Rho GTPase-activating protein 7 (also known as DLC1) is a tumour suppressor that functions as a Rho GTPase-activating protein (RhoGAP) and a negative regulator of specific Rho family proteins (RhoA-C and Cdc42) [, ].
The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers []. This domain is found to the N terminus of the RNA binding domain ().
Rho GTPase-activating protein 26 (ARHGAP26), also known as GTPase regulator associated with focal adhesion kinase (GRAF), is a GTPase-activating protein for the small GTPases of the Rho family RhoA and CDC42 [, ]. GRAF influences cytoskeletal changes mediated by Rho proteins []. It is recognised as a tumor suppressor []. GRAF contains an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, a Rho GAP domain, and a C-terminal SH3 domain. The SH3 domain of GRAF binds PKNbeta, a target of the small GTPase Rho [].
Proteins containing a RhoGAP (Rho GTPase Activating Protein) domain usually function to catalyse the hydrolysis of GTP that is bound to Rho, Rac and/or Cdc42, inactivating these regulators of the actin cytoskeleton. The 53 known human RhoGAP domain-containing proteins are the largest known group of Rho GTPase regulators and significantly outnumber the21 Rho GTPases they presumably regulate. This excess of GAP proteins probably indicates complex regulation of the Rho GTPases and is consistent with the existence of almost as many (48) human Dbl domain-containing Rho GEFs that act antagonistically to the RhoGAP proteins by activating the Rho GTPases. Phylogenetic analysis offers evidence for frequent domain duplication and for duplication of the entire genes containing these GAP domains [].
GRAF2, also called Rho GTPase activating protein 10 (ARHGAP10) or PS-GAP, is a GAP with activity towards Cdc42 and RhoA []. It regulates caspase-activated p21-activated protein kinase-2 (PAK-2p34). GRAF2 interacts with PAK-2p34, leading to its stabilization and decrease of cell death []. It is highly expressed in skeletal muscle, and is involved in alpha-catenin recruitment at cell-cell junctions []. GRAF2 contains an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, a Rho GAP domain, and a C-terminal SH3 domain. The SH3 domain of GRAF binds PKNbeta, a target of the small GTPase Rho [].
Rho-dependent transcription terminators participate in sophisticated genetic regulatory mechanisms, in both bacteria and phages; they occur in regulatory regions preceding the coding sequences of genes and within coding sequences, as well as at the end of transcriptional units, to prevent read through transcription. Rho is the main factor required for termination; it is a ring-shaped hexameric protein with ATPase and helicase activities. Rho-dependent termination occurs by binding of Rho to ribosome-free mRNA, C-rich sites being good candidates for binding. Rho's ATPase is activated by Rho-mRNA binding, and provides the energy for Rho translocation along the mRNA; translocation requires sliding of the message into the central hole of the hexamer. When a polymerase pause site is encountered, the actual termination occurs, and the transcript is released by Rho's helicase activity [].
Members of the Rho family of small G proteins transduce signals from plasma-membranereceptors and control cell adhesion, motility and shape by actin cytoskeleton formation.Like all other GTPases, Rho proteins act as molecular switches, with an activeGTP-bound form and an inactive GDP-bound form. The active conformation is promoted byguanine-nucleotide exchange factors, and the inactive state by GTPase-activating proteins(GAPs) which stimulate the intrinsic GTPase activity of small G proteins.This entry is a Rho/Rac/Cdc42-like GAP domain, that is found in a wide variety of large,multi-functional proteins [].A number of structure are known for this family[, , ].The domain is composed of seven α-helices.This domain is also known as the breakpoint cluster region-homology (BH) domain.
The GDP dissociation inhibitor for rho proteins, rho GDI, regulates GDP/GTP exchange by inhibiting the dissociation of GDP from them. The protein contains 204 amino acids, with a calculated Mr value of 23,421. Hydropathy analysis shows it to be largely hydrophilic, with a single hydrophobic region. Results of database searches suggest rho GDI is a novel protein, currently with no known homologue. The protein plays an important role in the activation of the superoxide (O2-)-generating NADPH oxidase of phagocytes. This process requires the interaction of membrane-associated cytochrome b559 with 3 cytosolic components: p47-phox, p67-phox and a heterodimer of the small G-protein p21rac1 and rho GDI []. The association of p21rac and GDI inhibits dissociation of GDP from p21rac, thereby maintaining it in an inactive form. The proteins are attached via a lipid tail on p21rac that binds to the hydrophobic region of GDI []. Dissociation of these proteins might be mediated by the release of lipids (e.g., arachidonate and phosphatidate) from membranes through the action of phospholipases []. The lipids may then compete with the lipid tail on p21rac for the hydrophobic pocket on GDI.
This entry represents a group of plant Rho GTPase-activating proteins, including RopGAP1-5 from Arabidopsis. RopGAP4 is a Rop deactivator, elevates ADH expression in response to oxygen deprivation but decreases tolerance to stress []. RopGAP3 and RopGAP4 mediate local activation of ARAC10/ROP11 to initiate the distinct pattern of secondary cell walls in xylem cells [].
Rho GTPase-activating protein 6 (RhoGAP6, also known as ARHGAP6) is both a GTPase-activating protein (GAP) with specificity for RhoA and a cytoskeletal protein that promotes actinremodelling []. It binds to and upregulates phospholipase C-delta, indicating a role for ARHGAP6 in enhanced activity of phospholipase C in hypertension [].
Rho GTPase activating protein 6 (ArhGAP6/RHOGAP6) shows GAP activity towards RhoA, but not towards Cdc42 and Rac1 []. ArhGAP6 is often deleted in microphthalmia with linear skin defects syndrome (MLS); MLS is a severe X-linked developmental disorder [].This family also includes ARHGAP36, which is a potent antagonist of PKA signalling [].
ARHGAP33 (also known as TCGAP) is a Rho GTPase-activating protein involved in insulin-stimulated glucose transport []. It is widely expressed in the brain where it is involved in regulating the outgrowth of axons and dendrites and is regulated by the protein tyrosine kinase Fyn []. It also plays a role in TrkB trafficking, which is essential for synapse development [].
The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers [].The Rho N-terminal domain consists of two subdomains: a three-helix bundle followed by a β-barrel. The β-barrel is an OB-type fold, which is found in a wide variety of single-stranded nucleic acid binding molecules that include cold shock proteins. An indented face on one side of this subdomain forms the primary RNA binding site of Rho [].
The Rho-ROCK pathway modulates the phosphorylation level of a variety of important signalling proteins and is thereby involved in miscellaneous cellular processes including cell migration, neurite outgrowth, and smooth muscle contraction. The enzyme activity of the two ROCK isoforms, ROCKI/ ROKbeta/p160(ROCK) and ROCKII/ROKalpha/Rho kinase, is auto-inhibited in the free state but is activated through direct binding to the small GTPase Rho in the GTP-bound form. ROCK proteins are composed of four domains: the N-terminal kinase domain, the long coiled-coil domain encompassing ~600 amino acid residues, the Rho-binding domain (RhoBD), and the C-terminal PH-like domain. The RhoBD is responsible for the recognition and binding of the active Rho proteins [, ]. The RhoBD forms long consecutive α-helices dimerized in a parallel coiled- coil. The polypeptide chains of the middle region of the coiled-coil are flexible with poor inter-helical contacts between two chains [, ]. This entry represents the RhoBD domain.
This entry represents Miro-1 (mitochondrial Rho GTPases 1) that belongs to the Miro family [].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 includes ARHGAP11A and ARHGAP11B from humans. ARHGAP11B gene arose from partial duplication of ARHGAP11A (which encodes a Rho guanosine triphosphatase-activating protein) on the human lineage after separation from the chimpanzee lineage []. A lack of 55 nucleotides in ARHGAP11B mRNA leads to loss of RhoGAP activity by GAP domain truncation and addition of a human-specific C-terminal amino acid sequence []. ARHGAP11B promotes basal progenitor amplification and is implicated in neocortex expansion [].
Neurotransmitter ligand-gated ion channels are transmembrane receptor-ion channel complexes that open transiently upon binding of specific ligands, allowing rapid transmission of signals at chemical synapses [, ]. Five of these ion channel receptor families have been shown to form a sequence-related superfamily:Nicotinic acetylcholine receptor (AchR), an excitatory cation channel in vertebrates and invertebrates; in vertebrate motor endplates it is composed of alpha, beta, gamma and delta/epsilon subunits; in neurons it is composed of alpha and non-alpha (or beta) subunits [].Glycine receptor, an inhibitory chloride ion channel composed of alpha and beta subunits [].Gamma-aminobutyric acid (GABA) receptor, an inhibitory chloride ion channel; at least four types of subunits (alpha, beta, gamma and delta) are known [].Serotonin 5HT3 receptor, of which there are seven major types (5HT3-5HT7) [].Glutamate receptor, an excitatory cation channel of which at least three types have been described (kainate, N-methyl-D-aspartate (NMDA) and quisqualate) [].These receptors possess a pentameric structure (made up of varying subunits), surrounding a central pore. All known sequences of subunits from neurotransmitter-gated ion-channels are structurally related. They are composed of a large extracellular glycosylated N-terminal ligand-binding domain, followed by three hydrophobic transmembrane regions which form the ionic channel, followed by an intracellular region of variable length. A fourth hydrophobic region is found at the C-terminal of the sequence [, ].Gamma-aminobutyric acid type A (GABAA) receptors are members of the neurotransmitter ligand-gated ion channels: they mediate neuronal inhibition on binding GABA. The effects of GABA on GABAA receptors are modulated by a range of therapeutically important drugs, including barbiturates, anaesthetics and benzodiazepines (BZs) []. The BZs are a diverse range of compounds, including widely prescribed drugs, such as librium and valium, and their interaction with GABAA receptorsprovides the most potent pharmacological means of distinguishing different GABAA receptor subtypes.GABAA receptors are pentameric membrane proteins that operate GABA-gated chloride channels []. Eight types of receptor subunit have been cloned, with multiple subtypes within some classes: alpha 1-6, beta 1-4, gamma 1-4, delta, epsilon, pi, rho 1-3 and theta [, ]. Subunits are typically 50-60kDa in size and comprise a long N-terminal extracellular domain, containing a putative signal peptide and a disulphide-bonded beta structural loop; 4 putative transmembrane (TM) domains; and a large cytoplasmic loop connecting the third and fourth TM domains. Amongst family members, the large cytoplasmic loop displays the most divergence in terms of primary structure, the TM domains showing the highest level of sequence conservation [].Most GABAA receptors contain one type of alpha and beta subunit, and a single gamma polypeptide in a ratio of 2:2:1 [], though in some cases other subunits such as epsilon or delta may replace gamma. The BZ binding site is located at the interface of adjacent alpha and gamma subunits; therefore, the type of alpha and gamma subunits present is instrumental in determining BZ selectivity and sensitivity. Receptors can be categorised into 3 groups based on their alpha subunit content and, hence, sensitivity to BZs: alpha 1-containing receptors have greatest sensitivity towards BZs (type I); alpha 2, 3 and 5-containing receptors have similar but distinguishable properties (type II); and alpha 4- and 6-containing assemblies have very low BZ affinity []. A conserved histidine residue in the alpha subunit of type I and II receptors is believed to be responsible for BZ affinity []. GABAA receptors can be characterised by their sensitivitytowards a selective antagonist, bicuculline. A GABA receptor has been identified that is insensitive to bicuculline and classical GABAA modulators but has an enhanced affinity for GABA. This receptor, unlike most GABAA receptors, is composed principally of rho subunits and was initially termed 'GABAC' in recognition of its altered pharmacology []. Despite these differences, rho subunits are generally considered to be part of the GABAAfamily of receptor proteins due to similarities in sequence and topology.Whilst early studies supported the view that rho subunits assembled to forma homopentamer, it has been shown that a mutant rho 1 protein is able tocoassemble with GABAA gamma 2 subunits as well as the glycine receptor alphasubunit. Rho subunit mRNA occurs prominently in both human and ratretina [], each subunit showing a characteristic pattern of spatial expression. In rat retina, rho 1 mRNA has been detected only in bipolarcells, whereas rho 2 transcripts have been detected in both bipolar andganglion cells. In retinal tissues, expression of rho 3 mRNA is exclusive toganglion cells. Reverse transcriptase PCR (RT-PCR) and in situhybridisation have shown rho transcripts also to be present in other regionsof the brain, specifically those involved in visual signal processing, suchas the superior colliculus and visual cortex.This entry represents the GABAA Rho subunits.
This entry represents the N-terminal domain of Rho guanine nucleotide exchange factor 5 (also known as Ephexin3 or TIM) and Rho guanine nucleotide exchange factor 5-like (also known as Rho guanine nucleotide exchange factor 35).
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 [].
Members of Rho family are small G proteins that transduce signals from plasma-membrane receptors and control cell adhesion, motility and shape by actin cytoskeleton formation. Like all other GTPases, Rho proteins act as molecular switches, with an active GTP-bound form and an inactive GDP-bound form. The active conformation is promoted by guanine-nucleotide exchange factors, and the inactive state by GTPase-activating proteins (GAPs), which stimulate the intrinsic GTPase activity of small G proteins.This entry represents Rho GTPase activating protein 27 (ARHGAP27, also known as CIN85-associated multi-domain-containing Rho GTPase-activating protein 1, CAMGAP1), a binding protein for Cbl-interacting protein of 85kDa (CIN85), an adaptor protein involved in the endocytic process of several receptor tyrosine kinases. It also has activity towards Rac1 and Cdc42 [].
Small GTPases form an independent superfamily within the larger class of regulatory GTP hydrolases. This superfamily contains proteins that control a vast number of important processes and possess a common, structurally preserved GTP-binding domain [, ]. Sequence comparisons of small G proteins from various species have revealed that they are conserved in primary structures at the level of 30-55% similarity [].Crystallographic analysis of various small G proteins revealed the presence of a 20kDa catalytic domain that is unique for the whole superfamily [, ]. The domain is built of five alpha helices (A1-A5),six β-strands (B1-B6) and five polypeptide loops (G1-G5). A structural comparison of the GTP- and GDP-bound form, allows one to distinguish two functional loop regions: switch I and switch II that surround the gamma-phosphate group of the nucleotide. The G1 loop (also called the P-loop) that connects the B1 strand and the A1 helix is responsible for the binding of the phosphate groups. The G3 loop provides residues for Mg2 and phosphate binding and is located at the N terminus of the A2 helix. The G1 and G3 loops are sequentially similar to Walker A and Walker B boxes that are found in other nucleotide binding motifs. The G2 loop connects the A1 helix and the B2 strand and contains a conserved Thr residue responsible for Mg2 binding. The guanine base is recognised by the G4 and G5 loops. The consensus sequence NKXD of the G4 loop contains Lys and Asp residues directly interacting with the nucleotide. Part of the G5 loop located between B6 and A5 acts as a recognition site for the guanine base [].The small GTPase superfamily can be divided into at least 8 different families, including:Arf small GTPases. GTP-binding proteins involved in protein trafficking by modulating vesicle budding and uncoating within the Golgi apparatus.Ran small GTPases. GTP-binding proteins involved in nucleocytoplasmic transport. Required for the import of proteins into the nucleus and also for RNA export.Rab small GTPases. GTP-binding proteins involved in vesicular traffic.Rho small GTPases. GTP-binding proteins that control cytoskeleton reorganisation.Ras small GTPases. GTP-binding proteins involved in signalling pathways.Sar1 small GTPases. Small GTPase component of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER).Mitochondrial Rho (Miro). Small GTPase domain found in mitochondrial proteins involved in mitochondrial trafficking.Roc small GTPases domain. Small GTPase domain always found associated with the COR domain.This entry represents the Rho subfamily of Ras-like small GTPases. The small GTPase-like protein LIP2 (light insensitive period 2) from Arabidopsis thalianais implicated in control of the plant circadian rhythm []. The crystal structures of a number of the members of this entry have been determined: Rnd3/RhoE [], RhoA []and Cdc42 [].
This entry represents the FF domain of the Rho GTPase activating proteins (GAPs). These are the key proteins that make the switch between the active guanosine-triphosphate-bound form of Rho guanosine triphosphatases (GTPases) and the inactive guanosine-diphosphate-bound form. Rho guanosine triphosphatases (GTPases) are a family of proteins with key roles in the regulation of actin cytoskeleton dynamics.The RhoGAP-FF1 domain have been implicated in binding to the transcription factor TFII-I; and phosphorylation of Tyr308 within the first FF domain inhibits this interaction. The RhoGAP-FF1 domain constitutes the first solved structure of an FF domain that lacks the first of the two highly conserved Phe residues, but the substitution of Phe by Tyr does not affect the domain fold [].
The SLIT-ROBO Rho GTPase-activating protein (srGAP) family consists of four members: srGAP1, -2, -3 and -4. They contain F-BAR, RhoGAP and SH3 domains. Their RhoGAP domain is involved in negative regulation of Rho GTPase activities important for cytoskeleton rearrangement []. The srGAP family members have an "inverse F-BAR"or IF-BAR domain that is distinct from other F-BAR domains such as FBP17. They are multifunctional adaptor proteins involved in various aspects of neuronal development [].srGAP2 acts through srGAP3 to modulate neuronal differentiation and neurite outgrowth of mouse neuroblastoma cells []. This entry also includes human srGAP2 duplication gene, SLIT-ROBO Rho GTPase-activating protein 2B and 2C (srGAP2B/C) []. srGAP2C encodes a truncated F-BAR domain protein that dimerises with srGAP2 to inhibit its function and thruogh this interaction with srGAP2 is involved in dendritic spine maturation [].
The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers []. This domain is found to the N terminus of the RNA binding domain ().
The GDP dissociation inhibitor for rho proteins, rho GDI, regulates GDP/GTP exchange by inhibiting the dissociation of GDP from them. The protein contains 204 amino acids, with a calculated Mr value of 23,421. Hydropathy analysis shows it to be largely hydrophilic, with a single hydrophobic region. Results of database searches suggest rho GDI is a novel protein, currently with no known homologue. The protein plays an important role in the activation of the superoxide (O2-)-generating NADPH oxidase of phagocytes. This process requires the interaction of membrane-associated cytochrome b559 with 3 cytosolic components: p47-phox, p67-phox and a heterodimer of the small G-protein p21rac1 and rho GDI []. The association of p21rac and GDI inhibits dissociation of GDP from p21rac, thereby maintaining it in an inactive form. The proteins are attached via a lipid tail on p21rac that binds to the hydrophobic region of GDI []. Dissociation of these proteins might be mediated by the release of lipids (e.g., arachidonate and phosphatidate) from membranes through the action of phospholipases []. The lipids may then compete with the lipid tail on p21rac for the hydrophobic pocket on GDI.The rhoGDI structural domain contains both a structured, immunoglobulin-like fold, and a highly flexible N terminus of 50-60 residues []. The N-terminal region becomes ordered upon complex formation and contributes more than 60% to the interface area [].
The function of Rho guanine nucleotide exchange factor 33 (ARHGEF33) is not clear. It contains the Dbl homology (DH) domain and may act as a guanine-nucleotide releasing factor.
Rho guanine nucleotide exchange factor 11, also known as PDZ-RhoGEF, is a guanine nucleotide exchange factor (GEFs) for Rho GTPase that plays critical roles in signalling []. PDZ-RhoGEF uses its PDZ domains to bind class B plexins and plays a role in axon guidance [, ]. It is involved in neurotrophin-induced neurite outgrowth [].
GTPases bind to guanosine triphosphate (GTP), hydrolyze gamma-phosphate,release guanosine diphosphate (GDP) and then rebind GTP, a process termed'GTPase cycling'. GTPases are regulated by GTPase activating proteins (GAPs) and guanine nucleotide exchange factors (GEFs). The Ras superfamily of small GTPases consists of five subgroups (Ras, Rho, Rab, Ran and Arf) that act as molecular switches in broad and diverse cellular pathways and processes. The Ras superfamily members contain five highly conserved sequence motifs, termed 'G-motifs', required for nucleotide-binding and catalytic activity. PseudoGTPases by definition would consist of a GTPase fold lacking one or more of these G motifs [].The p190RhoGAP proteins, p190RhoGAP-A (ARHGAP35) andp190RhoGAP-B (ARHGAP5), are key regulators of Rho GTP hydrolysis and arehighly important for maintenance of proper Rho signaling. They share a domainorganization containing a GTP-binding GTPase domain, four FF domains, twoGTPase-like folds (pG1 and pG2) and a C-terminal GAP domain. Their pG1 (pseudoGTPase1) and pG2 (pseudoGTPase2) domains lack conserved GTPase motifs and don't have nucleotide-binding activity []. This entry represents the pG2 domain.
GTPases bind to guanosine triphosphate (GTP), hydrolyze gamma-phosphate,release guanosine diphosphate (GDP) and then rebind GTP, a process termed'GTPase cycling'. GTPases are regulated by GTPase activating proteins (GAPs) and guanine nucleotide exchange factors (GEFs). The Ras superfamily of small GTPases consists of five subgroups (Ras, Rho, Rab, Ran and Arf) that act as molecular switches in broad and diverse cellular pathways and processes. The Ras superfamily members contain five highly conserved sequence motifs, termed 'G-motifs', required for nucleotide-binding and catalytic activity. PseudoGTPases by definition would consist of a GTPase fold lacking one or more of these G motifs [].The p190RhoGAP proteins, p190RhoGAP-A (ARHGAP35) andp190RhoGAP-B (ARHGAP5), are key regulators of Rho GTP hydrolysis and arehighly important for maintenance of proper Rho signaling. They share a domainorganization containing a GTP-binding GTPase domain, four FF domains, twoGTPase-like folds (pG1 and pG2) and a C-terminal GAP domain. Their pG1 (pseudoGTPase1) and pG2 (pseudoGTPase2) domains lack conserved GTPase motifs and don't have nucleotide-binding activity []. This entry represents the pG1 domain.
Rho GTPase-activating proteins (RhoGAPs or ARHGAPs) bind to Rho proteins and enhance the hydrolysis rates of bound GTP. ARHGAP9 functions as a GAP for Rac and Cdc42, but not for RhoA []. It negatively regulates cell migration and adhesion []. It also acts as a docking protein for the MAP kinases Erk2 and p38alpha, and may facilitate cross-talk between the Rho GTPase and MAPK pathways to control actin remodeling []. It contains SH3, WW, Pleckstin homology (PH), and RhoGAP domains. This entry represents the SH3 domain found in ARHGAP9.
This entry includes Rho guanine nucleotide exchange factors 10 and 17.ARHGEF10 is a Rho guanine nucleotide exchange factor that may play a role in developmental myelination of peripheral nerves []. It was found to regulate mitotic spindle formation and play a role in the regulation of the cell division cycle [].ARHGEF17 is a guanine nucleotide exchange for for RhoA GTPases; it contains a Dbl homology (DH) domain but lacks the typical pleckstrin homology domain [].
The SLIT-ROBO Rho GTPase-activating protein (srGAP) family consists of four members: srGAP1, -2, -3 and -4. They contain F-BAR, RhoGAP and SH3 domains. Their RhoGAP domain is involved in negative regulation of Rho GTPase activities important for cytoskeleton rearrangement []. The srGAP family members have an "inverse F-BAR"or IF-BAR domain that is distinct from other F-BAR domains such as FBP17. They are multifunctional adaptor proteins involved in various aspects of neuronal development [].This entry represents the F-BAR domain of srGAP1. srGAP1, also called Rho GTPase-Activating Protein 13 (ARHGAP13), is a Cdc42- and RhoA-specific GAP and is expressed later in the development of CNS (central nervous system) tissues. It is an important downstream signaling molecule of Robo1 [, ].
The RhoGAPs (GTPase-activating proteins) regulates Rho GTP hydrolysis and are important for proper Rho signalling. This entry represents a domain found in p190RhoGAP-A (ARHGAP35) and p190RhoGAP-B (ARHGAP5). 190RhoGAP-A/B contain a GTP-binding GTPase domain, four FF domains, two GTPase-like folds (pG1 and pG2) in the middle domain and a C-terminal GAP domain. This entry represents pG1 and pG2 which are important for GAP activity toward RhoA. 190RhoGAP-A/B were classified as pseudoGTPases as they lack nucleotide-binding activity. Crystal structures revealed a small GTPase fold in both cases with a central 6-stranded β-sheet surrounded by four α-helices [].
This entry includes a group of RhoGEFs, including Kalirin and TRIO from mammals. Kalirin and TRIO are encoded by separate genes in mammals and by a single one in invertebrates. Kalirin and TRIO share the same complex multidomain structure and display several splice variants. They are implicated in secretory granule (SG) maturation and exocytosis [, ]. The longest Kalirin and TRIO proteins have a Sec14 domain, a stretch of spectrin repeats, a RhoGEF(DH)/PH cassette (also called GEF1), an SH3 domain, a second RhoGEF(DH)/PH cassette (also called GEF2), a second SH3 domain, Ig/FNIII domains, and a kinase domain. The first RhoGEF(DH)/PH cassette catalyzes exchange on Rac1 and RhoG while the second RhoGEF(DH)/PH cassette is specific for RhoA. Kalirin and TRIO are closely related to p63RhoGEF and have PH domains of similar function. 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 [, ].Triple functional domain protein (TRIO) contains a protein kinase domain and two guanine nucleotide exchange factor (GEF) domains []. These functional domains suggest that it may play a role in signalling pathways controlling cell proliferation []. TRIO may form a complex with LAR transmembrane protein tyrosine phosphatase (PT-Pase), which localises to the ends of focal adhesions and plays an important part in coordinating cell-matrix and cytoskeletal rearrangements necessary for cell migration []. Its expression is associated with invasive tumor growth and rapid tumor cell proliferation in urinary bladder cancer [].Kalirin () promotes the exchange of GDP by GTP and stimulates the activity of specific Rho GTPases []. There are several Kalirin isoforms in humans and mice. Each Kalirin isoform is composed of a unique collection of domains and may have different functions []. In rat, isoforms 1 and 7 are necessary for neuronal development and axonal outgrowth, while isoform 6 is required for dendritic spine formation []. In humans, the major isoform of Kalirin in the adult brain is Kalirin-7, which plays a critical role in spine formation/synaptic plasticity. Kalirin-7 has been linked to neuropsychiatric and neurological diseases such as Alzheimer's, Huntingtin's, ischemic stroke, schizophrenia, depression, and cocaine addiction [, , ].
Rho family-interacting cell polarization regulator 2 (also known as protein FAM65B) is a plasma membrane-associated protein of hair cell stereocilia that is essential for hearing []. It is important for formation of the HDAC6-dysferlin protein complex during myogenic cell differentiation []. It is a RhoA inhibitor involved in T lymphocyte migration and neutrophil polarization [, ].
ARHGEF10 is a Rho guanine nucleotide exchange factor that may play a role in developmental myelination of peripheral nerves []. It was found to regulate mitotic spindle formation and play a role in the regulation of the cell division cycle [].
This entry represents the PX domain found in Rho GTPase-activating protein 32 (ARHGAP32, also known as RICS). RICS is a Rho GTPase-activating protein for cdc42 and Rac1. It is implicated in the regulation of postsynaptic signaling and neurite outgrowth. An N-terminal splicing variant of RICS containing additional PX and Src Homology 3 (SH3) domains, also called PX-RICS, is the main isoform expressed during neural development. PX-RICS is involved in neural functions including axon and dendrite extension, postnatal remodeling, and fine-tuning of neural circuits during early brain development []. The PX domain is involved in targeting of proteins to PI-enriched membranes, and may also be involved in protein-protein interaction []. The PX domain of PX-RICS specifically binds phosphatidylinositol 3-phosphate (PI3P), PI4P, and PI5P [].
Rho guanine nucleotide exchange factor 25 (ARHGEF25, GEFT), also known as p63RhoGEF, is a RhoA-specific guanine nucleotide exchange factor. It is found in vascular smooth muscle (SM) and may play a role in selective targetingof RhoA-mediated regulation of basal blood pressure through agonists that couple through G alpha(q/11) [, ]. It is thought to be involved in muscle regeneration, myogenesis, and adipogenesis regulation by modulating mesenchymal cell fate decisions [].
Formins are multidomain proteins conserved from plants to fungi and vertebrates. Due to their pivotal role in the organisation of the actin cytoskeleton formins are involved in processes as diverse as formation of filopodia, microspikes and lamellipodia, establishment and maintenance of cell polarity, vesicular trafficking, formation of adherens junctions, cytokinesis, embryonic development and signalling to the nucleus. Formins are defined by a conserved formin homology 2 (FH2) domain with actin nucleation activity preceded by a proline-rich formin homology 1 (FH1) domain. In most fungal and metazoan formins the FH1-FH2 core is accompanied by a less conserved N-terminal formin homology 3 (FH3) domain involved in targeting []. The Diaphanous-related formins are able to interact with activated Rho GTPases through a poorly defined N-terminal Rho GTPase binding domain (GBD) that overlaps with the formin homology 3 (FH3) domain. This binding releases the intramolecular inhibitory interaction between the GBD and a C-terminal Diaphanous autoregulatory domain (DAD) (see ) and renders the protein active. It has been proposed that the GBD and FH3 domains constitute a single domain also found in Dictyostelium guanine nucleotide exchange factors(RasGEFs) [].This entry represents the GBD/FH3 domain that is approximately 380 residues in length. Its role appears to be twofold. On one hand the N-terminal region of formins is involved in subcellular localisation through interaction with diverse targets. The low degree of sequence conservation of this region might correlate with the diversity of binding partners, not only Rho GTPases, and subcellular localisation patterns. On the other hand the GBD/FH3 domain is involved in regulation of activation by releasing of an intramolecular interaction between the DAD and the N terminus []. The GBD/FH3 domain is exclusively α-helical and is comprised of the N-terminal part of the GBD, an armadillo repeat region (ARR) and dimerisation subdomains [].
Rho guanine nucleotide exchange factor 11, also known as PDZ-RhoGEF, is a guanine nucleotide exchange factor (GEFs) for Rho GTPase that plays critical roles in signalling []. PDZ-RhoGEF uses its PDZ domains to bind class B plexins and plays a role in axon guidance [, ]. It is involved in neurotrophin-induced neurite outgrowth [].PDZ-RhoGEF contains an N-terminal PDZ domain, a regulators of G-protein signaling-like (RGSL) domain, a linker region, and C-terminal Dbl-homology (DH) and pleckstrin-homology (PH) domains which bind and catalyze the exchange of GDP for GTP on RhoA. This entry represents the PH domain [].
This entry represents the C-terminal coiled-coil (CC) region found in Rho guanine nucleotide exchange factors (GEFs) 6 and 7 (also known as alpha and betaPIX, respectively) []. This domain is upstream of the PDZ binding motif and is important for the multimerization of betaPIX [, ].
This entry represents a region that typically appears on the C terminus of EF hands in eukaryotic GTP-binding proteins such as Mitochondrial Rho GTPase 1 from Bos taurus (MIRO-1), the product of the gene Arht, which may be involved in mitochondrial homeostasis and apoptosis[]. The EF hand domains of these proteins may have a regulatory role related to Ca(2+) binding [].
The RGS domain is an essential part of the Rho guanine nucleotide exchange factor 11, also known as PDZ-RhoGEF (PDZ:Postsynaptic density 95, Disk large, Zona occludens-1; RhoGEF: Rho guanine nucleotide exchange factor; alias PRG), a member of RhoGEFs subfamily of the RGS protein family. The RhoGEFs are peripheral membrane proteins that regulate essential cellular processes, including cell shape, cell migration, and cell cycle progression, as well as 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 [, ]. RhoGEFs subfamily includes leukemia-associated RhoGEF protein (LARG), p115RhoGEF, 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 contrast to p115RhoGEF and LARG, PDZ-RhoGEF cannot serve as a GTPase-activating protein (GAP), due to the mutation of sites in the RGS domain region that are crucial for GAP activity [].
Alpha-PIX, also called Rho guanine nucleotide exchange factor 6 (ARHGEF6) or Cool (Cloned out of Library)-2, activates small GTPases by exchanging bound GDP for free GTP []. It acts as a GEF for both Cdc42 and Rac1, and is localized in dendritic spines where it regulates spine morphogenesis []. It controls dendritic length and spine density in the hippocampus. Mutations in the ARHGEF6 gene cause X-linked intellectual disability in humans [, ]. PIX proteins contain an N-terminal SH3 domain followed by RhoGEF (also called Dbl-homologous or DH) and Pleckstrin Homology (PH) domains, and a C-terminal leucine-zipper domain for dimerization. This entry represents the SH3 domain of alpha-PIX.
ARHGEF39 (also known as C9orf100) is a member of the Dbl-family guanine nucleotide exchange factors. It promotes cell proliferation and migration in hepatocellular carcinoma []. It may contribute to cell proliferation and migration in gastric cancer via Akt signalling []and predicts poor prognosis in non-small cell lung cancer patients [].
ARHGEF17 is a guanine nucleotide exchange for for RhoA GTPases; it contains a Dbl homology (DH) domain but lacks the typical pleckstrin homology domain [].
Beta-PIX, also called Rho guanine nucleotide exchange factor 7 (ARHGEF7) or Cool (Cloned out of Library)-1, activates small GTPases by exchanging bound GDP for free GTP. 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 [, , , ].PIX proteins contain an N-terminal SH3 domain followed by RhoGEF (also called Dbl-homologous or DH) and Pleckstrin Homology (PH) domains, and a C-terminal leucine-zipper domain for dimerization. The SH3 domain of PIX binds to an atypical PxxxPR motif in p21-activated kinases (PAKs) with high affinity. The binding of PAKs to PIX facilitate the localization of PAKs to focal complexes and also localizes PAKs to PIX targets Cdc43 and Rac, leading to the activation of PAKs [, ].This entry represents the SH3 domain of beta-PIX.
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 [].ARHGEF3 (also known as XPLN) is a guanine nucleotide exchange factor (GEF) for RhoA and RhoB GTPases []. It contains a tandem Dbl homology and a PH domain. This entry represents the PH domain.
ARHGEF9 (Rho guanine nucleotide exchange factor 9, also called PEM2 or collybistin) selectively activates Cdc42 by exchanging bound GDP for free GTP []. It is highly expressed in the brain and it interacts with gephyrin, a postsynaptic protein associated with GABA and glycine receptors. Mutations in the ARHGEF9 gene cause X-linked mental retardation with associated features like seizures, hyper-anxiety, aggressive behavior, and sensory hyperarousal [, , ]. ARHGEF9 contains a SH3 domain followed by RhoGEF (also called Dbl-homologous or DH) and Pleckstrin Homology (PH) domains [].This entry represents the SH3 domain of ARHGEF9.
This entry represents the PH domain found in Cdc24 from budding yeasts and Scd1 from fission yeasts. Cdc24 and Scd1 are guanine nucleotide exchange factors (GEFs) for Cdc42 [, ].
Rho GTPase-activating protein 26 (ARHGAP26), also known as GTPase regulator associated with focal adhesion kinase (GRAF), is a GTPase-activating protein for the small GTPases of the Rho family RhoA and CDC42 [, ]. GRAF influences cytoskeletal changes mediated by Rho proteins []. It is recognised as a tumor suppressor []. GRAF contains an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, a Rho GAP domain, and a C-terminal SH3 domain. The SH3 domain of GRAF binds PKNbeta, a target of the small GTPase Rho [].This entry represents the BAR domain of GRAF. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The BAR domain of GRAF directly interacts with its Rho GAP domain and inhibits its activity. Autoinhibited GRAF is capable of binding membranes and tubulating liposomes, showing that the membrane-tubulation and GAP-inhibitory functions of the BAR domain can occur simultaneously [].
This pleckstrin homology (PH) domain is found in some Rho guanine nucleotide exchange factors, such as ARHGEF18 (p114RhoGEF) []and ARHGEF1 (p115-RhoGEF) [].
This family consists of several bacterial modulator of Rho-dependent transcription termination (ROF) proteins. ROF binds transcription termination factor Rho and inhibits Rho-dependent termination in vivo[].
This entry represents Cdc42 effector protein 2 (also known as Binder of Rho GTPases 1). It is probably involved in the organisation of the actin cytoskeleton [, ].
This entry represents the SH3 domain of GRAF.Rho GTPase-activating protein 26 (ARHGAP26), also known as GTPase regulator associated with focal adhesion kinase (GRAF), is a GTPase-activating protein for the small GTPases of the Rho family RhoA and CDC42 [, ]. GRAF influences cytoskeletal changes mediated by Rho proteins []. It is recognised as a tumor suppressor []. GRAF contains an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, a Rho GAP domain, and a C-terminal SH3 domain. The SH3 domain of GRAF binds PKNbeta, a target of the small GTPase Rho [].
Alpha-catulin 1 (also known as catenin alpha-like protein 1, CTNNAL1) belongs to the alpha catenin family, whose members are involved in cell adhesion. CTNNAL1 may modulate Rho pathway signalling by providing a scaffold for the Lbc Rho guanine nucleotide exchange factor []. It is downregulated in asthma patients and animal models [].
The Rho-type GTPase Cdc42 regulates cell morphology and signal transduction in eukaryotic cells. The Cdc42 effector (CEP) or binder of Rho GTPase (BORG) proteins are involved in the organisation of the actin cytoskeleton []. They may function as negative regulators of Rho GTPase signaling [].This family consists of Cdc42 effector proteins, including CEP1-5 from humans.
Rho GTPase-activating proteins (RhoGAPs or ARHGAPs) bind to Rho proteins and enhance the hydrolysis rates of bound GTP. ARHGAP12 has been shown to display GAP activity towards Rac1. It plays a role in regulating hepatocyte growth factor (HGF)-driven cell growth and invasiveness []. It contains SH3, WW, Pleckstin homology (PH), and RhoGAP domains []. This entry represents the SH3 domain of ARHGAP12.
GRAF2, also called Rho GTPase activating protein 10 (ARHGAP10) or PS-GAP, is a GAP with activity towards Cdc42 and RhoA []. It regulates caspase-activated p21-activated protein kinase-2 (PAK-2p34). GRAF2 interacts with PAK-2p34, leading to its stabilization and decrease of cell death []. It is highly expressed in skeletal muscle, and is involved in alpha-catenin recruitment at cell-cell junctions []. GRAF2 contains an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, a Rho GAP domain, and a C-terminal SH3 domain. The SH3 domain of GRAF binds PKNbeta, a target of the small GTPase Rho []. This entry represents the SH3 domain of GRAF2.
Anillin (Rhotekin/RTKN; also called PLEKHK/Pleckstrin homology domain-containing family K) is an actin binding protein involved in cytokinesis. It interacts with GTP-bound Rho proteins and results in the inhibition of their GTPase activity. Dysregulation of the Rho signal transduction pathway has been implicated in many forms of cancer. Anillin proteins have a N-terminal HRI domain/ACC (anti-parallel coiled-coil) finger domain or Rho-binding domain binds small GTPases from the Rho family. The C-terminal PH domain helps target anillin to ectopic septin containing foci [, ].This entry represents the PH domain.
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 [, ].
This superfamily consists of several bacterial modulator of Rho-dependent transcription termination (ROF) proteins. ROF binds transcription termination factor Rho and inhibits Rho-dependent termination in vivo[].ROF (also known as YaeO) contains an N-terminal helix and a seven-stranded beta sandwich [].
This entry includes human CCDC85A/B/C and C. elegans Picc-1 protein. Picc-1 serves as a linker protein which helps to recruit the Rho GTPase-activating protein, pac-1, to adherens junctions []. Human CCDC85B suppresses the beta-catenin activity in a p53-dependent manner [].
Interactor of constitutive active ROPs (ICR) family includes ICR1-4 from plants. ICR1 acts as a scaffold, mediating interaction of ROPs with different proteins []. ROPs (Rho-related GTPases) are a subfamily of Rho small GTPases from plants.
Protein Shroom belongs to the Shroom family, whose members are linked to the actin cytoskeleton []. Shroom and Rho GTPase have distinct functions in regulating Rho-kinase localisation and planar polarised myosin contractility during convergent extension in Drosophila embryos [].
Bacterial transcription antitermination protein, NusG, is a component of thetranscription complex and interacts with the termination factor Rho and RNApolymerase [, ]. NusG is a bacterial transcriptional elongation factor involved in transcription termination and anti-termination [].
Costars significantly resembles the C-terminal region of the striated muscle activator of Rho signaling (STARS), a mammalian protein that regulates the serum response factor transcriptional activity through actin binding and Rho GTPase activation. Costars is involved in modulating actin dynamics and cell motility in Dictyostelium. Costars has been shown to directly bind to F-actin in vitro, however, it does not associate tightly with either G- or F-actin within the cellular context [].
This entry represenst a RhoGAP (GTPase-activator protein [GAP]for Rho-like small GTPases) domain present in ARAPs. ARAPs (also known as centaurin deltas) are dual GTPase activating proteins (GAPs) for Arf and Rho family GTPases, and contain, besides the Rho-GAP domain, an Arf-GAP, ankyrin repeat ras-associating, and PH domains. Since their Arf-GAP activity is PIP3-dependent, ARAPs are considered integration points for phosphoinositide, Arf and Rho signaling [, , , ].Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude [, , ].
This entry represents the SH3 domain of srGAP4. srGAP4 is highly expressed in hematopoietic cells and may play a role in lymphocyte differentiation []. It is able to stimulate the GTPase activity of three members of Rho GTPases, Rac1, Cdc42 and RhoA. In the nervous system, srGAP4 has been detected in differentiating neurites and may be involved in axon and dendritic growth [].The SLIT-ROBO Rho GTPase-activating protein (srGAP) family consists of four members: srGAP1, -2, -3 and -4. They contain F-BAR, RhoGAP and SH3 domains. Their RhoGAP domain is involved in negative regulation of Rho GTPase activities important for cytoskeleton rearrangement []. The srGAP family members have an "inverse F-BAR"or IF-BAR domain that is distinct from other F-BAR domains such as FBP17. They are multifunctional adaptor proteins involved in various aspects of neuronal development [].
The FAM65 family of proteins includes the members FAM65A (also known as Rho family-interacting cell polarization regulator 1), FAM65B (also known as Rho family-interacting cell polarization regulator 2) and FAM65C (also known as RIPOR family member 3). FAM65A has been shown to localise to the podocyte major processes and cell body in the kidney []. FAM65B is upregulated early during muscle cell differentiation [], and occurs in two isoforms, long and short, which are differentially expressed in different tissues. FAM65C also appears to occur in two isoforms, produced by alternative splicing.
Actin-binding LIM protein 2 (ABLIM2) may serve as a scaffold for signaling modules of the actin cytoskeleton and hence affect transcription. It binds to F-actin and synergistically enhances STARS (striated muscle activator of Rho signaling)-dependent activation of the serum-response factor (SRF), which is a transcription factor that affects embryo development in mammals [].
Actin-binding LIM protein 3 (ABLIM3) may serve as a scaffold for signaling modules of the actin cytoskeleton and hence affect transcription. It binds to F-actin and synergistically enhances STARS (striated muscle activator of Rho signaling)-dependent activation of the serum-response factor (SRF), which is a transcription factor that affect embryo development in mammals [].
Plakophilin-4 (protein p0071) is the most distantly related of the plakophilins []. Protein p0071 plays a role as a regulator of Rho activity during cytokinesis []. It is absent from desmosomes []and it is a major constituent of the myocardial composite junctions and of the diverse morphological forms of adherens junctions in which it forms stable complexes with specific catenins and 'classic' cadherins [].
Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase. It is a homohexamer []. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This entry represents the C-terminal ATP binding domain [, , ].
This domain is found in Diaphanous-related formins (Drfs). It binds the N-terminal GTPase-binding domain; this link is broken when GTP-bound Rho binds to the GBD and activates the protein. The addition of diaphanous activating domains (DAD) to mammalian cells induces actin filament formation, stabilises microtubules, and activates serum-response mediated transcription [].
RhoBTB3 is an atypical Rho GTPase that appears to have different functions compared to other RhoBTBs, such as RhoBTB1 and RhoBTB2. RhoBTB3 is only found in vertebrates and is a Rab9-regulated ATPase, rather than a GTPase, that participates in transport vesicle docking at the Golgi complex [].
This leucine-zipper domain can be found in MIP1 proteins and in putative Rho GTPase-activating proteins. MIP1 proteins, here largely from plants, are subunits of the TORC2 (rictor-mTOR) protein complex controlling cell growth and proliferation []. The leucine-zipper is likely to be the region that interacts with plant MADS-box factors [],
The Rho family GTPases Rho, Rac and CDC42 regulate a diverse array of cellular processes. Like all members of the Ras superfamily, the Rho proteins cycle between active GTP-bound and inactive GDP-bound conformational states.Activation of Rho proteins through release of bound GDP and subsequentbinding of GTP, is catalysed by guanine nucleotide exchange factors (GEFs) inthe Dbl family. The proteins encoded by members of the Dbl family share acommon domain, presented in this entry, of about 200 residues (designated the Dbl homology or DH domain) that has been shown to encode a GEF activity specific for a number of Rho family members. In addition, all family members possess a second, shared domain designated the pleckstrin homology (PH) domain (). Trio and its homologue UNC-73 are unique within the Dbl family insomuch as they encode two distinct DH/PH domain modules. The PH domain is invariably located immediately C-terminal to the DH domain and this invariant topography suggests a functional interdependence between these two structural modules. Biochemical data have established the role of the conserved DH domain in Rho GTPase interaction and activation, and the role of the tandem PH domain in intracellular targeting and/or regulation of DH domain function. The DH domain of Dbl has been shown to mediate oligomerisation that is mostly homophilic in nature. In addition to the tandem DH/PH domains Dbl family GEFs contain diverse structural motifs like serine/threonine kinase, RBD, PDZ, RGS, IQ, REM, Cdc25, RasGEF, CH, SH2, SH3, EF, spectrin or Ig.The DH domain is composed of three structurally conserved regions separated bymore variable regions. It does not share significant sequence homology withother subtypes of small G-protein GEF motifs such as the Cdc25 domain and theSec7 domain, which specifically interact with Ras and ARF family small GTPases, respectively, nor with other Rho protein interactive motifs, indicating that the Dbl family proteins are evolutionarily unique. The DH domain is composed of 11 alpha helices that are folded into a flattened, elongated α-helix bundle in which two of the three conserved regions, conserved region 1 (CR1) and conserved region 3 (CR3), are exposed near the centre of one surface. CR1 and CR3, together with a part of alpha-6 and the DH/PH junction site, constitute the Rho GTPase interacting pocket.
Diaphanous-related formins (Drfs) are a family of formin homology (FH) proteins that act as effectors of Rho small GTPases during growth factor-induced cytoskeletal remodelling, stress fibre formation, and cell division []. Drf proteins are characterised by a variety of shared domains: an N-terminal GTPase-binding domain (GBD), formin-homology domains FH1, FH2 () and FH3 (), and a C-terminal conserved Dia-autoregulatory domain (DAD) that binds the GBD.This entry represents the GBD, which is a bifunctional autoinhibitory domain that interacts with and is regulated by activated Rho family members. Mammalian Drf3 contains a CRIB-like motif within its GBD for binding to Cdc42, which is required for Cdc42 to activate and guide Drf3 towards the cell cortex where it remodels the actin skeleton [].
This superfamily contains the N-terminal domain of diaphanous, a subclass of formins whose members are regulated by the binding of a small GTP-binding protein of the Rho subfamily. These proteins are characterised by a variety of shared domains: an N-terminal GTPase-binding domain (GBD), formin-homology domains FH1, FH2 and FH3, and a C-terminal conserved Dia-autoregulatory domain (DAD) that binds the GBD. This N-terminal domain corresponds to the GBD, a bifunctional autoinhibitory domain that interacts with and is regulated by activated Rho family members. Mammalian Drf3 contains a CRIB-like motif within its GBD for binding to Cdc42, which is required for Cdc42 to activate and guide Drf3 towards the cell cortex where it remodels the actin skeleton [, ].
The RGS domain is an essential part of the leukemia-associated RhoGEF protein (LARG, also known as Rho guanine nucleotide exchange factor 12), a member of the RhoGEF 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 cellularresponses, 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 effector, the LARG protein also functions as a GTPase-activating protein (GAP) [].
RasGRF1 belong to the RasGRF family. It regulates both Ras and Rac signalling pathways []. It has been implicated in memory formation, postnatal growth, glucose homeostasis and photoreception [].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 [].
This entry represents the SH3 domain found in srGAP proteins 1, 2 and 3. srGAP1 (also called ARHGAP13) is a key GTPase activating protein (GAP) downstream of Slit-Robo pathway, and has been shown to inhibit neuronal migration and glioma cell invasion by reducing the activation of Cdc42 []. srGAP2 (ARHGAP34) regulates neuronal morphogenesis through the ability of its F-BAR domain to regulate membrane deformation and induce filopodia formation []. srGAP3 (ARHGAP14) interacts with lamellipodin at the cell membrane and regulates Rac-dependent cellular protrusions []. The SLIT-ROBO Rho GTPase-activating protein (srGAP) family consists of four members: srGAP1, -2, -3 and -4. They contain F-BAR, RhoGAP and SH3 domains. Their RhoGAP domain is involved in negative regulation of Rho GTPase activities important for cytoskeleton rearrangement []. The srGAP family members have an "inverse F-BAR"or IF-BAR domain that is distinct from other F-BAR domains such as FBP17. They are multifunctional adaptor proteins involved in various aspects of neuronal development [].
PKN1 is a serine/threonine protein kinase activated by the Rho family of small GTPases, and by fatty acids such as arachidonic and linoleic acids [, ]. It is expressed ubiquitously and is the most abundant PKN isoform in neurons []. PKN1 is implicated in a variety of functions including cytoskeletal reorganization, cardiac cell survival, cell adhesion, and glucose transport, among others [, ]. PKN1 contains three HR1 domains, a C2 domain, and a kinase domain.This entry represents the second HR1 domain of PKN1. HR1 domains are anti-parallel coiled-coil (ACC) domains that bind small GTPases from the Rho family; PKN1 binds the GTPases RhoA, RhoB, and RhoC, and can also interact weakly with Rac [].
Rho-associated protein kinases (ROCKs) were originally identified as small GTPase Rho effectors. Later, ROCKs were found actively phosphorylating many actin-binding proteins and intermediate filament proteins to modulate their functions []. Two ROCK isoforms have been identified:ROCK1 (ROKb, p160ROCK) and ROCK2. As major downstream effectors of the small GTPase RhoA, they regulate cellular contraction, motility, morphology, polarity, cell division, and gene expression [, , ].This entry represents the HR1 domain found in Rho-associated protein kinase 1 (ROCK1), which is essential for the formation of stress fibres []. ROCK1 contains an N-terminal extension, a catalytic kinase domain, and a long C-terminal extension, which contains a Rho-binding HR1 domain and a pleckstrin homology (PH) domain. ROCK1 is auto-inhibited by HR1 and PH domains interacting with the catalytic domain. HR1 domains are anti-parallel coiled-coil (ACC) domains that bind small GTPases from the Rho family [].
Rho-associated protein kinases (ROCKs) were originally identified as small GTPase Rho effectors. Later, ROCKs were found actively phosphorylating many actin-binding proteins and intermediate filament proteins to modulate their functions []. Two ROCK isoforms have been identified:ROCK1 (ROKb, p160ROCK) and ROCK2. As major downstream effectors of the small GTPase RhoA, they regulate cellular contraction, motility, morphology, polarity, cell division, and gene expression [, , ].This entry represents the HR1 domain found in Rho-associated protein kinase 2 (ROCK2), which is essential for the formation of stress fibres []. ROCK2 contains an N-terminal extension, a catalytic kinase domain, and a long C-terminal extension, which contains a Rho-binding HR1 domain and a pleckstrin homology (PH) domain. ROCK2 is auto-inhibited by HR1 and PH domains interacting with the catalytic domain. HR1 domains are anti-parallel coiled-coil (ACC) domains that bind small GTPases from the Rho family [].
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.
Myosin IX is a processive single-headed motor, which might play a role in signalling. Class IX myosins contain a GTPase-activating protein (GAP) domain in their tail region, which allows them to negatively regulate small Rho GTPases []. This entry represents the catalytic (head) domain, which has ATPase activity and belongs to the larger group of P-loop NTPases. The single head of class IX myosin exhibits characteristics of a processive motor [, ].
This family consists of erythromycin resistance gene leader peptides. These leader peptides are involved in the transcriptional attenuation control of the synthesis of the macrolide-lincosamide -streptogramin B resistance protein. It acts as a transcriptional attenuator, in contrast to other inducible erm genes. The mRNA leader sequence can fold in either of two mutually exclusive conformations, one of which is postulated to form in the absence of induction, and to contain two rho factor-independent terminators [].
This family contains a number of phage polarity suppression proteins (Psu) (approximately 190 residues long). The Psu protein of Bacteriophage P4causes suppression of transcriptional polarity in Escherichia coli by overcoming Rho termination factor activity []. It has the structure of a golf stick composed of seven helices. Psu is described to have a complicated knotted dimeric conformation. It binds to the hexameric capsomere on the P4 capsid to prevent DNA leakage [].
Protein Shroom3 (Shrm3) belongs to the Shroom family, whose members are linked to the actin cytoskeleton []. Shrm3 is an actin binding protein that directs Rho kinase- and RhoA-dependent apical constriction in the lens placode and partially facilitates invagination [, , , ]. It is recruited to adherens junctions by cadherin-binding ZA (zonula adherens) protein p120-catenin during lens pit morphogenesis []. It is necessary for neural tube closure in vertebrate development [, ].
This entry represents a group of Cdc42-binding proteins known as SPECs (for small protein effector of Cdc42), including SPEC1 and SPEC2 from humans. SPECs modulate the activity of the Rho GTPase Cdc42, which plays important roles in actin polymerization and kinase signaling []. SPEC1 and SPEC2 play a role in F-actin accumulation in activated T lymphocytes and may play a role in early contractile events in phagocytosis [].
The DH domain is composed of 11 alpha helices that are folded into a flattened, elongated α-helix bundle in which two of the three conserved regions, conserved region 1 (CR1) and conserved region 3 (CR3), are exposed near the centre of one surface. CR1 and CR3, together with a part of alpha-6 and the DH/PH junction site, constitute the Rho GTPase interacting pocket [, ].
Cell cycle progression protein 1 (CCPG1), also known as cell cycle progression restoration protein 8 (CPR8) [], is a scaffold protein that interacts with the Rho guanine nucleotide exchange factor Dbs and modulates its exchange specificity. CCPG1 binds to the Dbl homology/pleckstrin homology domain tandem motif of Dbs and inhibits its exchange activity toward RhoA, but not Cdc42 []. CCPG1 may be involved in cell cycle regulation [].
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 shownto 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 also includes Transducer of Cdc42-dependent actin assembly protein (TOCA) family proteins which contains a central HR1 (also known as Rho effector motif class 1, REM-1) which is closely related to Cdc42-interacting protein 4 (CIP4), effectors of the Rho family small G protein Cdc2 [].
Neurotransmitter ligand-gatedion channels are transmembrane receptor-ion channel complexes that open transiently upon binding of specific ligands, allowing rapid transmission of signals at chemical synapses [, ]. Five of these ion channel receptor families have been shown to form a sequence-related superfamily:Nicotinic acetylcholine receptor (AchR), an excitatory cation channel in vertebrates and invertebrates; in vertebrate motor endplates it is composed of alpha, beta, gamma and delta/epsilon subunits; in neurons it is composed of alpha and non-alpha (or beta) subunits [].Glycine receptor, an inhibitory chloride ion channel composed of alpha and beta subunits [].Gamma-aminobutyric acid (GABA) receptor, an inhibitory chloride ion channel; at least four types of subunits (alpha, beta, gamma and delta) are known [].Serotonin 5HT3 receptor, of which there are seven major types (5HT3-5HT7) [].Glutamate receptor, an excitatory cation channel of which at least three types have been described (kainate, N-methyl-D-aspartate (NMDA) and quisqualate) [].These receptors possess a pentameric structure (made up of varying subunits), surrounding a central pore. All known sequences of subunits from neurotransmitter-gated ion-channels are structurally related. They are composed of a large extracellular glycosylated N-terminal ligand-binding domain, followed by three hydrophobic transmembrane regions which form the ionic channel, followed by an intracellular region of variable length. A fourth hydrophobic region is found at the C-terminal of the sequence [, ].Gamma-aminobutyric acid type A (GABAA) receptors are members of the neurotransmitter ligand-gated ion channels: they mediate neuronal inhibition on binding GABA. The effects of GABA on GABAA receptors are modulated by a range of therapeutically important drugs, including barbiturates, anaesthetics and benzodiazepines (BZs) []. The BZs are a diverse range of compounds, including widely prescribed drugs, such as librium and valium, and their interaction with GABAA receptors provides the most potent pharmacological means of distinguishing different GABAA receptor subtypes.GABAA receptors are pentameric membrane proteins that operate GABA-gated chloride channels []. Eight types of receptor subunit have been cloned, with multiple subtypes within some classes: alpha 1-6, beta 1-4, gamma 1-4, delta, epsilon, pi, rho 1-3 and theta [, ]. Subunits are typically 50-60kDa in size and comprise a long N-terminal extracellular domain, containing a putative signal peptide and a disulphide-bonded beta structural loop; 4 putative transmembrane (TM) domains; and a large cytoplasmic loop connecting the third and fourth TM domains. Amongst family members, the large cytoplasmic loop displays the most divergence in terms of primary structure, the TM domains showing the highest level of sequence conservation [].Most GABAA receptors contain one type of alpha and beta subunit, and a single gamma polypeptide in a ratio of 2:2:1 [], though in some cases other subunits such as epsilon or delta may replace gamma. The BZ binding site is located at the interface of adjacent alpha and gamma subunits; therefore, the type of alpha and gamma subunits present is instrumental in determining BZ selectivity and sensitivity. Receptors can be categorised into 3 groups based on their alpha subunit content and, hence, sensitivity to BZs: alpha 1-containing receptors have greatest sensitivity towards BZs (type I); alpha 2, 3 and 5-containing receptors have similar but distinguishable properties (type II); and alpha 4- and 6-containing assemblies have very low BZ affinity []. A conserved histidine residue in the alpha subunit of type I and II receptors is believed to be responsible for BZ affinity []. GABAA receptors can be characterised by their sensitivitytowards a selective antagonist, bicuculline. A GABA receptor has been identified that is insensitive to bicuculline and classical GABAA modulators but has an enhanced affinity for GABA. This receptor, unlike most GABAA receptors, is composed principally of rho subunits and was initially termed 'GABAC' in recognition of its altered pharmacology []. Despite these differences, rho subunits are generally considered to be part of the GABAAfamily of receptor proteins due to similarities in sequence and topology.Whilst early studies supported the view that rho subunits assembled to forma homopentamer, it has been shown that a mutant rho 1 protein is able tocoassemble with GABAA gamma 2 subunits as well as the glycine receptor alphasubunit. Rho subunit mRNA occurs prominently in both human and ratretina [], each subunit showing a characteristic pattern of spatial expression. In rat retina, rho 1 mRNA has been detected only in bipolarcells, whereas rho 2 transcripts have been detected in both bipolar andganglion cells. In retinal tissues, expression of rho 3 mRNA is exclusive toganglion cells. Reverse transcriptase PCR (RT-PCR) and in situhybridisation have shown rho transcripts also to be present in other regionsof the brain, specifically those involved in visual signal processing, suchas the superior colliculus and visual cortex.This entry represents Rho 2 subunits.
Neurotransmitter ligand-gated ion channels are transmembrane receptor-ion channel complexes that open transiently upon binding of specific ligands, allowing rapid transmission of signals at chemical synapses [, ]. Five of these ion channel receptor families have been shown to form a sequence-related superfamily:Nicotinic acetylcholine receptor (AchR), an excitatory cation channel in vertebrates and invertebrates; in vertebrate motor endplates it is composed of alpha, beta, gamma and delta/epsilon subunits; in neurons it is composed of alpha and non-alpha (or beta) subunits [].Glycine receptor, an inhibitory chloride ion channel composed of alpha and beta subunits [].Gamma-aminobutyric acid (GABA) receptor, an inhibitory chloride ion channel; at least four types of subunits (alpha, beta, gamma and delta) are known [].Serotonin 5HT3 receptor, of which there are seven major types (5HT3-5HT7) [].Glutamate receptor, an excitatory cation channel of which at least three types have been described (kainate, N-methyl-D-aspartate (NMDA) and quisqualate) [].These receptors possess a pentameric structure (made up of varying subunits), surrounding a central pore. All known sequences of subunits from neurotransmitter-gated ion-channels are structurally related. They are composed of a large extracellular glycosylated N-terminal ligand-binding domain, followed by three hydrophobic transmembrane regions which form the ionic channel, followed by an intracellular region of variable length. A fourth hydrophobic region is found at the C-terminal of the sequence [, ].Gamma-aminobutyric acid type A (GABAA) receptors are members of the neurotransmitter ligand-gated ion channels: they mediate neuronal inhibition on binding GABA. The effects of GABA on GABAA receptors are modulated by a range of therapeutically important drugs, including barbiturates, anaesthetics and benzodiazepines (BZs) []. The BZs are a diverse range of compounds, including widely prescribed drugs, such as librium and valium, and their interaction with GABAA receptors provides the most potent pharmacological means of distinguishing different GABAA receptor subtypes.GABAA receptors are pentameric membrane proteins that operate GABA-gated chloride channels []. Eight types of receptor subunit have been cloned, with multiple subtypes within some classes: alpha 1-6, beta 1-4, gamma 1-4, delta, epsilon, pi, rho 1-3 and theta [, ]. Subunits are typically 50-60kDa in size and comprise a long N-terminal extracellular domain, containing a putative signal peptide and a disulphide-bonded beta structural loop; 4 putative transmembrane (TM) domains; and a large cytoplasmic loop connecting the third and fourth TM domains. Amongst family members, the large cytoplasmic loop displays the most divergence in terms of primary structure, the TM domains showing the highest level of sequence conservation [].Most GABAA receptors contain one type of alpha and beta subunit, and a single gamma polypeptide in a ratio of 2:2:1 [], though in some cases other subunits such as epsilon or delta may replace gamma. The BZ binding site is located at the interface of adjacent alpha and gamma subunits; therefore, the type of alpha and gamma subunits present is instrumental in determining BZ selectivity and sensitivity. Receptors can be categorised into 3 groups based on their alpha subunit content and, hence, sensitivity to BZs: alpha 1-containing receptors have greatest sensitivity towards BZs (type I); alpha 2, 3 and 5-containing receptors have similar but distinguishable properties (type II); and alpha 4- and 6-containing assemblies have very low BZ affinity []. A conserved histidine residue in the alpha subunit of type I and II receptors is believed to be responsible for BZ affinity []. GABAA receptors can be characterised by their sensitivitytowards a selective antagonist, bicuculline. A GABA receptor has been identified that is insensitive to bicuculline and classical GABAA modulators but has an enhanced affinity for GABA. This receptor, unlike most GABAA receptors, is composed principally of rho subunits and was initially termed 'GABAC' in recognition of its altered pharmacology []. Despite these differences, rho subunitsare generally considered to be part of the GABAAfamily of receptor proteins due to similarities in sequence and topology.Whilst early studies supported the view that rho subunits assembled to forma homopentamer, it has been shown that a mutant rho 1 protein is able tocoassemble with GABAA gamma 2 subunits as well as the glycine receptor alphasubunit. Rho subunit mRNA occurs prominently in both human and ratretina [], each subunit showing a characteristic pattern of spatial expression. In rat retina, rho 1 mRNA has been detected only in bipolarcells, whereas rho 2 transcripts have been detected in both bipolar andganglion cells. In retinal tissues, expression of rho 3 mRNA is exclusive toganglion cells. Reverse transcriptase PCR (RT-PCR) and in situhybridisation have shown rho transcripts also to be present in other regionsof the brain, specifically those involved in visual signal processing, suchas the superior colliculus and visual cortex.This entry represents Rho 1 subunits.
This group of sequences are characterised by a cysteine protease domain, corresponding to MEROPS peptidase family C58 (clan CA), found in proteins of bacteria that include plant pathogens (Pseudomonas syringae), root nodule bacteria, and intracellular pathogens (e.g. Yersinia pestis, Haemophilus ducreyi, Pasteurella multocida, Chlamydia trachomatis) of animal hosts. The domain features a catalytic triad of Cys, His, and Asp. Sequences can be extremely divergent outside of a few well-conserved motifs. YopT, a virulence effector protein of Y. pestis, cleaves and releases host cell Rho GTPases from the membrane, thereby disrupting the actin cytoskeleton. Members of the family from pathogenic bacteria are likely to be pathogenesis factors [].
This entry represents the PH domain found in the N terminus of type II inositol 1,4,5-trisphosphate 5-phosphatase (INPP5B). The structure of this domain has been revealed []. INPP5B hydrolyses phosphatidylinositol 4,5-bisphosphate (PtIns(4,5)P2) and the signalling molecule phosphatidylinositol 1,4,5-trisphosphate (PtIns(1,4,5)P3), and thereby modulates cellular signalling events [].INPP5B contains a PH domain, a 5-phosphatase domain, an ASH domain and a Rho-GAP domain. It shares ~45% sequence identity with OCRL1 (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 [].
