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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SMALL G PROTEIN RAP2A WITH GDP
 
Authors :  J. Cherfils, J. Menetrey, G. Le Bras
Date :  01 Aug 97  (Deposition) - 24 Dec 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Gtp-Binding Protein, Small G Protein, Rap2, Gdp, Ras (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Cherfils, J. Menetrey, G. Le Bras, I. Janoueix-Lerosey, J. De Gunzburg, J. R. Garel, I. Auzat
Crystal Structures Of The Small G Protein Rap2A In Complex With Its Substrate Gtp, With Gdp And With Gtpgammas.
Embo J. V. 16 5582 1997
PubMed-ID: 9312017  |  Reference-DOI: 10.1093/EMBOJ/16.18.5582
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RAP2A
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:17 , GDP A:170 , HOH A:171 , HOH A:172 , HOH A:173 , HOH A:174BINDING SITE FOR RESIDUE MG A 168
2AC2SOFTWAREASP A:38 , HOH A:227 , HOH A:239 , HOH A:240BINDING SITE FOR RESIDUE MG A 169
3AC3SOFTWAREGLY A:13 , VAL A:14 , GLY A:15 , LYS A:16 , SER A:17 , ALA A:18 , PHE A:28 , ILE A:29 , GLU A:30 , LYS A:31 , ASN A:116 , LYS A:117 , ASP A:119 , LEU A:120 , SER A:146 , ALA A:147 , MG A:168 , HOH A:171 , HOH A:172 , HOH A:173 , HOH A:179BINDING SITE FOR RESIDUE GDP A 170

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1KAO)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1KAO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1KAO)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RASPS51421 small GTPase Ras family profile.RAP2A_HUMAN1-183  1A:1-167

(-) Exons   (2, 2)

Asymmetric/Biological Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002453041aENSE00000853869chr13:98086476-98087038563RAP2A_HUMAN1-1051051A:1-105105
1.3bENST000002453043bENSE00001128147chr13:98116459-981202443786RAP2A_HUMAN105-183791A:105-16763

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:167
 aligned with RAP2A_HUMAN | P10114 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:167
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       
          RAP2A_HUMAN     1 MREYKVVVLGSGGVGKSALTVQFVTGTFIEKYDPTIEDFYRKEIEVDSSPSVLEILDTAGTEQFASMRDLYIKNGQGFILVYSLVNQQSFQDIKPMRDQIIRVKRYEKVPVILVGNKVDLESEREVSSSEGRALAEEWGCPFMETSAKSKTMVDELFAEIVRQMNYA 167
               SCOP domains d1kaoa_ A: Rap2a                                                                                                                                                        SCOP domains
               CATH domains 1kaoA00 A:1-167 P-loop containing nucleotide triphosphate hydrolases                                                                                                    CATH domains
               Pfam domains ----Ras-1kaoA01 A:5-166                                                                                                                                               - Pfam domains
         Sec.struct. author ..eeeeeee......hhhhhhhhhh............eeeeeeeee..eeeeeeeee.......hhhhhhhhhh..eeeeeee...hhhhhhhhhhhhhhhhh......eeeeeee.hhhhhh....hhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE RAS  PDB: A:1-167 UniProt: 1-183                                                                                                                                        PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:1-105 UniProt: 1-105                                                                   -------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------------------Exon 1.3b  PDB: A:105-167 UniProt: 105-183 [INCOMPLETE]         Transcript 1 (2)
                 1kao A   1 MREYKVVVLGSGGVGKSALTVQFVTGTFIEKYDPTIEDFYRKEIEVDSSPSVLEILDTAGTEQFASMRDLYIKNGQGFILVYSLVNQQSFQDIKPMRDQIIRVKRYEKVPVILVGNKVDLESEREVSSSEGRALAEEWGCPFMETSAKSKTMVDELFAEIVRQMNYA 167
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Family: Ras (176)

(-) Gene Ontology  (27, 27)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RAP2A_HUMAN | P10114)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003924    GTPase activity    Catalysis of the reaction: GTP + H2O = GDP + phosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0032486    Rap protein signal transduction    A series of molecular signals within the cell that are mediated by a member of the Rap family of proteins switching to a GTP-bound active state.
    GO:0031532    actin cytoskeleton reorganization    A process that is carried out at the cellular level which results in dynamic structural changes to the arrangement of constituent parts of cytoskeletal structures comprising actin filaments and their associated proteins.
    GO:0034613    cellular protein localization    Any process in which a protein is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell.
    GO:0035690    cellular response to drug    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0045198    establishment of epithelial cell apical/basal polarity    The specification and formation of the apicobasal polarity of an epithelial cell.
    GO:0045184    establishment of protein localization    The directed movement of a protein to a specific location.
    GO:0030033    microvillus assembly    Formation of a microvillus, a thin cylindrical membrane-covered projection on the surface of a cell.
    GO:0030336    negative regulation of cell migration    Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration.
    GO:0031954    positive regulation of protein autophosphorylation    Any process that activates or increases the frequency, rate or extent of the phosphorylation by a protein of one or more of its own residues.
    GO:0001934    positive regulation of protein phosphorylation    Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein.
    GO:0072659    protein localization to plasma membrane    A process in which a protein is transported to, or maintained in, a specific location in the plasma membrane.
    GO:0046328    regulation of JNK cascade    Any process that modulates the frequency, rate or extent of signal transduction mediated by the JNK cascade.
    GO:0048814    regulation of dendrite morphogenesis    Any process that modulates the frequency, rate or extent of dendrite morphogenesis.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0007264    small GTPase mediated signal transduction    Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0030496    midbody    A thin cytoplasmic bridge formed between daughter cells at the end of cytokinesis. The midbody forms where the contractile ring constricts, and may persist for some time before finally breaking to complete cytokinesis.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0055037    recycling endosome    An organelle consisting of a network of tubules that functions in targeting molecules, such as receptors transporters and lipids, to the plasma membrane.
    GO:0055038    recycling endosome membrane    The lipid bilayer surrounding a recycling endosome.

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        RAP2A_HUMAN | P101142rap 3rap

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