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(-) Description

Title :  CRYSTAL STRUCTURE OF THE VPS9 DOMAIN OF RABEX-5
 
Authors :  A. Delprato, E. Merithew, D. G. Lambright
Date :  06 Jul 04  (Deposition) - 21 Sep 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  A
Keywords :  Vps9 Domain, Rab5 Guanine-Nucleotide Exchange Factor, Gef, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Delprato, E. Merithew, D. G. Lambright
Structure, Exchange Determinants, And Family-Wide Rab Specificity Of The Tandem Helical Bundle And Vps9 Domains Of Rabex-5
Cell(Cambridge, Mass. ) V. 118 607 2004
PubMed-ID: 15339665  |  Reference-DOI: 10.1016/J.CELL.2004.08.009
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RAB5 GDP/GTP EXCHANGE FACTOR
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentVPS9
    GeneRABGEF1
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRABEX-5

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric/Biological Unit (2, 10)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2MSE9Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:274 , HIS A:297BINDING SITE FOR RESIDUE MG A 1

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1VPS9PS51205 VPS9 domain profile.RABX5_HUMAN449-592  1A:232-375

(-) Exons   (0, 0)

(no "Exon" information available for 1TXU)

(-) 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:254
 aligned with RABX5_HUMAN | Q9UJ41 from UniProtKB/Swiss-Prot  Length:708

    Alignment length:293
                                   321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601   
          RABX5_HUMAN   312 ETDRVSKEFIEFLKTFHKTGQEIYKQTKLFLEGMHYKRDLSIEEQSECAQDFYHNVAERMQTRGKERRFHHVGQAGLELLTSGDPPASASQSAGNTGVEPPHPAVPPERVEKIMDQIEKYIMTRLYKYVFCPETTDDEKKDLAIQKRIRALRWVTPQMLCVPVNEDIPEVSDMVVKAITDIIEMDSKRVPRDKLACITKCSKHIFNAIKITKNEPASADDFLPTLIYIVLKGNPPRLQSNIQYITRFCNPSRLMTGEDGYYFTNLCCAVAFIEKLDAQSLNLSQEDFDRYMSG 604
               SCOP domains d1txua_ A: Rab5 GDP/GTP exchange factor (Rabex-5)                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------VPS9-1txuA01 A:268-371                                                                                  ---------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.---------------------------------------....hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------VPS9  PDB: A:232-375 UniProt: 449-592                                                                                                           ------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1txu A 134 ETDRVSKEFIEFLKTFHKTGQEIYKQTKLFLEGmHYKRDLSIEEQSECAQDFYHNVAERmQTRGK---------------------------------------VPPERVEKImDQIEKYImTRLYKYVFCPETTDDEKKDLAIQKRIRALRWVTPQmLCVPVNEDIPEVSDmVVKAITDIIEmDSKRVPRDKLACITKCSKHIFNAIKITKNEPASADDFLPTLIYIVLKGNPPRLQSNIQYITRFCNPSRLmTGEDGYYFTNLCCAVAFIEKLDAQSLNLSQEDFDRYmSG 387
                                   143       153       163   |   173       183       193    |    -         -         -         -    |  204   |   214 |     224       234       244       254       264  |    274   |   284       294       304       314       324       334       344   |   354       364       374       384|  
                                                           167-MSE                   193-MSE8                                     199      208-MSE 216-MSE                             252-MSE        267-MSE    278-MSE                                                               348-MSE                              385-MSE

   Legend:   → Mismatch (orange background)
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    → 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  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (28, 28)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RABX5_HUMAN | Q9UJ41)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0017137    Rab GTPase binding    Interacting selectively and non-covalently with Rab protein, any member of the Rab subfamily of the Ras superfamily of monomeric GTPases.
    GO:0017112    Rab guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Rab 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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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).
    GO:0061630    ubiquitin protein ligase activity    Catalysis of the transfer of ubiquitin to a substrate protein via the reaction X-ubiquitin + S -> X + S-ubiquitin, where X is either an E2 or E3 enzyme, the X-ubiquitin linkage is a thioester bond, and the S-ubiquitin linkage is an amide bond: an isopeptide bond between the C-terminal glycine of ubiquitin and the epsilon-amino group of lysine residues in the substrate or, in the linear extension of ubiquitin chains, a peptide bond the between the C-terminal glycine and N-terminal methionine of ubiquitin residues.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006897    endocytosis    A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
    GO:1900235    negative regulation of Kit signaling pathway    Any process that stops, prevents or reduces the frequency, rate or extent of Kit signaling pathway.
    GO:0046580    negative regulation of Ras protein signal transduction    Any process that stops, prevents, or reduces the frequency, rate or extent of Ras protein signal transduction.
    GO:0050728    negative regulation of inflammatory response    Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response.
    GO:1900165    negative regulation of interleukin-6 secretion    Any process that stops, prevents or reduces the frequency, rate or extent of interleukin-6 secretion.
    GO:0002686    negative regulation of leukocyte migration    Any process that stops, prevents, or reduces the frequency, rate, or extent of leukocyte migration.
    GO:0033004    negative regulation of mast cell activation    Any process that stops, prevents, or reduces the frequency, rate, or extent of mast cell activation.
    GO:0043305    negative regulation of mast cell degranulation    Any process that stops, prevents, or reduces the rate of mast cell degranulation.
    GO:0001933    negative regulation of protein phosphorylation    Any process that stops, prevents or reduces the rate of addition of phosphate groups to amino acids within a protein.
    GO:0048261    negative regulation of receptor-mediated endocytosis    Any process that stops, prevents, or reduces the frequency, rate or extent of receptor mediated endocytosis, the uptake of external materials by cells, utilizing receptors to ensure specificity of transport.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0006612    protein targeting to membrane    The process of directing proteins towards a membrane, usually using signals contained within the protein.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
    GO:0060368    regulation of Fc receptor mediated stimulatory signaling pathway    Any process that modulates the rate, frequency or extent of the Fc receptor mediated stimulatory signaling pathway. The Fc receptor mediated stimulatory signaling pathway is a series of molecular signals generated as a consequence of a the binding of the Fc portion of an immunoglobulin by an Fc receptor capable of activating or perpetuating an immune response. The Fc portion of an immunoglobulin is its C-terminal constant region.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005769    early endosome    A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    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:0031982    vesicle    Any small, fluid-filled, spherical organelle enclosed by membrane.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        RABX5_HUMAN | Q9UJ412c7m 2c7n 2ot3 4n3x 4n3y 4n3z 4q9u

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