• The other cluster was a relatively open 4Fe cluster with a mix of sulfur and oxygen bridging atoms bound by seven amino acid residues including three cysteines, two glutamates, one histidine and a stable persulfido-cysteine, previously seen only as an intermediate active site species (RESID:AA0269). (proteininformationresource.org)
  • This region includes two folding domains and all seven of the cofactor binding residues observed in the Desulfovibrio vulgaris structure. (proteininformationresource.org)
  • The proteins encoded by members of the Dbl family share a common 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. (embl-heidelberg.de)
  • Typically Rho proteins are 190-250 residues long and consist only of the GTPase domain and short terminal C-terminal extensions. (biomedcentral.com)
  • The homology models are validated by predicting the effect of mutating hot spot residues in the interface, and residues important for the specificity of interaction with different Ras proteins. (crg.es)
  • Ligand-binding characteristics and related structural features of the expressed goldfish kainate receptors: identification of a conserved disulfide bond and three residues important for ligand binding. (aspetjournals.org)
  • 3) Mutations of Q12, A53, and Y54 of GFKAR beta indicate that these three residues are important for ligand binding (particularly L-glutamate), which is consistent with the sequence homology to bacterial periplasmic binding proteins. (aspetjournals.org)
  • These proteins share a core structure, the conserved G-box (GDP/GTP) binding domain, of approximately 170 residues [ 3 ]. (oncotarget.com)
  • Based on mutagenesis we suggested that the tips of two adjacent helical domains form a composite membrane-binding surface involving hydrophobic and positively charged residues. (researchatlanta.org)
  • We found that residues at the Cyclothiazide tip of the helical domain directly insert into membranes. (researchatlanta.org)
  • Two basic residues are key in binding with phosphoinositides: one forms hydrogen bonds with the 3-phosphate of PI(3)P and another forms hydrogen bonds with the 4-and 5-hydroxyl groups of PI(3)P. (nih.gov)
  • Most of the ERCC1 protein is related at the sequence level to the C-terminus of the XPF protein, but residues in the nuclease domain are not present. (dict.cc)
  • HOMOLOBIND identifies residues in protein sequences with significant similarity to structurally characterized binding sites. (fredpdavis.com)
  • The homology transfer procedure predicts residues in ligand and protein binding sites with estimated true positive rates of 98% and 88%, respectively, at 1% false positive rates. (fredpdavis.com)
  • Binding of phosphatidylinositol 3,4,5-trisphosphate to the pleckstrin homology domain of protein kinase B induces a conformational change. (cathdb.info)
  • Members of this subfamily contain PX and Pleckstrin Homology (PH) domains in addition to the catalytic domain. (nih.gov)
  • It contains a catalytic domain, a central coiled-coil domain, and a C-terminal region containing a Rho-binding domain (RBD), a zinc finger, and a pleckstrin homology (PH) domain, in addition to other motifs. (umbc.edu)
  • ICAM-1 has 7 potential N-linked glycosylation sites and shares considerable amino acid sequence homology with ICAM-3 (CD50) and ICAM-2 (CD102). (thermofisher.com)
  • The nickel-containing chain of carbon-monoxide dehydrogenase also has a domain with some sequence similarities to the hybrid cluster proteins. (proteininformationresource.org)
  • It does not share significant sequence homology with other subtypes of small G-protein GEF motifs such as the Cdc25 domain and the Sec7 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. (embl-heidelberg.de)
  • Click on the pictures below to see domain assignment details for that sequence. (cam.ac.uk)
  • All members contain the sequence motifs characteristic of all GTP-binding proteins, bind to GDP and GTP with high affinity. (biomedcentral.com)
  • Based on a limited sequence homology among members of the Ras association (RA) and Ras binding (RB) sub-domain families of the ubiquitin super-family, we have built structural homology models of Ras proteins in complex with different RA and RB domains, using the FOLD-X software. (crg.es)
  • Human G-CSF R is 863 amino acids (aa) in length, with a 604 aa extracellular domain, a 26 aa transmembrane domain, and a 183 aa cytoplasmic domain that include a 23 amino acid signal sequence. (rndsystems.com)
  • Results The tip of the helical domain is a primary membrane-binding site Mammalian EHDs share a sequence identity of 70 - 85% and display a common domain architecture (Figure 1A B). Based on their location in the crystal structure and mutagenesis. (researchatlanta.org)
  • The structural comparison of binding sites is especially useful when applied on distantly related proteins as a comparison solely based on the amino acid sequence is not sufficient in such cases. (uni-marburg.de)
  • The DH domain is composed of three structurally conserved regions separated by more variable regions. (embl-heidelberg.de)
  • Low-molecular-weight kainate receptors from nonmammalian vertebrate brain belong structurally to the ionotropic glutamate receptor superfamily. (aspetjournals.org)
  • 2007 X-ray structure analysis showed that the G domains of EHD2 and dynamin are structurally related (Daumke et al. (researchatlanta.org)
  • 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. (embl-heidelberg.de)
  • We generated a library of FLNa fragments to examine their F-actin binding to define the structural properties of FLNa that enable its various functions. (rupress.org)
  • They are small (21-25 kDa) molecules that share structural homology and become activated only when bound to GTP. (biomedcentral.com)
  • A structural feature that distinguishes the Rho proteins from other small GTPases is the so-called Rho insert domain located between a β strand and an α helix within the small GTPase domain [ 1 - 3 ]. (biomedcentral.com)
  • A critical step in our approach is to use different templates of Ras complexes, in order to account for the structural variation among the RA and RB domains. (crg.es)
  • In this study, two previously cloned goldfish kainate receptor subunits (GFKAR alpha and GFKAR beta) were transiently expressed in human embryonic kidney 293 cells, and their ligand-binding properties and some associated structural features were characterized, resulting in the following findings. (aspetjournals.org)
  • These data lend further evidence in support of a model of glutamate receptor topology with three transmembrane segments and reveal several general structural features of the extracellular ligand-binding domain of the kainate receptors. (aspetjournals.org)
  • These results are consistent with the notion that the ligand-binding domain has close structural similarities to bacterial periplasmic binding proteins. (aspetjournals.org)
  • Protein S, a Ca(2+)-binding spore-coat protein from the soil bacterium Myxococcus xanthus exhibits a high degree of sequential and structural homology with gammaB-crystallin from the vertebrate eye lens. (protabank.org)
  • 2012 Despite recent progress in Cyclothiazide structural studies our previous structural analysis did not reveal the conformational changes associated with membrane-binding of EHD2. (researchatlanta.org)
  • Structural determinants required for the interaction between Rho GTPase and the GTPase-activating domain of p190. (embl-heidelberg.de)
  • Here, we present three 3D structural models of human Mfsd2a derived by homology modelling using MelB- and LacY-based crystal structures, and refined by biochemical analysis. (neurosciencenews.com)
  • In addition to a conserved sodium-binding site, three unique structural features were identified: A phosphate headgroup binding site, a hydrophobic cleft to accommodate a hydrophobic hydrocarbon tail, and three sets of ionic locks that stabilize the outward-open conformation. (neurosciencenews.com)
  • 11] The resultant mutations were interpreted to result in local structural changes in the ACVR1 protein, as revealed by interrogating homology models of the native and mutated ACVR1 kinase domains. (medscape.com)
  • Members of the IL-1 R family contain extracellular Ig-like domains and mediate signaling through an intracellular Toll/IL-1 R (TIR) domain. (rndsystems.com)
  • 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. (embl-heidelberg.de)
  • intracellular domain. (nexelis.com)
  • It shares about 30% homology with members of the fibroblast growth factor receptor/platelet-derived growth factor receptor superfamily, and contains a single putative transmembrane domain and a conserved intracellular tyrosine kinase domain, whereas lacks an extracellular domain for binding specific ligands [ 8 ]. (biomedcentral.com)
  • A comparison of the conserved with the variable regions of the intracellular domain of the prolactin receptor: consequences for molecular modeling. (tueventoenvivo.com)
  • Additionally, it is shown whether each cytokine belongs to the beta-trefoil, four helix bundle, or cysteine-knot superfamily and their subfamily designation. (rndsystems.com)
  • Serine/Threonine Kinases (STKs), Citron Rho-interacting kinase (CRIK) subfamily, catalytic (c) domain. (umbc.edu)
  • The CRIK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. (umbc.edu)
  • ICAM-1 (CD54) is an 85-110 kDa single-chain type 1 integral membrane glycoprotein with an extracellular domain of five immunoglobulin superfamily repeats, a transmembrane region and a cytoplasmic domain. (thermofisher.com)
  • FLNa dimeric subunits have N-terminal spectrin family F-actin binding domains (ABDs) and an elongated flexible segment of 24 immunoglobulin (Ig) repeats. (rupress.org)
  • We find that Ig repeats 9-15 contain an F-actin-binding domain necessary for high avidity F-actin binding. (rupress.org)
  • Ig repeats 16-24, where most FLNa-binding partners interact, do not bind F-actin, and thus F-actin does not compete with Ig repeat 23 ligand, FilGAP. (rupress.org)
  • Ig repeats 16-24 have a compact structure that suggests their unfolding may accommodate pre-stress-mediated stiffening of F-actin networks, partner binding, mechanosensing, and mechanoprotection properties of FLNa. (rupress.org)
  • Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases Also called Dbl-homologous (DH) domain. (embl-heidelberg.de)
  • Activation of Rho proteins through release of bound GDP and subsequent binding of GTP, is catalysed by guanine nucleotide exchange factors (GEFs) in the Dbl family. (embl-heidelberg.de)
  • Small G-proteins, monomeric GTPases, or the RAS (Rat sarcoma) superfamily are a large family of small guanine nucleotide-binding proteins with molecular weights ranging from 20 to 30 kDa [ 1 , 2 ]. (oncotarget.com)
  • The G domains of EHDs bind to adenine rather than guanine nucleotides (Lee et al. (researchatlanta.org)
  • DyNamin Binding Protein (DNMBP), also called Tuba, is a Cdc42-specific Guanine nucleotide Exchange Factor (GEF) that binds dynamin and various actin regulatory proteins. (nih.gov)
  • Analysis of [3H]kainate binding to wild-type and cysteine mutations of GFKAR beta indicate that in the absence of the disulfide bond, the affinity for kainate is increased 3-fold. (aspetjournals.org)
  • The betagamma-crystallin superfamily consists of a class of homologous two-domain proteins with Greek-key fold. (protabank.org)
  • Cytokines in the TNF superfamily bind to oligomeric, type I or type II transmembrane proteins that have multiple extracellular cysteine-rich domains. (rndsystems.com)
  • BCMA is a type III membrane protein containing one extracellular cysteine rich domain. (nexelis.com)
  • The C-terminal EH domains interact with linear peptide motifs containing an Asn-Pro-Phe (NPF) motif (de Beer et al. (researchatlanta.org)
  • Cell activation by G-CSF is mediated by a type I membrane protein belonging to the cytokine receptor superfamily. (rndsystems.com)
  • Their importance has been even further enhanced by the homology now identified between them and the membrane attack complex/perforin (MACPF) family of proteins, which includes several components of the complement cascade as well as perforin itself. (ox.ac.uk)
  • Phospholipase D (PLD) catalyzes the hydrolysis of the phosphodiester bond of phosphatidylcholine to generate membrane-bound phosphatidic acid and choline. (nih.gov)
  • BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. (nih.gov)
  • regulatory switch in EHD2 and demonstrate the versatility of EPR to study structure and function of dynamin superfamily proteins. (researchatlanta.org)
  • 2007 Similar to other dynamin superfamily members EHDs can tubulate negatively charged liposomes and oligomerize in ring-like structures around them (Daumke et al. (researchatlanta.org)
  • G domains of EHD2 stably dimerize via a nucleotide-independent interface which is not conserved in other dynamin superfamily proteins. (researchatlanta.org)
  • A second interface in the G domain promotes nucleotide-dependent assembly in dynamin and septin superfamily proteins (Schwefel et al. (researchatlanta.org)
  • Rho GTPases work as sensitive molecular switches existing either in an inactive, GDP-bound form or an active GTP-bound form. (biomedcentral.com)
  • Like all other GTPases, Rho proteins act as molecular switches, with an active GTP-bound form and an inactive GDP-bound form. (embl-heidelberg.de)
  • All IL-1 family members share a conserved beta-trefoil structure and bind to members of the IL-1 receptor (IL-1 R) family. (rndsystems.com)
  • This superfamily is further subdivided into the class I and class II cytokine receptor families. (rndsystems.com)
  • These cytokines belong to the cysteine-knot superfamily and bind to members of the IL-17 receptor family. (rndsystems.com)
  • ICAM-1 binds to integrins of type CD11a/CD18 (leukocyte adhesion molecule, LFA-1), or CD11b/CD18 (Mac-1) and is exploited by Rhinovirus as a receptor. (thermofisher.com)
  • BCMA, B cell maturation antigen, is a member of the TNF receptor superfamily. (nexelis.com)
  • Binding of G-CSF to its receptor induces dimerization or oligomerization of the receptor activating cytoplasmic tyrosine kinases. (rndsystems.com)
  • It was determined that Ear2 negatively regulates renin expression by competing with retinoic acid receptor/ retinoid X receptor (RAR/RXR) for binding to the retinoic acid response elements (RARE) on the renin enhancer [ 13 ]. (biomedcentral.com)
  • Protein binding site comparisons are frequently used receptor-based techniques in early stages of the drug development process. (uni-marburg.de)
  • Results DIM, but not I3C, increased adipocyte differentiation through upregulation of peroxisome proliferator‐activated receptor γ and CCAAT/enhancer‐binding protein α. (researchgate.net)
  • It transfers binding sites from LIGBASE ( http://salilab.org/ligbase ) and PIBASE ( http://fredpdavis.com/pibase ) through ASTRAL/ASTEROIDS ( http://astral.berkeley.edu ) alignments onto SUPERFAMILY ( http://supfam.org ) domain assignments. (fredpdavis.com)
  • In this chapter I aim to provide an overview of our understanding of the interaction between CDCs and other members of what is now called the MACPF/CDC superfamily, with their target membranes. (ox.ac.uk)
  • While not all MACPF domains are involved in pore formation-for example, C6 and C8beta--they are all apparently involved in action on membranes. (ox.ac.uk)
  • The PX domain is involved in targeting of proteins to PI-enriched membranes, and may also be involved in protein-protein interaction. (nih.gov)
  • The BAR domain of DNMBP may be involved in binding to membranes. (nih.gov)
  • Many members of the TNF superfamily regulate apoptosis and/or immune cell functions, such as T cell co-stimulation, natural killer cell activation, and B cell homeostasis. (rndsystems.com)
  • The superfamily is classified into five subfamilies based on the cellular processes that they regulate [ 2 ]. (oncotarget.com)
  • One protein that has been identified to bind to and regulate the renin enhancer is Ear2 [ 13 ]. (biomedcentral.com)
  • The cystic fibrosis transmembrane conductance regulator (CFTR) is a member of the ATP binding cassette (ABC) transporter superfamily. (ucl.ac.uk)
  • Importantly, the work identifies new binding features of the transporter, providing insight into the transport mechanism of Mfsd2a. (neurosciencenews.com)
  • Major Facilitator Superfamily Domain containing 2A (Mfsd2a) was recently characterized as a sodium-dependent lysophosphatidylcholine (LPC) transporter expressed at the blood-brain barrier endothelium. (neurosciencenews.com)
  • It comprises the following groups of actin-binding domains: Actinin-type (including spectrin, fimbrin, ABP-280) Calponin-type A comprehensive review of proteins containing this type of actin-binding domains is given in. (wikipedia.org)
  • Actin binding domains present in duplicate at the N-termini of spectrin-like proteins (including dystrophin, alpha-actinin). (embl.de)
  • A number of actin-binding proteins, including spectrin, alpha-actinin and fimbrin, contain a 250 amino acid stretch called the actin binding domain (ABD). (embl.de)
  • The CH domain is involved in actin binding in some members of the family. (wikipedia.org)
  • The Periodic Table of Cytokine and Chemokine Families poster includes members of the tumor necrosis factor (TNF) superfamily, and cytokines belonging to the different families of interleukins, interferons, and chemokines. (rndsystems.com)
  • Columns 11 through 13 in the poster show the members of the tumor necrosis factor (TNF) superfamily. (rndsystems.com)
  • Like all members of the Ras superfamily, the Rho proteins cycle between active GTP-bound and inactive GDP-bound conformational states. (embl-heidelberg.de)
  • BCMA and TACI have both been shown to bind to APRIL and BAFF, members of the TNF ligand superfamily. (nexelis.com)
  • [ 5 ] BMPs are members of the transforming growth factor-beta superfamily and play a role in the development of bone and other tissues. (medscape.com)
  • The receptors for these cytokines contain extracellular Ig-like domains, similar to the IL-1 R family, but they have cytoplasmic domains with tyrosine kinase activity. (rndsystems.com)
  • Catalytic domain of the Protein Serine/Threonine Kinase, Citron Rho-interacting kinase. (umbc.edu)
  • Proteins in this family form homotrimers or in some cases, heterotrimers, and share a common extracellular domain known as the TNF homology domain (THD). (rndsystems.com)
  • Trio and its homologue UNC-73 are unique within the Dbl family insomuch as they encode two distinct DH/PH domain modules. (embl-heidelberg.de)
  • The Rho family of GTP-binding proteins has been implicated in the regulation of various cellular functions including actin cytoskeleton-dependent morphological change. (embl-heidelberg.de)
  • An amino-terminal portion conserved among a subset of Dbl family proteins is sufficient for the binding of Gbetagamma. (embl-heidelberg.de)
  • Rho GTPases represent a family of small GTP-binding proteins involved in cell cytoskeleton organization, migration, transcription, and proliferation. (biomedcentral.com)
  • Within their GTPase domains, they share approximately 30% amino acid identity with the Ras proteins and 40-95% identity within the family. (biomedcentral.com)
  • In turn, GTP-bound active GTPases can interact with a plethora of different effectors which mediate the different cellular functions of this family of proteins. (biomedcentral.com)
  • The domain is about 100 amino acids in length and is composed of four alpha helices. (wikipedia.org)
  • The DH domain is composed of 11 alpha helices that are folded into a flattened, elongated alpha-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. (embl-heidelberg.de)
  • The domain is composed of seven alpha helices. (embl-heidelberg.de)
  • Moving to the right, the next eight families shown in the poster belong to the four-helix bundle cytokine superfamily. (rndsystems.com)
  • This gene is highly expressed in fetal brain and encodes a protein of relative molecular mass 91K, named oligophrenin-1, which contains a domain typical of a Rho-GTPase-activating protein (rhoGAP). (embl-heidelberg.de)
  • Proteins of the myosin superfamily are ATP-dependent molecular motors that travel unidirectionally along actin filaments. (ciliate.org)
  • In this work, we explored possible conformational states of the CFTR gating cycle by means of homology modeling. (ucl.ac.uk)
  • Further fine mapping in a large population with over 1,000 F 2 plants narrowed this region to 39.08 Kb harboring two genes, Cla97C01G008760 and Cla97C01G008770 , which encode phytoene synthase ( ClPsy1 ) and GATA zinc finger domain-containing protein, respectively. (researchsquare.com)
  • Human BCMA is a 184 amino acid (aa) protein consisting of a 54 aa extracellular domain, a 23 aa transmembrane domain, and a 107 aa. (nexelis.com)
  • These mutations typically led to a truncation in the cytoplasmic domain of the G-CSF R leading to maturation arrest of neutrophil precursors in the bone marrow and neutropenia in peripheral blood (2). (rndsystems.com)
  • The N-terminal CH domain has the intrinsic ability to bind actin, albeit with lower affinity than the complete ABD, whereas the C-terminal CH bind actin extremely weakly or not at all. (embl.de)
  • Calorimetric analysis of the Ca(2+)-binding betagamma-crystallin homolog protein S from Myxococcus xanthus: intrinsic stability and mutual stabilization of domains. (protabank.org)
  • The p53 interacting partner protein NUMB (homology of numb protein) preserves this intrinsic cellular asymmetry by preventing ubiquitin-mediated proteolysis of p53 catalyzed by the MDM2 E3 ubiquitin ligase 11 . (nature.com)
  • Dimerization, mediated by FLNa Ig repeat 24, accounts for rigid high-angle FLNa/F-actin branching resistant to bending by thermal forces, and high avidity F-actin binding and cross-linking. (rupress.org)
  • BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. (nih.gov)
  • Transitions between open and closed states of CFTR are regulated by ATP binding and hydrolysis on the cystosolic nucleotide binding domains (NBDs), which are coupled with the transmembrane domains (TMDs) forming the pathway for anion permeation. (ucl.ac.uk)
  • 2012 EHDs are composed of an N-terminal Cyclothiazide extended GTPase domain (G domain) followed by a helical domain and a C-terminal Eps15-homology (EH) domain. (researchatlanta.org)
  • The structure of the GTPase-activating domain from p50rhoGAP. (embl-heidelberg.de)
  • In particular, we propose that Arg 85 and Asn 194 are involved in binding G proteins and enhancing GTPase activity. (embl-heidelberg.de)
  • 1998 In the EHD2 dimer EH domains bind on top of the opposing G domains and may block the nucleotide-dependent assembly interface of the G domain. (researchatlanta.org)
  • These domains cross-link actin filaments into bundles and networks. (embl.de)
  • This region is an homology domain that is observed in at least four homeomorphic superfamilies [8] and is presented as an alignment in Figure 1. (proteininformationresource.org)
  • Carbohydrate-binding module 3 / Carbohydrate-binding module 3 superfamily / CBM3 (carbohydrate binding type-3) domain profile. (pdbj.org)
  • The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. (nih.gov)
  • Based on these results, we can establish energy thresholds above, or below which, we can predict with 96% confidence that a RA/RB domain will or will not interact with Ras. (crg.es)
  • Recognizing and defining true Ras binding domains II: in silico prediction based on homology modelling and energy calculations. (crg.es)
  • In the present work, accelerated methods for the comparison of protein binding sites as well as an extended procedure for the assessment of ligand poses in protein binding sites are presented. (uni-marburg.de)
  • Methods for the assessment of ligand poses in protein binding sites are also used in the early phase of drug development within docking programs. (uni-marburg.de)
  • The myosin heavy chain proteins are comprised of three domains: a head (motor) domain responsible for ATP hydrolysis at the N-terminus, a neck (lever arm) region, and a C-terminal tail region. (ciliate.org)