Reviewed, UniProtKB/Swiss-Prot P54787 (VPS9_YEAST)

Names and origin

Protein names

Recommended name:
    Vacuolar protein sorting-associated protein 9
Alternative name(s):
    Vacuolar protein-targeting protein 9

Gene names

Name:	VPS9
Synonyms:	VPT9
Ordered Locus Names:	YML097C

Organism

Saccharomyces cerevisiae (Baker's yeast) [Complete proteome]

Taxonomic identifier

4932 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

Protein attributes

Sequence length	451 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	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.
Subunit structure	Homodimer.
Subcellular location	Cytoplasm.
Domain	The CUE domain (Coupling of ubiquitin conjugation to ER degradation) is monoubiquitin-binding and is required for intramolecular ubiquitination.
Miscellaneous	Present with 4280 molecules/cell in log phase SD medium. Ref.4
Sequence similarities	Contains 1 CUE domain. Contains 1 VPS9 domain.

Ontologies

Keywords
Biological process	Ubl conjugation pathway
Cellular component	Cytoplasm
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	modification-dependent protein catabolic process Inferred from electronic annotation. Source: UniProtKB-KW protein targeting to vacuole Ref.1 Inferred from mutant phenotype. Source: SGD
Cellular component	cytosol Ref.1 Inferred from direct assay. Source: SGD
Molecular function	guanyl-nucleotide exchange factor activity Inferred from direct assay. Source: SGD identical protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
itself		1	EBI-20495,EBI-20495

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 451

451

Vacuolar protein sorting-associated protein 9

PRO_0000191324

Regions

Domain

170 – 312

143

VPS9

Domain

408 – 451

44

CUE

Motif

229 – 237

9

GBH motif I

Motif

249 – 257

9

GBH motif II

Motif

287 – 295

9

GBH motif III

Compositional bias

332 – 341

10

Glu/Lys-rich

Amino acid modifications

Modified residue

375

1

Phosphoserine Ref.5

Experimental info

Sequence conflict

172

1

N → T in AAA62233. Ref.2

Sequence conflict

305

1

S → N in CAA86640. Ref.3

Sequence conflict

314

1

D → E in CAA86640. Ref.3

Sequence conflict

327

1

L → F in CAA86640. Ref.3

Sequence conflict

345

1

V → I in CAA86640. Ref.3

Secondary structure

1

.

.

.

.

.

.

.

451

Helix Strand Turn

Details...

Helix

399 – 419

21

Helix

425 – 432

8

Helix

439 – 450

12

Sequences

	Sequence		Length	Mass (Da)
	P54787-1 [UniParc]. Last modified October 1, 1996. Version 1. Checksum: 3DE1EBC723C13AA0	FASTA	451	52,394
	10 20 30 40 50 60 MTDDEKREIL KEFDPFSQLE QANGNPDKDV KFKKDDPNRA AAEETNRDIS AQDKGDEEPF 70 80 90 100 110 120 YDFQIFIKQL QTPGADPLVK YTKSFLRNFL AQRLLWTVSE EIKLISDFKT FIYDKFTLYE 130 140 150 160 170 180 PFRSLDNSKM RNAKEGMEKL IMGKLYSRCF SPSLYEILQK PLDDEHMKDL TNDDTLLEKI 190 200 210 220 230 240 RHYRFISPIM LDIPDTMPNA RLNKFVHLAS KELGKINRFK SPRDKMVCVL NASKVIFGLL 250 260 270 280 290 300 KHTKLEQNGA DSFIPVLIYC ILKGQVRYLV SNVNYIERFR SPDFIRGEEE YYLSSLQAAL 310 320 330 340 350 360 NFIMSLTERS LTIDDHEDFE EAYQRNLKQL AEEKEEEEKK KQLEVPDELQ PNGTLLKPLD 370 380 390 400 410 420 EVTNIVISKF NELFSPIGEP TQEEALKSEQ SNKEEDVSSL IKKIEENERK DTLNTLQNMF 430 440 450 PDMDPSLIED VCIAKKSRIG PCVDALLSLS E

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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: 8628304] [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]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome XIII." Bowman S., Churcher C.M., Badcock K., Brown D., Chillingworth T., Connor R., Dedman K., Devlin K., Gentles S., Hamlin N., Hunt S., Jagels K., Lye G., Moule S., Odell C., Pearson D., Rajandream M.A., Rice P. , Skelton J., Walsh S.V., Whitehead S., Barrell B.G. Nature 387:90-93(1997) [PubMed: 9169872] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[4]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed: 14562106] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[5]	"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: 18407956] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-375, MASS SPECTROMETRY.
[6]	"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: 12787502] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 398-451 IN COMPLEX WITH UBIQUITIN.
[7]	"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: 12628920] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 398-449 IN COMPLEX WITH UBIQUITIN.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

U50142 Genomic DNA. Translation: AAC49314.1.
U20373 Genomic DNA. Translation: AAA62233.1.
Z46660 Genomic DNA. Translation: CAA86640.1.

PIR

S49629.

RefSeq

NP_013612.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1MN3	X-ray	2.30	A	398-451	[»]
1P3Q	X-ray	1.70	Q/R	398-451	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:4526N.

IntAct

P54787. 6 interactions.

STRING

P54787.

Proteomic databases

PeptideAtlas

P54787.

Genome annotation databases

Ensembl

YML097C; YML097C; YML097C; Saccharomyces cerevisiae. [Genome view]

GeneID

854876.

KEGG

sce:YML097C.

Organism-specific databases

CYGD

YML097c.

SGD

S000004563. VPS9.

Phylogenomic databases

HOGENOM

P54787.

OrthoDB

EOG9XWHFH

Gene expression databases

ArrayExpress

P54787.

Genevestigator

P54787.

GermOnline

YML097C. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR003892. CUE.
IPR009060. UBA-like.
IPR003123. VPS9.
IPR013995. VPS9_sub.
[Graphical view]

Pfam

PF02845. CUE. 1 hit.
PF02204. VPS9. 1 hit.
[Graphical view]

SMART

SM00546. CUE. 1 hit.
SM00167. VPS9. 1 hit.
[Graphical view]

PROSITE

PS51140. CUE. 1 hit.
PS51205. VPS9. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

VPS9_YEAST

Accession

Primary (citable) accession number: P54787

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1996
Last sequence update:	October 1, 1996
Last modified:	November 24, 2009
This is version 87 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)