VPS9_YEAST
ID VPS9_YEAST Reviewed; 451 AA.
AC P54787; D6W0I8;
DT 01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
DT 05-OCT-2010, sequence version 2.
DT 03-AUG-2022, entry version 184.
DE RecName: Full=Vacuolar protein sorting-associated protein 9;
DE AltName: Full=Vacuolar protein-targeting protein 9;
GN Name=VPS9; Synonyms=VPT9; OrderedLocusNames=YML097C;
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].
RX PubMed=8628304; DOI=10.1128/mcb.16.5.2369;
RA Burd C.G., Mustol P.A., Schu P.V., Emr S.D.;
RT "A yeast protein related to a mammalian Ras-binding protein, Vps9p, is
RT required for localization of vacuolar proteins.";
RL Mol. Cell. Biol. 16:2369-2377(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=SF838-9D;
RA Whitters E.A., Piper R.C., Stevens T.H.;
RT "VPS9, a gene whose product is required for Golgi to vacuole trafficking,
RT shares similarity to mammalian ras inhibitors.";
RL Submitted (MAR-1995) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169872;
RA Bowman S., Churcher C.M., Badcock K., Brown D., Chillingworth T.,
RA Connor R., Dedman K., Devlin K., Gentles S., Hamlin N., Hunt S., Jagels K.,
RA Lye G., Moule S., Odell C., Pearson D., Rajandream M.A., Rice P.,
RA Skelton J., Walsh S.V., Whitehead S., Barrell B.G.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XIII.";
RL Nature 387:90-93(1997).
RN [4]
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 [5]
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 [6]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-375, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT "A multidimensional chromatography technology for in-depth phosphoproteome
RT analysis.";
RL Mol. Cell. Proteomics 7:1389-1396(2008).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 398-451 IN COMPLEX WITH UBIQUITIN.
RX PubMed=12787502; DOI=10.1016/s0092-8674(03)00364-7;
RA Prag G., Misra S., Jones E.A., Ghirlando R., Davies B.A., Horazdovsky B.F.,
RA Hurley J.H.;
RT "Mechanism of ubiquitin recognition by the CUE domain of Vps9p.";
RL Cell 113:609-620(2003).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 398-449 IN COMPLEX WITH UBIQUITIN.
RX PubMed=12628920; DOI=10.1093/emboj/cdg140;
RA Shih S.C., Prag G., Francis S.A., Sutanto M.A., Hurley J.H., Hicke L.;
RT "A ubiquitin-binding motif required for intramolecular monoubiquitylation,
RT the CUE domain.";
RL EMBO J. 22:1273-1281(2003).
CC -!- FUNCTION: Required for vacuolar protein sorting; may be required for
CC the consumption of transport vesicles containing vacuolar protein
CC precursors. May bind a Rab GTPase such as VPS21.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:12628920,
CC ECO:0000269|PubMed:12787502}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm.
CC -!- DOMAIN: The CUE domain (Coupling of ubiquitin conjugation to ER
CC degradation) is monoubiquitin-binding and is required for
CC intramolecular ubiquitination.
CC -!- MISCELLANEOUS: Present with 4280 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
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DR EMBL; U50142; AAC49314.1; -; Genomic_DNA.
DR EMBL; U20373; AAA62233.1; -; Genomic_DNA.
DR EMBL; Z46660; CAA86640.1; -; Genomic_DNA.
DR EMBL; BK006946; DAA09802.1; -; Genomic_DNA.
DR PIR; S49629; S49629.
DR RefSeq; NP_013612.1; NM_001182457.1.
DR PDB; 1MN3; X-ray; 2.30 A; A=398-451.
DR PDB; 1P3Q; X-ray; 1.70 A; Q/R=398-451.
DR PDBsum; 1MN3; -.
DR PDBsum; 1P3Q; -.
DR AlphaFoldDB; P54787; -.
DR SMR; P54787; -.
DR BioGRID; 35046; 583.
DR DIP; DIP-4526N; -.
DR IntAct; P54787; 6.
DR MINT; P54787; -.
DR STRING; 4932.YML097C; -.
DR iPTMnet; P54787; -.
DR MaxQB; P54787; -.
DR PaxDb; P54787; -.
DR PRIDE; P54787; -.
DR EnsemblFungi; YML097C_mRNA; YML097C; YML097C.
DR GeneID; 854876; -.
DR KEGG; sce:YML097C; -.
DR SGD; S000004563; VPS9.
DR VEuPathDB; FungiDB:YML097C; -.
DR eggNOG; KOG2319; Eukaryota.
DR GeneTree; ENSGT00390000015057; -.
DR HOGENOM; CLU_007625_3_2_1; -.
DR InParanoid; P54787; -.
DR OMA; DVCIAKK; -.
DR BioCyc; YEAST:G3O-32682-MON; -.
DR EvolutionaryTrace; P54787; -.
DR PRO; PR:P54787; -.
DR Proteomes; UP000002311; Chromosome XIII.
DR RNAct; P54787; protein.
DR GO; GO:0005829; C:cytosol; IDA:SGD.
DR GO; GO:0005769; C:early endosome; IDA:SGD.
DR GO; GO:0030139; C:endocytic vesicle; IBA:GO_Central.
DR GO; GO:0005085; F:guanyl-nucleotide exchange factor activity; IDA:SGD.
DR GO; GO:0031267; F:small GTPase binding; IBA:GO_Central.
DR GO; GO:0043130; F:ubiquitin binding; IDA:SGD.
DR GO; GO:0006895; P:Golgi to endosome transport; IMP:SGD.
DR GO; GO:0032511; P:late endosome to vacuole transport via multivesicular body sorting pathway; IMP:SGD.
DR GO; GO:0036010; P:protein localization to endosome; IGI:SGD.
DR GO; GO:0006623; P:protein targeting to vacuole; IMP:SGD.
DR GO; GO:0000011; P:vacuole inheritance; IMP:SGD.
DR CDD; cd14369; CUE_VPS9_like; 1.
DR Gene3D; 1.20.1050.80; -; 1.
DR InterPro; IPR003892; CUE.
DR InterPro; IPR041545; DUF5601.
DR InterPro; IPR009060; UBA-like_sf.
DR InterPro; IPR003123; VPS9.
DR InterPro; IPR045046; Vps9-like.
DR InterPro; IPR041804; Vps9_CUE.
DR InterPro; IPR037191; VPS9_dom_sf.
DR PANTHER; PTHR23101; PTHR23101; 1.
DR Pfam; PF02845; CUE; 1.
DR Pfam; PF18151; DUF5601; 1.
DR Pfam; PF02204; VPS9; 1.
DR SMART; SM00546; CUE; 1.
DR SMART; SM00167; VPS9; 1.
DR SUPFAM; SSF109993; SSF109993; 1.
DR SUPFAM; SSF46934; SSF46934; 1.
DR PROSITE; PS51140; CUE; 1.
DR PROSITE; PS51205; VPS9; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Phosphoprotein; Reference proteome;
KW Ubl conjugation pathway.
FT CHAIN 1..451
FT /note="Vacuolar protein sorting-associated protein 9"
FT /id="PRO_0000191324"
FT DOMAIN 170..312
FT /note="VPS9"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00550"
FT DOMAIN 408..451
FT /note="CUE"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00468"
FT REGION 15..54
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 229..237
FT /note="GBH motif I"
FT MOTIF 249..257
FT /note="GBH motif II"
FT MOTIF 287..295
FT /note="GBH motif III"
FT COMPBIAS 26..54
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 375
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18407956"
FT CONFLICT 172
FT /note="N -> T (in Ref. 2; AAA62233)"
FT /evidence="ECO:0000305"
FT CONFLICT 305
FT /note="N -> S (in Ref. 1; AAC49314 and 2; AAA62233)"
FT /evidence="ECO:0000305"
FT CONFLICT 314
FT /note="E -> D (in Ref. 1; AAC49314 and 2; AAA62233)"
FT /evidence="ECO:0000305"
FT CONFLICT 327
FT /note="F -> L (in Ref. 1; AAC49314 and 2; AAA62233)"
FT /evidence="ECO:0000305"
FT CONFLICT 345
FT /note="I -> V (in Ref. 1; AAC49314 and 2; AAA62233)"
FT /evidence="ECO:0000305"
FT HELIX 401..419
FT /evidence="ECO:0007829|PDB:1P3Q"
FT HELIX 425..434
FT /evidence="ECO:0007829|PDB:1P3Q"
FT HELIX 441..443
FT /evidence="ECO:0007829|PDB:1P3Q"
FT HELIX 445..448
FT /evidence="ECO:0007829|PDB:1P3Q"
SQ SEQUENCE 451 AA; 52483 MW; 6631766C00D3A22B CRC64;
MTDDEKREIL KEFDPFSQLE QANGNPDKDV KFKKDDPNRA AAEETNRDIS AQDKGDEEPF
YDFQIFIKQL QTPGADPLVK YTKSFLRNFL AQRLLWTVSE EIKLISDFKT FIYDKFTLYE
PFRSLDNSKM RNAKEGMEKL IMGKLYSRCF SPSLYEILQK PLDDEHMKDL TNDDTLLEKI
RHYRFISPIM LDIPDTMPNA RLNKFVHLAS KELGKINRFK SPRDKMVCVL NASKVIFGLL
KHTKLEQNGA DSFIPVLIYC ILKGQVRYLV SNVNYIERFR SPDFIRGEEE YYLSSLQAAL
NFIMNLTERS LTIEDHEDFE EAYQRNFKQL AEEKEEEEKK KQLEIPDELQ PNGTLLKPLD
EVTNIVISKF NELFSPIGEP TQEEALKSEQ SNKEEDVSSL IKKIEENERK DTLNTLQNMF
PDMDPSLIED VCIAKKSRIG PCVDALLSLS E
