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Protein

Vacuolar protein sorting-associated protein 9

Gene

VPS9

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Required for vacuolar protein sorting; may be required for the consumption of transport vesicles containing vacuolar protein precursors. May bind a Rab GTPase such as VPS21.

GO - Molecular functioni

  • guanyl-nucleotide exchange factor activity Source: SGD
  • ubiquitin binding Source: SGD

GO - Biological processi

  • Golgi to endosome transport Source: SGD
  • late endosome to vacuole transport via multivesicular body sorting pathway Source: SGD
  • positive regulation of GTPase activity Source: GOC
  • protein localization to endosome Source: SGD
  • protein targeting to vacuole Source: SGD
  • vacuole inheritance Source: SGD
Complete GO annotation...

Keywords - Biological processi

Ubl conjugation pathway

Enzyme and pathway databases

BioCyciYEAST:G3O-32682-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Vacuolar protein sorting-associated protein 9
Alternative name(s):
Vacuolar protein-targeting protein 9
Gene namesi
Name:VPS9
Synonyms:VPT9
Ordered Locus Names:YML097C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XIII

Organism-specific databases

EuPathDBiFungiDB:YML097C.
SGDiS000004563. VPS9.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 451451Vacuolar protein sorting-associated protein 9PRO_0000191324Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei375 – 3751PhosphoserineCombined sources

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP54787.
PeptideAtlasiP54787.

PTM databases

iPTMnetiP54787.

Interactioni

Subunit structurei

Homodimer.2 Publications

GO - Molecular functioni

  • ubiquitin binding Source: SGD

Protein-protein interaction databases

BioGridi35046. 254 interactions.
DIPiDIP-4526N.
IntActiP54787. 5 interactions.
MINTiMINT-516456.

Structurei

Secondary structure

1
451
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi401 – 41919Combined sources
Helixi425 – 43410Combined sources
Helixi441 – 4433Combined sources
Helixi445 – 4484Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1MN3X-ray2.30A398-451[»]
1P3QX-ray1.70Q/R398-451[»]
ProteinModelPortaliP54787.
SMRiP54787. Positions 70-317, 398-451.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP54787.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini170 – 312143VPS9PROSITE-ProRule annotationAdd
BLAST
Domaini408 – 45144CUEPROSITE-ProRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi229 – 2379GBH motif I
Motifi249 – 2579GBH motif II
Motifi287 – 2959GBH motif III

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi332 – 34110Glu/Lys-rich

Domaini

The CUE domain (Coupling of ubiquitin conjugation to ER degradation) is monoubiquitin-binding and is required for intramolecular ubiquitination.

Sequence similaritiesi

Contains 1 CUE domain.PROSITE-ProRule annotation
Contains 1 VPS9 domain.PROSITE-ProRule annotation

Phylogenomic databases

GeneTreeiENSGT00530000063341.
HOGENOMiHOG000141911.
InParanoidiP54787.
OMAiEDVCIAK.
OrthoDBiEOG7MPRRD.

Family and domain databases

InterProiIPR003892. CUE.
IPR009060. UBA-like.
IPR003123. VPS9.
[Graphical view]
PfamiPF02845. CUE. 1 hit.
PF02204. VPS9. 1 hit.
[Graphical view]
SMARTiSM00546. CUE. 1 hit.
SM00167. VPS9. 1 hit.
[Graphical view]
SUPFAMiSSF46934. SSF46934. 1 hit.
PROSITEiPS51140. CUE. 1 hit.
PS51205. VPS9. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P54787-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTDDEKREIL KEFDPFSQLE QANGNPDKDV KFKKDDPNRA AAEETNRDIS
60 70 80 90 100
AQDKGDEEPF YDFQIFIKQL QTPGADPLVK YTKSFLRNFL AQRLLWTVSE
110 120 130 140 150
EIKLISDFKT FIYDKFTLYE PFRSLDNSKM RNAKEGMEKL IMGKLYSRCF
160 170 180 190 200
SPSLYEILQK PLDDEHMKDL TNDDTLLEKI RHYRFISPIM LDIPDTMPNA
210 220 230 240 250
RLNKFVHLAS KELGKINRFK SPRDKMVCVL NASKVIFGLL KHTKLEQNGA
260 270 280 290 300
DSFIPVLIYC ILKGQVRYLV SNVNYIERFR SPDFIRGEEE YYLSSLQAAL
310 320 330 340 350
NFIMNLTERS LTIEDHEDFE EAYQRNFKQL AEEKEEEEKK KQLEIPDELQ
360 370 380 390 400
PNGTLLKPLD EVTNIVISKF NELFSPIGEP TQEEALKSEQ SNKEEDVSSL
410 420 430 440 450
IKKIEENERK DTLNTLQNMF PDMDPSLIED VCIAKKSRIG PCVDALLSLS

E
Length:451
Mass (Da):52,483
Last modified:October 5, 2010 - v2
Checksum:i6631766C00D3A22B
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti172 – 1721N → T in AAA62233 (Ref. 2) Curated
Sequence conflicti305 – 3051N → S in AAC49314 (PubMed:8628304).Curated
Sequence conflicti305 – 3051N → S in AAA62233 (Ref. 2) Curated
Sequence conflicti314 – 3141E → D in AAC49314 (PubMed:8628304).Curated
Sequence conflicti314 – 3141E → D in AAA62233 (Ref. 2) Curated
Sequence conflicti327 – 3271F → L in AAC49314 (PubMed:8628304).Curated
Sequence conflicti327 – 3271F → L in AAA62233 (Ref. 2) Curated
Sequence conflicti345 – 3451I → V in AAC49314 (PubMed:8628304).Curated
Sequence conflicti345 – 3451I → V in AAA62233 (Ref. 2) Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U50142 Genomic DNA. Translation: AAC49314.1.
U20373 Genomic DNA. Translation: AAA62233.1.
Z46660 Genomic DNA. Translation: CAA86640.1.
BK006946 Genomic DNA. Translation: DAA09802.1.
PIRiS49629.
RefSeqiNP_013612.1. NM_001182457.1.

Genome annotation databases

EnsemblFungiiYML097C; YML097C; YML097C.
GeneIDi854876.
KEGGisce:YML097C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U50142 Genomic DNA. Translation: AAC49314.1.
U20373 Genomic DNA. Translation: AAA62233.1.
Z46660 Genomic DNA. Translation: CAA86640.1.
BK006946 Genomic DNA. Translation: DAA09802.1.
PIRiS49629.
RefSeqiNP_013612.1. NM_001182457.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1MN3X-ray2.30A398-451[»]
1P3QX-ray1.70Q/R398-451[»]
ProteinModelPortaliP54787.
SMRiP54787. Positions 70-317, 398-451.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi35046. 254 interactions.
DIPiDIP-4526N.
IntActiP54787. 5 interactions.
MINTiMINT-516456.

PTM databases

iPTMnetiP54787.

Proteomic databases

MaxQBiP54787.
PeptideAtlasiP54787.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYML097C; YML097C; YML097C.
GeneIDi854876.
KEGGisce:YML097C.

Organism-specific databases

EuPathDBiFungiDB:YML097C.
SGDiS000004563. VPS9.

Phylogenomic databases

GeneTreeiENSGT00530000063341.
HOGENOMiHOG000141911.
InParanoidiP54787.
OMAiEDVCIAK.
OrthoDBiEOG7MPRRD.

Enzyme and pathway databases

BioCyciYEAST:G3O-32682-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP54787.
NextBioi977816.
PROiP54787.

Family and domain databases

InterProiIPR003892. CUE.
IPR009060. UBA-like.
IPR003123. VPS9.
[Graphical view]
PfamiPF02845. CUE. 1 hit.
PF02204. VPS9. 1 hit.
[Graphical view]
SMARTiSM00546. CUE. 1 hit.
SM00167. VPS9. 1 hit.
[Graphical view]
SUPFAMiSSF46934. SSF46934. 1 hit.
PROSITEiPS51140. CUE. 1 hit.
PS51205. VPS9. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "A yeast protein related to a mammalian Ras-binding protein, Vps9p, is required for localization of vacuolar proteins."
    Burd C.G., Mustol P.A., Schu P.V., Emr S.D.
    Mol. Cell. Biol. 16:2369-2377(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "VPS9, a gene whose product is required for Golgi to vacuole trafficking, shares similarity to mammalian ras inhibitors."
    Whitters E.A., Piper R.C., Stevens T.H.
    Submitted (MAR-1995) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: SF838-9D.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  4. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  5. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  6. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
    Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
    Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-375, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  7. "Mechanism of ubiquitin recognition by the CUE domain of Vps9p."
    Prag G., Misra S., Jones E.A., Ghirlando R., Davies B.A., Horazdovsky B.F., Hurley J.H.
    Cell 113:609-620(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 398-451 IN COMPLEX WITH UBIQUITIN.
  8. "A ubiquitin-binding motif required for intramolecular monoubiquitylation, the CUE domain."
    Shih S.C., Prag G., Francis S.A., Sutanto M.A., Hurley J.H., Hicke L.
    EMBO J. 22:1273-1281(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 398-449 IN COMPLEX WITH UBIQUITIN.

Entry informationi

Entry nameiVPS9_YEAST
AccessioniPrimary (citable) accession number: P54787
Secondary accession number(s): D6W0I8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: October 5, 2010
Last modified: May 11, 2016
This is version 141 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 4280 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 XIII
    Yeast (Saccharomyces cerevisiae) chromosome XIII: entries and gene names

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.