OCRL1 []. The PH domain connects to the 5-phosphatase domain, which has a Dnase I-like fold [].
Unconventional myosin-IXa (MYO9A) belongs to class IX myosin that contains an extra Rho-specific GAP (GTPase-activating protein) domain in the tail region []. In mice, MYO9A homologue, Myr7 regulates Rho by stimulating it's GTPase activity in neurons and has a role in the regulation of neuronal morphology and function []. In humans, there are two proteins in class IX, MYO9A and MYO9B. Class IX myosins may carry its own Rho-GAP tail using its motor head domain to sites that require down-regulation of Rho-dependent signalling [].Myosin constitutes a large superfamily of actin-dependent molecular motors. Myosin binds to actins and moves along actin filaments by using the energy from ATP hydrolysis. Myosin is involved in muscular contraction, cytokinesis, membrane trafficking and signal transduction [, ]. Myosins are typically composed of three functional domains:Motor head domain whose core sequence is highly conserved in all the myosin classes. This domain binds to actin and uses ATP hydrolysis to generate force to move along actin filaments. Neck domain composed of a long helix of variable length depending on the number of IQ motifs (has a consensus sequence of IQXXXRGXXXR) []. This domain acts as a linker and as a lever arm. The neck domain also serves as a binding site for moysin light chains, which are calmodulin-like proteins that have regulatory functions. Tail domain is the most diverse domain and vary in length and in sequence. Many myosin tails form coiled-coil structure that allow the molecules to dimerise and produce two-headed molecules. This domain mediates interaction with cargo molecules and/or other myosin subunits.
Protein kinase C (PKC) is a member of a family of Ser/Thr phosphotransferases that are involved in many cellular signaling pathways. Fungi have only one or two PKCs in contrast to mammals, which have at least 9 []. Saccharomyces cerevisiae contains a single PKC isozyme, Pkc1p, which contains all of the regulatory motifs found in mammalian PKCs []. In addition to its main function in maintaining cell integrity, fungi PKCs have been implicated in the regulation of diverse processes such as the organization of the actin cytoskeleton, autophagy and apoptosis, cell cycle control, cytokinesis and genetic stability [, ]. PKC has two antiparallel coiled-coiled regions (ACC finger domain) known as HR1 (PKC homology region 1/ Rho binding domain) upstream of the C2 domain and two C1 domains downstream.The C2 domain was first identified in PKC. 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. Many C2 domains, like those of PKC, are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions [, , , , ].This entry represents the C2 domain of fungal PKC-like proteins.
This globular domain is named fido after the Fic and Doc proteins where it is found. It is approximately 125 to 150 residues long, and is present in proteins from all kingdoms of life [, , , ], including:Fic (filamentation induced by cAMP) from diverse bacteria. It contains a longer insert in the fido domain.Doc (death on curing) proteins from phage P1 and several bacteria. All these proteins contain a minimal stand-alone version of the fido domain.HypE (Huntingtin associated protein E) from animal. In humans, HypE is thought to interact with Huntingtin, one of the major proteins in the Huntington's disease protein interaction network. Proteins related to HypE are also found in several bacteria and some archaea. HypE proteins contain a longer insert in their fido domain and are typically multidomain proteins.Type IV secretion system effector AnkX from Legionella.VopS, a type III secretion system effector from Vibrio that causes eukaryotic cell cytotoxicity.IbpA (virulence factor p76) from Haemophilus somnus. It includes an N-terminal haemagglutination activity domain, two fido domains and a peptidase C58 domain.BepA, an anti-apoptotic bacterial effector protein, which is a type IV secretion system substrate.The fido domain of Vibrio VopS covalently modifies Rho GTPase threonine with AMP to inhibit downstream signaling events in host cells. The AMPylation activity extends to a eukaryotic fido domain in Drosophila fic homologue CG9523. AMPylation represents a newly discovered posttranslational modification used to stably modify proteins with AMP. This signaling mechanism is predicted to be functionally similar to other posttranslation modifications such as phosphorylation, SUMOylation or acetylation, because the added moiety changes the activity of the modified protein. The covalent attachment of AMP by a phosphodiester bond is predicted to be reversible and is bulky enough to provide a docking site for a putative AMP binding domain [].The fido domain contains a central motif conserved in most sequences (H-x-F-x-[DE]-[AG]-N-[GK]-R), with the motif His contributing to fic AMPylation. The fido domain adopts an α-helical fold, arranged as a six-helix up and down bundle [, , ].
This entry represents a group of plant CRIB domain-containing proteins including RIC1-11 (exclude 2 and 4) from Arabidopsis. They belong to the RIC (ROP-interactive CRIB motif-containing protein) family. RIC1 is inactivated by active ROP2 in the lobe-forming regions of pavement cells, which suppresses MT assembly, but promotes fine F-actin assembly and thereby induces outgrowth of the region. In contrast, RIC1 is activated by active ROP6 in the neck-forming regions of pavement cells, and then promotes the assembly of MTs, which limits the expansion of the region and results in the formation of a narrow neck. RIC1 also positively regulates the auxin effect and negatively regulates the ABA effect during root growth and lateral root development [].RIC7 functions as downstream effector of active ROP2 which is involved in the prevention of excessive stomatal opening upon light stimulation []. It is also involved in pollen tube growth regulation through its interaction with ROP1 [].The RIC (ROP-interactive CRIB motif-containing protein) family members act as Rho GTPase (Rop) targets that function in distinct Rop signaling pathways []. RICs interact with multiple ROP GTPases via their conserved CRIB motif, and link ROP proteins to diverse target molecules that bind to their variable domains []. RICs share several consensus amino acid residues upstream of the CRIB motif and a consensus PSWMXDFK block downstream of the CRIB motif. Unlike other group members, members of group V, consisting of RIC4 and RIC2, lack the PSWMXDFK block and contain a relatively long N terminus in front of the CRIB motif and a short C terminus [].
Secretion of virulence factors in Gram-negative bacteria involves transportation of the protein across two membranes to reach the cell exterior. There have been four secretion systems described in animal enteropathogens, such as Salmonella and Yersinia, with further sequence similarities in plant pathogens like Ralstonia and Erwinia [].The type III secretion system is of great interest, as it is used to transport virulence factors from the pathogen directly into the host cell and is only triggered when the bacterium comes into close contact with the host. The protein subunits of the system are very similar to those of bacterial flagellar biosynthesis. However, while the latter forms a ring structure to allow secretion of flagellin and is an integral part ofthe flagellum itself [], type III subunits in the outer membrane translocate secreted proteins through a channel-like structure.Exotoxins secreted by the type III system do not possess a secretion signal, and are considered unique for this reason []. Yersinia secrete a Rho GTPase-activating protein, YopE [, ], that disrupts the host cell actin cytoskeleton. YopE is regulated by another bacterial gene, SycE [], that enables the exotoxin to remain soluble in the bacterial cytoplasm. A similar protein, exoenzyme S from Pseudomonas aeruginosa, has both ADP-ribosylation and GTPase activity [, ]. This entry also includes ADP-ribosyltransferase toxin AexT from Aeromonas salmonicida that is directly involved in the toxicity for RTG-2 (rainbow trout gonad) fish cells [].This entry also includes Exoenzyme T (ExoT) from Pseudomonas aeruginosa. ExoT contains an N-terminal GTPase-activating protein (GAP) domain and a C-terminal ADP-ribosyltransferase (ADPRT) domain. Its ADPRT domain induces atypical anoikis by transforming an innocuous cellular protein, Crk, into a cytotoxin, which interferes with integrin survival signaling. Its GAP domain activity induces mitochondrial disruption in the target host cell by activating host caspases 3 and 9 that execute cellular death [].
Myosin phosphatase-RhoA interacting protein (M-RIP) is proposed to play a role in myosin phosphatase regulation by RhoA. M-RIP contains two PH domains followed by a Rho binding domain (Rho-BD), and a C-terminal myosin binding subunit (MBS) binding domain (MBS-BD). The amino terminus of M-RIP with its adjacent PH domains and polyproline motifs mediates binding to both actin and Galpha. M-RIP brings RhoA and MBS into close proximity where M-RIP can target RhoA to the myosin phosphatase complex to regulate the myosin phosphorylation state. M-RIP does this via its C-terminal coiled-coil domain which interacts with the MBS leucine zipper domain of myosin phosphatase, while its Rho-BD, directly binds RhoA in a nucleotide-independent manner [, ].PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner []. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity []. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane []. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes [].
This globular domain is named fido after the Fic and Doc proteins where it is found. It is approximately 125 to 150 residues long, and is present in proteins from all kingdoms of life [, , , ], including:Fic (filamentation induced by cAMP) from diverse bacteria. It contains a longer insert in the fido domain.Doc (death on curing) proteins from phage P1 and several bacteria. All these proteins contain a minimal stand-alone version of the fido domain.HypE (Huntingtin associated protein E) from animal. In humans, HypE is thought to interact with Huntingtin, one of the major proteins in the Huntington's disease protein interaction network. Proteins related to HypE are also found in several bacteria and some archaea. HypE proteins contain a longer insert in their fido domain and are typically multidomain proteins.Type IV secretion system effector AnkX from Legionella.VopS, a type III secretion system effector from Vibrio that causes eukaryotic cell cytotoxicity.IbpA (virulence factor p76) from Haemophilus somnus. It includes an N-terminal haemagglutination activity domain, two fido domains and a peptidase C58 domain.BepA, an anti-apoptotic bacterial effector protein, which is a type IV secretion system substrate.The fido domain of Vibrio VopS covalently modifies Rho GTPase threonine with AMP to inhibit downstream signaling events in host cells. The AMPylation activity extends to a eukaryotic fido domain in Drosophila fic homologue CG9523. AMPylation represents a newly discovered posttranslational modification used to stably modify proteins with AMP. This signaling mechanism is predicted to be functionally similar to other posttranslation modifications such as phosphorylation, SUMOylation or acetylation, because the added moiety changes the activity of the modified protein. The covalent attachment of AMP by a phosphodiester bond is predicted to be reversible and is bulky enough to provide a docking site for a putative AMP binding domain [].The fido domain contains a central motif conserved in most sequences (H-x-F-x-[DE]-[AG]-N-[GK]-R), with the motif His contributing to fic AMPylation. The fido domain adopts an α-helical fold, arranged as a six-helix up and down bundle [, , ].
FGD4 (also known as FRABIN) is a member of the FGD family and is a small RhoGTPase Cdc42-guanine nucleotide exchange factor. It is associated with Charcot-Marie-Tooth neuropathy type 4 (CMT4), a group of progressive motor and sensory axonal and demyelinating neuropathies that are distinguished from other forms of CMT by autosomal recessive inheritance []. FGD4 has been shown to regulate Schwann cell endocytosis []. This entry represents the N-terminal PH domain of FGD4. FGDs have a RhoGEF (DH) domain, followed by an N-terminal PH domain, a FYVE domain and a C-terminal PH domain. All FGDs are guanine nucleotide exchange factors that activates the Rho GTPase Cdc42, an important regulator of membrane trafficking. The RhoGEF domain is responsible for GEF catalytic activity, while the N-terminal PH domain is involved in intracellular targeting of the DH domain []. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner []. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity []. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane []. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes [].
Pleckstrin homology (PH) domains are small modular domains that occur in a large variety of proteins. The domains can bind phosphatidylinositol within biological membranes and proteins such as the beta/gamma subunits of heterotrimeric G proteins []and protein kinase C []. Through these interactions, PH domains play a role in recruiting proteins to different membranes, thus targeting them to appropriate cellular compartments or enabling them to interact with other components of the signal transduction pathways.PH domains have been found to possess inserted domains (such as in PLC gamma, syntrophins) and to be inserted within other domains. Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids.The 3D structure of several PH domains has been determined []. All known cases have a common structure consisting of two perpendicular anti-parallel β-sheets, followedby a C-terminal amphipathic helix. The loops connecting the β-strands differ greatly in length, making the PH domain relatively difficult to detect. There are no totally invariant residues within the PH domain.Proteins reported to contain one more PH domains belong to the following families:Pleckstrin, the protein where this domain was first detected, is the major substrate of protein kinase C in platelets. Pleckstrin is one of the rare proteins to contains two PH domains.Ser/Thr protein kinases such as the Akt/Rac family, the beta-adrenergic receptor kinases, the mu isoform of PKC and the trypanosomal NrkA family.Tyrosine protein kinases belonging to the Btk/Itk/Tec subfamily.Insulin Receptor Substrate 1 (IRS-1).Regulators of small G-proteins like guanine nucleotide releasing factor GNRP (Ras-GRF) (which contains 2 PH domains), guanine nucleotide exchange proteins like vav, dbl, SoS and Saccharomyces cerevisiae CDC24, GTPase activating proteins like rasGAP and BEM2/IPL2, and the human break point cluster protein bcr.Cytoskeletal proteins such as dynamin (see ), Caenorhabditis elegans kinesin-like protein unc-104 (see ), spectrin beta-chain, syntrophin (2 PH domains) and S. cerevisiae nuclear migration protein NUM1.Mammalian phosphatidylinositol-specific phospholipase C (PI-PLC) (see ) isoforms gamma and delta. Isoform gamma contains two PH domains, the second one is split into two parts separated by about 400 residues.Oxysterol binding proteins OSBP, S. cerevisiae OSH1 and YHR073w.Mouse protein citron, a putative rho/rac effector that binds to the GTP-bound forms of rho and rac.Several S. cerevisiae proteins involved in cell cycle regulation and bud formation like BEM2, BEM3, BUD4 and the BEM1-binding proteins BOI2 (BEB1) and BOI1 (BOB1).C. elegans protein MIG-10.C. elegans hypothetical proteins C04D8.1, K06H7.4 and ZK632.12.S. cerevisiae hypothetical proteins YBR129c and YHR155w.
