GDI1_YEAST
ID GDI1_YEAST Reviewed; 451 AA.
AC P39958; D3DM41;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1995, sequence version 1.
DT 03-AUG-2022, entry version 171.
DE RecName: Full=Rab GDP-dissociation inhibitor;
DE Short=Rab GDI;
DE AltName: Full=Secretory pathway GDP dissociation inhibitor;
GN Name=GDI1; Synonyms=SEC19; OrderedLocusNames=YER136W;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND FUNCTION.
RX PubMed=8157010; DOI=10.1002/j.1460-2075.1994.tb06436.x;
RA Garrett M.D., Zahner J.E., Cheney C.M., Novick P.J.;
RT "GDI1 encodes a GDP dissociation inhibitor that plays an essential role in
RT the yeast secretory pathway.";
RL EMBO J. 13:1718-1728(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169868;
RA Dietrich F.S., Mulligan J.T., Hennessy K.M., Yelton M.A., Allen E.,
RA Araujo R., Aviles E., Berno A., Brennan T., Carpenter J., Chen E.,
RA Cherry J.M., Chung E., Duncan M., Guzman E., Hartzell G., Hunicke-Smith S.,
RA Hyman R.W., Kayser A., Komp C., Lashkari D., Lew H., Lin D., Mosedale D.,
RA Nakahara K., Namath A., Norgren R., Oefner P., Oh C., Petel F.X.,
RA Roberts D., Sehl P., Schramm S., Shogren T., Smith V., Taylor P., Wei Y.,
RA Botstein D., Davis R.W.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome V.";
RL Nature 387:78-81(1997).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [4]
RP INTERACTION WITH YPT10.
RX PubMed=10394895; DOI=10.1007/s004380050001;
RA Louvet O., Roumanie O., Barthe C., Peypouquet M.-F., Schaeffer J.,
RA Doignon F., Crouzet M.;
RT "Characterization of the ORF YBR264c in Saccharomyces cerevisiae, which
RT encodes a new yeast Ypt that is degraded by a proteasome-dependent
RT mechanism.";
RL Mol. Gen. Genet. 261:589-600(1999).
RN [5]
RP FUNCTION.
RX PubMed=11118206; DOI=10.1093/emboj/19.24.6713;
RA Eitzen G., Will E., Gallwitz D., Haas A., Wickner W.;
RT "Sequential action of two GTPases to promote vacuole docking and fusion.";
RL EMBO J. 19:6713-6720(2000).
RN [6]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=14562095; DOI=10.1038/nature02026;
RA Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA Weissman J.S., O'Shea E.K.;
RT "Global analysis of protein localization in budding yeast.";
RL Nature 425:686-691(2003).
RN [7]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [8]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19779198; DOI=10.1126/science.1172867;
RA Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
RT "Global analysis of Cdk1 substrate phosphorylation sites provides insights
RT into evolution.";
RL Science 325:1682-1686(2009).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) IN COMPLEX WITH YPT1.
RX PubMed=14576435; DOI=10.1126/science.1087761;
RA Rak A., Pylypenko O., Durek T., Watzke A., Kushnir S., Brunsveld L.,
RA Waldmann H., Goody R.S., Alexandrov K.;
RT "Structure of Rab GDP-dissociation inhibitor in complex with prenylated
RT YPT1 GTPase.";
RL Science 302:646-650(2003).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (1.48 ANGSTROMS) IN COMPLEX WITH YPT1.
RX PubMed=16395334; DOI=10.1038/sj.emboj.7600921;
RA Pylypenko O., Rak A., Durek T., Kushnir S., Dursina B.E., Thomae N.H.,
RA Constantinescu A.T., Brunsveld L., Watzke A., Waldmann H., Goody R.S.,
RA Alexandrov K.;
RT "Structure of doubly prenylated Ypt1:GDI complex and the mechanism of GDI-
RT mediated Rab recycling.";
RL EMBO J. 25:13-23(2006).
RN [11]
RP X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS).
RX PubMed=18426803; DOI=10.1074/jbc.m709718200;
RA Ignatev A., Kravchenko S., Rak A., Goody R.S., Pylypenko O.;
RT "A structural model of the GDP dissociation inhibitor rab membrane
RT extraction mechanism.";
RL J. Biol. Chem. 283:18377-18384(2008).
CC -!- FUNCTION: Regulates the GDP/GTP exchange reaction of SEC4 by inhibiting
CC the dissociation of GDP from it, and the subsequent binding of GTP to
CC SEC4. Plays an essential role in the yeast secretory pathway
CC (PubMed:8157010). Extracts GDP-bound YPT7 from vacuolar membranes,
CC antagonizing vacuolar membrane fusion (PubMed:11118206).
CC {ECO:0000269|PubMed:11118206, ECO:0000269|PubMed:8157010}.
CC -!- SUBUNIT: Interacts with the GDP-bound form of Rab GTPase YPT1.
CC Interacts with YPT10. {ECO:0000269|PubMed:10394895,
CC ECO:0000269|PubMed:14576435}.
CC -!- INTERACTION:
CC P39958; P07560: SEC4; NbExp=3; IntAct=EBI-7517, EBI-16858;
CC P39958; P36017: VPS21; NbExp=4; IntAct=EBI-7517, EBI-29399;
CC P39958; P01123: YPT1; NbExp=6; IntAct=EBI-7517, EBI-29496;
CC P39958; P38146: YPT10; NbExp=6; IntAct=EBI-7517, EBI-29357;
CC P39958; P38555: YPT31; NbExp=5; IntAct=EBI-7517, EBI-29379;
CC P39958; P51996: YPT32; NbExp=3; IntAct=EBI-7517, EBI-29384;
CC P39958; P36018: YPT52; NbExp=3; IntAct=EBI-7517, EBI-29407;
CC P39958; Q99260: YPT6; NbExp=5; IntAct=EBI-7517, EBI-29503;
CC P39958; P32939: YPT7; NbExp=3; IntAct=EBI-7517, EBI-29509;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}.
CC -!- MISCELLANEOUS: Present with 7280 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the Rab GDI family. {ECO:0000305}.
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DR EMBL; S69371; AAB30540.1; -; Genomic_DNA.
DR EMBL; U18916; AAC03234.1; -; Genomic_DNA.
DR EMBL; BK006939; DAA07795.1; -; Genomic_DNA.
DR PIR; S44446; S44446.
DR RefSeq; NP_011062.1; NM_001179026.1.
DR PDB; 1UKV; X-ray; 1.50 A; G=1-451.
DR PDB; 2BCG; X-ray; 1.48 A; G=1-451.
DR PDB; 3CPH; X-ray; 2.90 A; G/H=1-451.
DR PDB; 3CPI; X-ray; 2.30 A; G/H=1-451.
DR PDB; 3CPJ; X-ray; 2.35 A; G=1-451.
DR PDBsum; 1UKV; -.
DR PDBsum; 2BCG; -.
DR PDBsum; 3CPH; -.
DR PDBsum; 3CPI; -.
DR PDBsum; 3CPJ; -.
DR AlphaFoldDB; P39958; -.
DR SMR; P39958; -.
DR BioGRID; 36882; 270.
DR DIP; DIP-785N; -.
DR IntAct; P39958; 20.
DR MINT; P39958; -.
DR STRING; 4932.YER136W; -.
DR iPTMnet; P39958; -.
DR UCD-2DPAGE; P39958; -.
DR MaxQB; P39958; -.
DR PaxDb; P39958; -.
DR PRIDE; P39958; -.
DR EnsemblFungi; YER136W_mRNA; YER136W; YER136W.
DR GeneID; 856876; -.
DR KEGG; sce:YER136W; -.
DR SGD; S000000938; GDI1.
DR VEuPathDB; FungiDB:YER136W; -.
DR eggNOG; KOG1439; Eukaryota.
DR GeneTree; ENSGT00950000182994; -.
DR HOGENOM; CLU_021695_0_0_1; -.
DR InParanoid; P39958; -.
DR OMA; DHYGGES; -.
DR BioCyc; YEAST:G3O-30297-MON; -.
DR Reactome; R-SCE-6798695; Neutrophil degranulation.
DR Reactome; R-SCE-8876198; RAB GEFs exchange GTP for GDP on RABs.
DR EvolutionaryTrace; P39958; -.
DR PRO; PR:P39958; -.
DR Proteomes; UP000002311; Chromosome V.
DR RNAct; P39958; protein.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005096; F:GTPase activator activity; IEA:UniProtKB-KW.
DR GO; GO:0005093; F:Rab GDP-dissociation inhibitor activity; IDA:SGD.
DR GO; GO:0015031; P:protein transport; IEA:UniProtKB-KW.
DR GO; GO:0007264; P:small GTPase mediated signal transduction; IEA:InterPro.
DR GO; GO:0016192; P:vesicle-mediated transport; IMP:SGD.
DR Gene3D; 3.50.50.60; -; 1.
DR InterPro; IPR036188; FAD/NAD-bd_sf.
DR InterPro; IPR018203; GDP_dissociation_inhibitor.
DR InterPro; IPR000806; RabGDI.
DR PANTHER; PTHR11787; PTHR11787; 1.
DR Pfam; PF00996; GDI; 1.
DR PRINTS; PR00892; RABGDI.
DR PRINTS; PR00891; RABGDIREP.
DR SUPFAM; SSF51905; SSF51905; 2.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; GTPase activation; Protein transport;
KW Reference proteome; Transport.
FT CHAIN 1..451
FT /note="Rab GDP-dissociation inhibitor"
FT /id="PRO_0000056684"
FT REGION 106..112
FT /note="Interaction with YPT1"
FT /evidence="ECO:0000269|PubMed:14576435"
FT REGION 234..259
FT /note="Interaction with YPT1"
FT /evidence="ECO:0000269|PubMed:14576435"
FT STRAND 11..15
FT /evidence="ECO:0007829|PDB:2BCG"
FT HELIX 19..30
FT /evidence="ECO:0007829|PDB:2BCG"
FT STRAND 35..38
FT /evidence="ECO:0007829|PDB:2BCG"
FT STRAND 40..44
FT /evidence="ECO:0007829|PDB:2BCG"
FT HELIX 46..48
FT /evidence="ECO:0007829|PDB:2BCG"
FT HELIX 53..60
FT /evidence="ECO:0007829|PDB:2BCG"
FT HELIX 67..74
FT /evidence="ECO:0007829|PDB:2BCG"
FT HELIX 77..79
FT /evidence="ECO:0007829|PDB:2BCG"
FT STRAND 82..85
FT /evidence="ECO:0007829|PDB:2BCG"
FT STRAND 88..90
FT /evidence="ECO:0007829|PDB:2BCG"
FT HELIX 94..101
FT /evidence="ECO:0007829|PDB:2BCG"
FT HELIX 104..106
FT /evidence="ECO:0007829|PDB:2BCG"
FT STRAND 110..112
FT /evidence="ECO:0007829|PDB:2BCG"
FT STRAND 116..120
FT /evidence="ECO:0007829|PDB:2BCG"
FT STRAND 123..126
FT /evidence="ECO:0007829|PDB:2BCG"
FT HELIX 131..136
FT /evidence="ECO:0007829|PDB:2BCG"
FT STRAND 138..140
FT /evidence="ECO:0007829|PDB:3CPJ"
FT HELIX 142..157
FT /evidence="ECO:0007829|PDB:2BCG"
FT HELIX 163..165
FT /evidence="ECO:0007829|PDB:2BCG"
FT TURN 171..173
FT /evidence="ECO:0007829|PDB:2BCG"
FT HELIX 176..182
FT /evidence="ECO:0007829|PDB:2BCG"
FT HELIX 187..196
FT /evidence="ECO:0007829|PDB:2BCG"
FT STRAND 201..203
FT /evidence="ECO:0007829|PDB:2BCG"
FT HELIX 204..207
FT /evidence="ECO:0007829|PDB:2BCG"
FT STRAND 208..210
FT /evidence="ECO:0007829|PDB:2BCG"
FT HELIX 211..227
FT /evidence="ECO:0007829|PDB:2BCG"
FT STRAND 231..235
FT /evidence="ECO:0007829|PDB:2BCG"
FT HELIX 241..252
FT /evidence="ECO:0007829|PDB:2BCG"
FT STRAND 256..258
FT /evidence="ECO:0007829|PDB:2BCG"
FT STRAND 265..268
FT /evidence="ECO:0007829|PDB:2BCG"
FT TURN 270..272
FT /evidence="ECO:0007829|PDB:2BCG"
FT STRAND 275..280
FT /evidence="ECO:0007829|PDB:2BCG"
FT STRAND 283..286
FT /evidence="ECO:0007829|PDB:2BCG"
FT STRAND 290..292
FT /evidence="ECO:0007829|PDB:2BCG"
FT HELIX 294..296
FT /evidence="ECO:0007829|PDB:2BCG"
FT HELIX 298..300
FT /evidence="ECO:0007829|PDB:2BCG"
FT STRAND 301..317
FT /evidence="ECO:0007829|PDB:2BCG"
FT STRAND 322..324
FT /evidence="ECO:0007829|PDB:3CPI"
FT STRAND 326..332
FT /evidence="ECO:0007829|PDB:2BCG"
FT HELIX 334..336
FT /evidence="ECO:0007829|PDB:2BCG"
FT STRAND 343..349
FT /evidence="ECO:0007829|PDB:2BCG"
FT HELIX 350..352
FT /evidence="ECO:0007829|PDB:2BCG"
FT STRAND 360..367
FT /evidence="ECO:0007829|PDB:2BCG"
FT HELIX 373..376
FT /evidence="ECO:0007829|PDB:2BCG"
FT HELIX 378..381
FT /evidence="ECO:0007829|PDB:2BCG"
FT HELIX 382..384
FT /evidence="ECO:0007829|PDB:2BCG"
FT STRAND 388..402
FT /evidence="ECO:0007829|PDB:2BCG"
FT TURN 405..407
FT /evidence="ECO:0007829|PDB:2BCG"
FT STRAND 408..411
FT /evidence="ECO:0007829|PDB:2BCG"
FT STRAND 419..421
FT /evidence="ECO:0007829|PDB:2BCG"
FT HELIX 422..436
FT /evidence="ECO:0007829|PDB:2BCG"
SQ SEQUENCE 451 AA; 51206 MW; 48CF8D45FC031772 CRC64;
MDQETIDTDY DVIVLGTGIT ECILSGLLSV DGKKVLHIDK QDHYGGEAAS VTLSQLYEKF
KQNPISKEER ESKFGKDRDW NVDLIPKFLM ANGELTNILI HTDVTRYVDF KQVSGSYVFK
QGKIYKVPAN EIEAISSPLM GIFEKRRMKK FLEWISSYKE DDLSTHQGLD LDKNTMDEVY
YKFGLGNSTK EFIGHAMALW TNDDYLQQPA RPSFERILLY CQSVARYGKS PYLYPMYGLG
ELPQGFARLS AIYGGTYMLD TPIDEVLYKK DTGKFEGVKT KLGTFKAPLV IADPTYFPEK
CKSTGQRVIR AICILNHPVP NTSNADSLQI IIPQSQLGRK SDIYVAIVSD AHNVCSKGHY
LAIISTIIET DKPHIELEPA FKLLGPIEEK FMGIAELFEP REDGSKDNIY LSRSYDASSH
FESMTDDVKD IYFRVTGHPL VLKQRQEQEK Q
