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(-) Description

Title :  RA DOMAIN OF GUANINE NUCLEOTIDE EXCHANGE FACTOR FOR RAP1
 
Authors :  T. Nagashima, N. Tochio, T. Kigawa, F. Hayashi, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  28 May 04  (Deposition) - 28 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Ubiquitin Fold, Ra, Guanine Nucleotide Exchange, Rap1, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Nagashima, N. Tochio, T. Kigawa, F. Hayashi, S. Yokoyama
Ra Domain Of Guanine Nucleotide Exchange Factor For Rap1
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RAP GUANINE NUCLEOTIDE EXCHANGE FACTOR 5
    Chains: A
    Engineered: YES
    Expression System Plasmid: P030804-93
    Expression System Vector Type: PLASMID
    Fragment: RA DOMAIN
    Gene: KAZUSA CDNA HA06833
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CELL-FREE PROTEIN SYNTHESIS
    Synonym: GUANINE NUCLEOTIDE EXCHANGE FACTOR FOR RAP1, RELATED TO EPAC, REPAC, M-RAS-REGULATED RAP GEF, MR-GEF

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1WGY)

(-) Sites  (0, 0)

(no "Site" information available for 1WGY)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RASGEF_CATPS50009 Ras guanine-nucleotide exchange factors catalytic domain profile.RPGF5_HUMAN345-579  1A:99-104

(-) Exons   (0, 0)

(no "Exon" information available for 1WGY)

(-) Sequences/Alignments

NMR Structure
   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:104
 aligned with RPGF5_HUMAN | Q92565 from UniProtKB/Swiss-Prot  Length:580

    Alignment length:147
                                   243       253       263       273       283       293       303       313       323       333       343       353       363       373       
          RPGF5_HUMAN   234 RGTVTETEEIFCHVYITEHSYVSVKAKVSSIAQEILKVVAEKIQYAEEDLALVAITFSGEKHELQPNDLVISKSLEASGRIYVYRKDLADTLNPFAENEESQQRSMRILGMNTWDLALELMNFDWSLFNSIHEQELIYFTFSRQGSG 380
               SCOP domains d1wgya_ A: Rap guanine nucleotide exchange factor 5, RapGEF5                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeee.....eeee.......hhhhhhhhhhhhh.hhh.eeeeee........................eeeeee.............-------------------------------------------...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------RASGEF_CAT  PDB: A:99-104            PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wgy A   1 GSSGSSGEEIFCHVYITEHSYVSVKAKVSSIAQEILKVVAEKIQYAEEDLALVAITFSGEKHELQPNDLVISKSLEASGRIYVYRKDLADTLNPFAEN-------------------------------------------SGPSSG 104
                                    10        20        30        40        50        60        70        80        90       | -         -         -         -         - |     
                                                                                                                            98                                          99
   Legend:   → Mismatch (orange background)
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  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)

NMR Structure
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1WGY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1WGY)

(-) Gene Ontology  (8, 8)

NMR Structure(hide GO term definitions)
Chain A   (RPGF5_HUMAN | Q92565)
molecular function
    GO:0030742    GTP-dependent 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) using energy from the hydrolysis of GTP.
    GO:0017034    Rap guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Rap family. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    GO:0005088    Ras guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Ras superfamily. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    GO:0005085    guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
biological process
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    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:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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