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P39958

- GDI1_YEAST

UniProt

P39958 - GDI1_YEAST

Protein

Rab GDP-dissociation inhibitor

Gene

GDI1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 117 (01 Oct 2014)
      Sequence version 1 (01 Feb 1995)
      Previous versions | rss
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    Functioni

    Regulates the GDP/GTP exchange reaction of SEC4 by inhibiting the dissociation of GDP from it, and the subsequent binding of GTP to SEC4. Plays an essential role in the yeast secretory pathway.1 Publication

    GO - Molecular functioni

    1. GTPase activator activity Source: UniProtKB-KW
    2. protein binding Source: IntAct
    3. Rab GDP-dissociation inhibitor activity Source: SGD

    GO - Biological processi

    1. protein transport Source: UniProtKB-KW
    2. regulation of catalytic activity Source: GOC
    3. vesicle-mediated transport Source: SGD

    Keywords - Molecular functioni

    GTPase activation

    Keywords - Biological processi

    Protein transport, Transport

    Enzyme and pathway databases

    BioCyciYEAST:G3O-30297-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Rab GDP-dissociation inhibitor
    Short name:
    Rab GDI
    Alternative name(s):
    Secretory pathway GDP dissociation inhibitor
    Gene namesi
    Name:GDI1
    Synonyms:SEC19
    Ordered Locus Names:YER136W
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome V

    Organism-specific databases

    CYGDiYER136w.
    SGDiS000000938. GDI1.

    Subcellular locationi

    Cytoplasm 1 Publication

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 451451Rab GDP-dissociation inhibitorPRO_0000056684Add
    BLAST

    Proteomic databases

    MaxQBiP39958.
    PaxDbiP39958.
    PeptideAtlasiP39958.

    2D gel databases

    UCD-2DPAGEP39958.

    Expressioni

    Gene expression databases

    GenevestigatoriP39958.

    Interactioni

    Subunit structurei

    Interacts with the GDP-bound form of Rab GTPase YPT1. Interacts with YPT10.2 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    YPT1P011235EBI-7517,EBI-29496
    YPT10P381464EBI-7517,EBI-29357
    YPT31P385556EBI-7517,EBI-29379
    YPT52P360183EBI-7517,EBI-29407
    YPT6Q992603EBI-7517,EBI-29503

    Protein-protein interaction databases

    BioGridi36882. 35 interactions.
    DIPiDIP-785N.
    IntActiP39958. 16 interactions.
    MINTiMINT-502785.
    STRINGi4932.YER136W.

    Structurei

    Secondary structure

    1
    451
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi11 – 155
    Helixi19 – 3012
    Beta strandi35 – 384
    Beta strandi40 – 445
    Helixi46 – 483
    Helixi53 – 608
    Helixi67 – 748
    Helixi77 – 793
    Beta strandi82 – 854
    Beta strandi88 – 903
    Helixi94 – 1018
    Helixi104 – 1063
    Beta strandi110 – 1123
    Beta strandi116 – 1205
    Beta strandi123 – 1264
    Helixi131 – 1366
    Beta strandi138 – 1403
    Helixi142 – 15716
    Helixi163 – 1653
    Turni171 – 1733
    Helixi176 – 1827
    Helixi187 – 19610
    Beta strandi201 – 2033
    Helixi204 – 2074
    Beta strandi208 – 2103
    Helixi211 – 22717
    Beta strandi231 – 2355
    Helixi241 – 25212
    Beta strandi256 – 2583
    Beta strandi265 – 2684
    Turni270 – 2723
    Beta strandi275 – 2806
    Beta strandi283 – 2864
    Beta strandi290 – 2923
    Helixi294 – 2963
    Helixi298 – 3003
    Beta strandi301 – 31717
    Beta strandi322 – 3243
    Beta strandi326 – 3327
    Helixi334 – 3363
    Beta strandi343 – 3497
    Helixi350 – 3523
    Beta strandi360 – 3678
    Helixi373 – 3764
    Helixi378 – 3814
    Helixi382 – 3843
    Beta strandi388 – 40215
    Turni405 – 4073
    Beta strandi408 – 4114
    Beta strandi419 – 4213
    Helixi422 – 43615

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1UKVX-ray1.50G1-451[»]
    2BCGX-ray1.48G1-451[»]
    3CPHX-ray2.90G/H1-451[»]
    3CPIX-ray2.30G/H1-451[»]
    3CPJX-ray2.35G1-451[»]
    ProteinModelPortaliP39958.
    SMRiP39958. Positions 5-446.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP39958.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni106 – 1127Interaction with YPT1
    Regioni234 – 25926Interaction with YPT1Add
    BLAST

    Sequence similaritiesi

    Belongs to the Rab GDI family.Curated

    Phylogenomic databases

    eggNOGiCOG5044.
    GeneTreeiENSGT00530000063044.
    HOGENOMiHOG000163825.
    KOiK17255.
    OMAiKKYGNYN.
    OrthoDBiEOG72C58R.

    Family and domain databases

    InterProiIPR018203. GDP_dissociation_inhibitor.
    IPR000806. RabGDI.
    [Graphical view]
    PfamiPF00996. GDI. 1 hit.
    [Graphical view]
    PRINTSiPR00892. RABGDI.
    PR00891. RABGDIREP.

    Sequencei

    Sequence statusi: Complete.

    P39958-1 [UniParc]FASTAAdd to Basket

    « Hide

    MDQETIDTDY DVIVLGTGIT ECILSGLLSV DGKKVLHIDK QDHYGGEAAS    50
    VTLSQLYEKF KQNPISKEER ESKFGKDRDW NVDLIPKFLM ANGELTNILI 100
    HTDVTRYVDF KQVSGSYVFK QGKIYKVPAN EIEAISSPLM GIFEKRRMKK 150
    FLEWISSYKE DDLSTHQGLD LDKNTMDEVY YKFGLGNSTK EFIGHAMALW 200
    TNDDYLQQPA RPSFERILLY CQSVARYGKS PYLYPMYGLG ELPQGFARLS 250
    AIYGGTYMLD TPIDEVLYKK DTGKFEGVKT KLGTFKAPLV IADPTYFPEK 300
    CKSTGQRVIR AICILNHPVP NTSNADSLQI IIPQSQLGRK SDIYVAIVSD 350
    AHNVCSKGHY LAIISTIIET DKPHIELEPA FKLLGPIEEK FMGIAELFEP 400
    REDGSKDNIY LSRSYDASSH FESMTDDVKD IYFRVTGHPL VLKQRQEQEK 450
    Q 451
    Length:451
    Mass (Da):51,206
    Last modified:February 1, 1995 - v1
    Checksum:i48CF8D45FC031772
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    S69371 Genomic DNA. Translation: AAB30540.1.
    U18916 Genomic DNA. Translation: AAC03234.1.
    BK006939 Genomic DNA. Translation: DAA07795.1.
    PIRiS44446.
    RefSeqiNP_011062.1. NM_001179026.1.

    Genome annotation databases

    EnsemblFungiiYER136W; YER136W; YER136W.
    GeneIDi856876.
    KEGGisce:YER136W.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    S69371 Genomic DNA. Translation: AAB30540.1 .
    U18916 Genomic DNA. Translation: AAC03234.1 .
    BK006939 Genomic DNA. Translation: DAA07795.1 .
    PIRi S44446.
    RefSeqi NP_011062.1. NM_001179026.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1UKV X-ray 1.50 G 1-451 [» ]
    2BCG X-ray 1.48 G 1-451 [» ]
    3CPH X-ray 2.90 G/H 1-451 [» ]
    3CPI X-ray 2.30 G/H 1-451 [» ]
    3CPJ X-ray 2.35 G 1-451 [» ]
    ProteinModelPortali P39958.
    SMRi P39958. Positions 5-446.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 36882. 35 interactions.
    DIPi DIP-785N.
    IntActi P39958. 16 interactions.
    MINTi MINT-502785.
    STRINGi 4932.YER136W.

    2D gel databases

    UCD-2DPAGE P39958.

    Proteomic databases

    MaxQBi P39958.
    PaxDbi P39958.
    PeptideAtlasi P39958.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YER136W ; YER136W ; YER136W .
    GeneIDi 856876.
    KEGGi sce:YER136W.

    Organism-specific databases

    CYGDi YER136w.
    SGDi S000000938. GDI1.

    Phylogenomic databases

    eggNOGi COG5044.
    GeneTreei ENSGT00530000063044.
    HOGENOMi HOG000163825.
    KOi K17255.
    OMAi KKYGNYN.
    OrthoDBi EOG72C58R.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-30297-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P39958.
    NextBioi 983252.
    PROi P39958.

    Gene expression databases

    Genevestigatori P39958.

    Family and domain databases

    InterProi IPR018203. GDP_dissociation_inhibitor.
    IPR000806. RabGDI.
    [Graphical view ]
    Pfami PF00996. GDI. 1 hit.
    [Graphical view ]
    PRINTSi PR00892. RABGDI.
    PR00891. RABGDIREP.
    ProtoNeti Search...

    Publicationsi

    1. "GDI1 encodes a GDP dissociation inhibitor that plays an essential role in the yeast secretory pathway."
      Garrett M.D., Zahner J.E., Cheney C.M., Novick P.J.
      EMBO J. 13:1718-1728(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    3. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    4. "Characterization of the ORF YBR264c in Saccharomyces cerevisiae, which encodes a new yeast Ypt that is degraded by a proteasome-dependent mechanism."
      Louvet O., Roumanie O., Barthe C., Peypouquet M.-F., Schaeffer J., Doignon F., Crouzet M.
      Mol. Gen. Genet. 261:589-600(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH YPT10.
    5. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
    6. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    7. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
      Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
      Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    8. "Structure of Rab GDP-dissociation inhibitor in complex with prenylated YPT1 GTPase."
      Rak A., Pylypenko O., Durek T., Watzke A., Kushnir S., Brunsveld L., Waldmann H., Goody R.S., Alexandrov K.
      Science 302:646-650(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) IN COMPLEX WITH YPT1.

    Entry informationi

    Entry nameiGDI1_YEAST
    AccessioniPrimary (citable) accession number: P39958
    Secondary accession number(s): D3DM41
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1995
    Last sequence update: February 1, 1995
    Last modified: October 1, 2014
    This is version 117 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present with 7280 molecules/cell in log phase SD medium.1 Publication

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families
    3. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    4. Yeast chromosome V
      Yeast (Saccharomyces cerevisiae) chromosome V: entries and gene names

    External Data

    Dasty 3