P12868 (PEP5_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Vacuolar membrane protein PEP5

Alternative name(s):
Carboxypeptidase Y-deficient protein 5
Vacuolar biogenesis protein END1
Vacuolar morphogenesis protein 1
Vacuolar protein sorting-associated protein 11
Vacuolar protein-targeting protein 11

Gene names

Name:	PEP5
Synonyms:	END1, VAM1, VPL9, VPS11, VPT11
Ordered Locus Names:	YMR231W
ORF Names:	YM9959.13

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	1029 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Required for vacuolar biogenesis and for trafficking of hydrolase precursors to the vacuole. Mediates transport at the vacuolar membrane where it may be responsible for tethering transport vesicles on the target membranes. It is required for gluconeogenic growth of yeast. Acts as component of the HOPS complex that acts during the docking stage of vacuole fusion. HOPS is an effector for the vacuolar Rab GTPase YPT7 and is required for vacuolar SNARE complex assembly. It remains bound to SNARE complexes after vacuole fusion. Ref.5 Ref.7
Subunit structure	Component of the HOPS complex which is composed of PEP5, VPS16, PEP3, VPS33, VPS39 and VPS41. HOPS associates with phosphoinositides and the PX domain of VAM7. Interacts with PEP3, PEP7 and VAM7. Ref.5 Ref.7
Subcellular location	Vacuole membrane; Peripheral membrane protein; Cytoplasmic side.
Miscellaneous	Present with 1200 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the VPS11 family. Contains 1 clathrin repeat. Contains 1 RING-type zinc finger.

Ontologies

Keywords
Biological process	Protein transport Transport
Cellular component	Membrane Vacuole
Domain	Zinc-finger
Ligand	Metal-binding Zinc
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	Golgi to endosome transport Inferred from genetic interaction PubMed 11422941. Source: SGD histone catabolic process Inferred from mutant phenotype PubMed 22570702. Source: SGD histone ubiquitination Inferred from direct assay PubMed 22570702. Source: SGD late endosome to vacuole transport Inferred from genetic interaction PubMed 11422941. Source: SGD protein transport Inferred from electronic annotation. Source: UniProtKB-KW regulation of SNARE complex assembly Inferred from direct assay PubMed 18385512. Source: SGD regulation of vacuole fusion, non-autophagic Inferred from direct assay PubMed 18385512. Source: SGD vacuole fusion, non-autophagic Inferred from mutant phenotype PubMed 10944212. Source: SGD vesicle docking involved in exocytosis Inferred from mutant phenotype Ref.5. Source: SGD
Cellular_component	CORVET complex Inferred from direct assay PubMed 17488625. Source: SGD HOPS complex Inferred from physical interaction PubMed 10944212. Source: SGD fungal-type vacuole membrane Inferred from direct assay PubMed 10944212. Source: SGD
Molecular_function	ubiquitin-protein ligase activity Inferred from direct assay PubMed 22570702. Source: SGD zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
PEP3	P27801	7	EBI-6450,EBI-13130

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 1029	1029	Vacuolar membrane protein PEP5		PRO_0000055995
Regions
	Zinc finger	928 – 973	46	RING-type
Amino acid modifications
	Modified residue	608	1	Phosphothreonine Ref.8 Ref.9
	Modified residue	609	1	Phosphothreonine Ref.9
Experimental info
	Sequence conflict	37	1	A → R in CAA33413. Ref.2
	Sequence conflict	619 – 625	7	VFYSYKT → MFFTVTKH in CAA33413. Ref.2
	Sequence conflict	769 – 770	2	TK → KQ in CAA33413. Ref.2

Sequences

	Sequence		Length	Mass (Da)
	P12868 [UniParc]. Last modified August 1, 1991. Version 2. Checksum: E5216AD3C285CF34	FASTA	1,029	117,478
	10 20 30 40 50 60 MSLSSWRQFQ LFENIPIRDP NFGGDSLLYS DPTLCAATIV DPQTLIIAVN SNIIKVVKLN 70 80 90 100 110 120 QSQVIHEFQS FPHDFQITFL KVINGEFLVA LAESIGKPSL IRVYKLEKLP NREQLYHSQV 130 140 150 160 170 180 ELKNGNNTYP ISVVSISNDL SCIVVGFING KIILIRGDIS RDRGSQQRII YEDPSKEPIT 190 200 210 220 230 240 ALFLNNDATA CFAATTSRIL LFNTTGRNRG RPSLVLNSKN GLDLNCGSFN PATNEFICCL 250 260 270 280 290 300 SNFIEFFSSS GKKHQFAFDL SLRKRIFCVD KDHILIVTEE TGVPTTSISV NELSPTIINR 310 320 330 340 350 360 IFIIDAKNKI ISLNFVVSSA IIDIFSTSQS GKNITYLLTS EGVMHRITPK SLENQINIII 370 380 390 400 410 420 QKELYPFALQ LAKQHSLSPL DVQEIHKKYG DYLFKKGLRK EATDQYIQCL DVVETSEIIS 430 440 450 460 470 480 KFGVKEVPDP ESMRNLADYL WSLIKNSISQ RDHVTLLLIV LIKLKDVEGI DTFIQHFDRK 490 500 510 520 530 540 GIWNEGVVMD DMDDVTFFYS DNDFFDLDLI LELMKESDFK RLSYRLAKKY SKDSLIIVDI 550 560 570 580 590 600 LLNLLHNPVK AIKYIKSLPI DETLRCLVTY SKKLLEESPN ETNALLIEVF TGKFKPSTFE 610 620 630 640 650 660 VDLDRRDTTG DFSENIRTVF YSYKTFFNYM NSNGTSDAMS ESSEASHEHE EPTYHPPKPS 670 680 690 700 710 720 IVFSSFVTKP FEFVVFLEAC LACYQQYEGF DEDRQVILTT LYDLYLNLAQ NDVPERIDDW 730 740 750 760 770 780 RSRATGVLRE SNKLVYSAAS NNTSKRVDNS IMLLISHMDQ SSASAKDKTK IDIASFANDN 790 800 810 820 830 840 PEMDLLSTFR AMTLNEEPST CLKFLEKYGT EEPKLLQVAL SYFVSNKLIF KEMGGNEVLK 850 860 870 880 890 900 EKVLRPIIEG ERMPLLDIIK ALSRTNVAHF GLIQDIIIDH VKTEDTEIKR NEKLIESYDK 910 920 930 940 950 960 ELKEKNKKLK NTINSDQPLH VPLKNQTCFM CRLTLDIPVV FFKCGHIYHQ HCLNEEEDTL 970 980 990 1000 1010 1020 ESERKLFKCP KCLVDLETSN KLFEAQHEVV EKNDLLNFAL NSEEGSRDRF KVITEFLGRG AISYSDITI

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Isolation and characterization of PEP5, a gene essential for vacuolar biogenesis in Saccharomyces cerevisiae." Woolford C.A., Dixon C.K., Manolson M.F., Wright R., Jones E.W. Genetics 125:739-752(1990) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Characterization of the END1 gene required for vacuole biogenesis and gluconeogenic growth of budding yeast." Dulic V., Riezman H. EMBO J. 8:1349-1359(1989) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[4]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[5]	"Pep3p/Pep5p complex: a putative docking factor at multiple steps of vesicular transport to the vacuole of Saccharomyces cerevisiae." Srivastava A., Woolford C.A., Jones E.W. Genetics 156:105-122(2000) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, INTERACTION WITH PEP3 AND PEP7.
[6]	"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] [Europe PMC] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[7]	"Purification of active HOPS complex reveals its affinities for phosphoinositides and the SNARE Vam7p." Stroupe C., Collins K.M., Fratti R.A., Wickner W. EMBO J. 25:1579-1589(2006) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION IN THE HOPS COMPLEX, FUNCTION OF THE HOPS COMPLEX, INTERACTION WITH VAM7.
[8]	"Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases." Smolka M.B., Albuquerque C.P., Chen S.H., Zhou H. Proc. Natl. Acad. Sci. U.S.A. 104:10364-10369(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-608, MASS SPECTROMETRY.
[9]	"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 THR-608 AND THR-609, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	X54466 Genomic DNA. Translation: CAA38348.1. X15355 Genomic DNA. Translation: CAA33413.1. Z49939 Genomic DNA. Translation: CAA90202.1. BK006946 Genomic DNA. Translation: DAA10131.1.
PIR	S57598.
RefSeq	NP_013958.1. NM_001182738.1.
3D structure databases
ProteinModelPortal	P12868.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-4409N.
IntAct	P12868. 13 interactions.
MINT	MINT-545862.
STRING	4932.YMR231W.
Proteomic databases
PaxDb	P12868.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YMR231W; YMR231W; YMR231W.
GeneID	855271.
KEGG	sce:YMR231W.
Organism-specific databases
CYGD	YMR231w.
SGD	S000004844. PEP5.
Phylogenomic databases
eggNOG	NOG294563.
GeneTree	ENSGT00390000015058.
HOGENOM	HOG000074719.
OMA	YLLIVSP.
OrthoDB	EOG47WRWW.
Gene expression databases
Genevestigator	P12868.
GermOnline	YMR231W. Saccharomyces cerevisiae.
Family and domain databases
Gene3D	2.130.10.10. 1 hit. 3.30.40.10. 1 hit.
InterPro	IPR016528. VPS11. IPR024763. VPS11_C. IPR015943. WD40/YVTN_repeat-like_dom. IPR017986. WD40_repeat_dom. IPR001965. Znf_PHD. IPR001841. Znf_RING. IPR013083. Znf_RING/FYVE/PHD. [Graphical view]
Pfam	PF12451. VPS11_C. 1 hit. [Graphical view]
PIRSF	PIRSF007860. VPS11. 1 hit.
SMART	SM00249. PHD. 1 hit. SM00184. RING. 1 hit. [Graphical view]
SUPFAM	SSF50978. WD40_like. 1 hit.
PROSITE	PS00518. ZF_RING_1. False negative. PS50089. ZF_RING_2. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	978885.

Entry information

Entry name

PEP5_YEAST

Accession

Primary (citable) accession number: P12868
Secondary accession number(s): D6W057

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1989
Last sequence update:	August 1, 1991
Last modified:	May 1, 2013
This is version 125 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program