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Protein

E3 ubiquitin-protein ligase PEP5

Gene

PEP5

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 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 (PubMed:3062374, PubMed:10978279, PubMed:10944212, PubMed:16601699). Acts as component of the CORVET complex that is required for transport between endosome and vacuole. CORVET is an effector for the endosomal Rab GTPase VPS21 (PubMed:17488625). Probable ubiquitin-protein ligase involved in the degradation-related ubiquitination of histones. Contributes to the post-translational regulation of histone protein levels by polyubiquitination of excess histones for subsequent degradation (PubMed:22570702).6 Publications

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri928 – 97346RING-typePROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  1. ligase activity Source: UniProtKB-KW
  2. ubiquitin-protein transferase activity Source: SGD
  3. zinc ion binding Source: InterPro

GO - Biological processi

  1. Golgi to endosome transport Source: SGD
  2. histone catabolic process Source: SGD
  3. histone ubiquitination Source: SGD
  4. intracellular protein transport Source: InterPro
  5. late endosome to vacuole transport Source: SGD
  6. regulation of SNARE complex assembly Source: SGD
  7. regulation of vacuole fusion, non-autophagic Source: SGD
  8. vacuole fusion, non-autophagic Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

Protein transport, Transport, Ubl conjugation pathway

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

BioCyciYEAST:G3O-32912-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
E3 ubiquitin-protein ligase PEP51 Publication (EC:6.3.2.-1 Publication)
Alternative name(s):
Carboxypeptidase Y-deficient protein 51 Publication
Histone E3 ligase PEP51 Publication
Vacuolar biogenesis protein END11 Publication
Vacuolar morphogenesis protein 11 Publication
Vacuolar protein sorting-associated protein 111 Publication
Vacuolar protein-targeting protein 111 Publication
Gene namesi
Name:PEP51 Publication
Synonyms:END11 Publication, VAM11 Publication, VPL91 Publication, VPS111 Publication, VPT111 Publication
Ordered Locus Names:YMR231W
ORF Names:YM9959.13
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311 Componenti: Chromosome XIII

Organism-specific databases

CYGDiYMR231w.
SGDiS000004844. PEP5.

Subcellular locationi

Vacuole membrane 1 Publication; Peripheral membrane protein 1 Publication; Cytoplasmic side 1 Publication

GO - Cellular componenti

  1. CORVET complex Source: SGD
  2. fungal-type vacuole membrane Source: SGD
  3. HOPS complex Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Membrane, Vacuole

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 10291029E3 ubiquitin-protein ligase PEP5PRO_0000055995Add
BLAST

Proteomic databases

MaxQBiP12868.
PaxDbiP12868.

Expressioni

Gene expression databases

GenevestigatoriP12868.

Interactioni

Subunit structurei

Component of the homotypic vacuole fusion and vacuole protein sorting (HOPS) complex, which is composed of a core of the 4 class C Vps proteins PEP5/VPS11, PEP3/VPS18, VPS16, VPS33 associated to VAM6/VPS39 and VPS41/VAM2. HOPS associates with phosphoinositides and the PX domain of VAM7. Component of the class C core vacuole/endosome tethering (CORVET) complex, which is composed of a core of the 4 class C Vps proteins PEP5/VPS11, PEP3/VPS18, VPS16, VPS33 associated to VPS3/PEP6 and VPS8. Interacts with PEP3, PEP7 and VAM7. Interacts with the E2 ubiquitin-conjugating enzyme UBC4 and histones H3 and H4.5 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
PEP3P278017EBI-6450,EBI-13130
VPS33P207955EBI-6450,EBI-20395

Protein-protein interaction databases

BioGridi35409. 69 interactions.
DIPiDIP-4409N.
IntActiP12868. 13 interactions.
MINTiMINT-545862.
STRINGi4932.YMR231W.

Structurei

3D structure databases

ProteinModelPortaliP12868.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Repeati406 – 583178CHCRPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the VPS11 family.Curated
Contains 1 CHCR (clathrin heavy-chain) repeat.PROSITE-ProRule annotation
Contains 1 RING-type zinc finger.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri928 – 97346RING-typePROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiNOG294563.
GeneTreeiENSGT00390000015058.
HOGENOMiHOG000074719.
InParanoidiP12868.
OMAiGMHEDVL.
OrthoDBiEOG7GN2W1.

Family and domain databases

Gene3Di2.130.10.10. 1 hit.
3.30.40.10. 1 hit.
InterProiIPR000547. Clathrin_H-chain/VPS_repeat.
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]
PANTHERiPTHR23323:SF24. PTHR23323:SF24. 1 hit.
PfamiPF12451. VPS11_C. 1 hit.
[Graphical view]
SMARTiSM00249. PHD. 1 hit.
SM00184. RING. 1 hit.
[Graphical view]
SUPFAMiSSF50978. SSF50978. 1 hit.
PROSITEiPS50236. CHCR. 1 hit.
PS50089. ZF_RING_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P12868-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSLSSWRQFQ LFENIPIRDP NFGGDSLLYS DPTLCAATIV DPQTLIIAVN
60 70 80 90 100
SNIIKVVKLN QSQVIHEFQS FPHDFQITFL KVINGEFLVA LAESIGKPSL
110 120 130 140 150
IRVYKLEKLP NREQLYHSQV ELKNGNNTYP ISVVSISNDL SCIVVGFING
160 170 180 190 200
KIILIRGDIS RDRGSQQRII YEDPSKEPIT ALFLNNDATA CFAATTSRIL
210 220 230 240 250
LFNTTGRNRG RPSLVLNSKN GLDLNCGSFN PATNEFICCL SNFIEFFSSS
260 270 280 290 300
GKKHQFAFDL SLRKRIFCVD KDHILIVTEE TGVPTTSISV NELSPTIINR
310 320 330 340 350
IFIIDAKNKI ISLNFVVSSA IIDIFSTSQS GKNITYLLTS EGVMHRITPK
360 370 380 390 400
SLENQINIII QKELYPFALQ LAKQHSLSPL DVQEIHKKYG DYLFKKGLRK
410 420 430 440 450
EATDQYIQCL DVVETSEIIS KFGVKEVPDP ESMRNLADYL WSLIKNSISQ
460 470 480 490 500
RDHVTLLLIV LIKLKDVEGI DTFIQHFDRK GIWNEGVVMD DMDDVTFFYS
510 520 530 540 550
DNDFFDLDLI LELMKESDFK RLSYRLAKKY SKDSLIIVDI LLNLLHNPVK
560 570 580 590 600
AIKYIKSLPI DETLRCLVTY SKKLLEESPN ETNALLIEVF TGKFKPSTFE
610 620 630 640 650
VDLDRRDTTG DFSENIRTVF YSYKTFFNYM NSNGTSDAMS ESSEASHEHE
660 670 680 690 700
EPTYHPPKPS IVFSSFVTKP FEFVVFLEAC LACYQQYEGF DEDRQVILTT
710 720 730 740 750
LYDLYLNLAQ NDVPERIDDW RSRATGVLRE SNKLVYSAAS NNTSKRVDNS
760 770 780 790 800
IMLLISHMDQ SSASAKDKTK IDIASFANDN PEMDLLSTFR AMTLNEEPST
810 820 830 840 850
CLKFLEKYGT EEPKLLQVAL SYFVSNKLIF KEMGGNEVLK EKVLRPIIEG
860 870 880 890 900
ERMPLLDIIK ALSRTNVAHF GLIQDIIIDH VKTEDTEIKR NEKLIESYDK
910 920 930 940 950
ELKEKNKKLK NTINSDQPLH VPLKNQTCFM CRLTLDIPVV FFKCGHIYHQ
960 970 980 990 1000
HCLNEEEDTL ESERKLFKCP KCLVDLETSN KLFEAQHEVV EKNDLLNFAL
1010 1020
NSEEGSRDRF KVITEFLGRG AISYSDITI
Length:1,029
Mass (Da):117,478
Last modified:August 1, 1991 - v2
Checksum:iE5216AD3C285CF34
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti37 – 371A → R in CAA33413 (PubMed:2670552).Curated
Sequence conflicti619 – 6257VFYSYKT → MFFTVTKH in CAA33413 (PubMed:2670552).Curated
Sequence conflicti769 – 7702TK → KQ in CAA33413 (PubMed:2670552).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X54466 Genomic DNA. Translation: CAA38348.1.
X15355 Genomic DNA. Translation: CAA33413.1.
Z49939 Genomic DNA. Translation: CAA90202.1.
BK006946 Genomic DNA. Translation: DAA10131.1.
PIRiS57598.
RefSeqiNP_013958.1. NM_001182738.1.

Genome annotation databases

EnsemblFungiiYMR231W; YMR231W; YMR231W.
GeneIDi855271.
KEGGisce:YMR231W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X54466 Genomic DNA. Translation: CAA38348.1.
X15355 Genomic DNA. Translation: CAA33413.1.
Z49939 Genomic DNA. Translation: CAA90202.1.
BK006946 Genomic DNA. Translation: DAA10131.1.
PIRiS57598.
RefSeqiNP_013958.1. NM_001182738.1.

3D structure databases

ProteinModelPortaliP12868.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi35409. 69 interactions.
DIPiDIP-4409N.
IntActiP12868. 13 interactions.
MINTiMINT-545862.
STRINGi4932.YMR231W.

Proteomic databases

MaxQBiP12868.
PaxDbiP12868.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYMR231W; YMR231W; YMR231W.
GeneIDi855271.
KEGGisce:YMR231W.

Organism-specific databases

CYGDiYMR231w.
SGDiS000004844. PEP5.

Phylogenomic databases

eggNOGiNOG294563.
GeneTreeiENSGT00390000015058.
HOGENOMiHOG000074719.
InParanoidiP12868.
OMAiGMHEDVL.
OrthoDBiEOG7GN2W1.

Enzyme and pathway databases

BioCyciYEAST:G3O-32912-MONOMER.

Miscellaneous databases

NextBioi978885.
PROiP12868.

Gene expression databases

GenevestigatoriP12868.

Family and domain databases

Gene3Di2.130.10.10. 1 hit.
3.30.40.10. 1 hit.
InterProiIPR000547. Clathrin_H-chain/VPS_repeat.
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]
PANTHERiPTHR23323:SF24. PTHR23323:SF24. 1 hit.
PfamiPF12451. VPS11_C. 1 hit.
[Graphical view]
SMARTiSM00249. PHD. 1 hit.
SM00184. RING. 1 hit.
[Graphical view]
SUPFAMiSSF50978. SSF50978. 1 hit.
PROSITEiPS50236. CHCR. 1 hit.
PS50089. ZF_RING_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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(1989) [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(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  4. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  5. "Proteinase mutants of Saccharomyces cerevisiae."
    Jones E.W.
    Genetics 85:23-33(1976) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION.
  6. "Two yeast mutants defective in endocytosis are defective in pheromone response."
    Chvatchko Y., Howald I., Riezman H.
    Cell 46:355-364(1985) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION.
  7. "Protein sorting in Saccharomyces cerevisiae: isolation of mutants defective in the delivery and processing of multiple vacuolar hydrolases."
    Robinson J.S., Klionsky D.J., Banta L.M., Emr S.D.
    Mol. Cell. Biol. 8:4936-4948(1987) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  8. "Characterization of genes required for protein sorting and vacuolar function in the yeast Saccharomyces cerevisiae."
    Rothman J.H., Howald I., Stevens T.H.
    EMBO J. 8:2057-2065(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION.
  9. "Genes for directing vacuolar morphogenesis in Saccharomyces cerevisiae. I. Isolation and characterization of two classes of vam mutants."
    Wada Y., Ohsumi Y., Anraku Y.
    J. Biol. Chem. 267:18665-18670(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION.
  10. "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(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH PEP3 AND PEP7.
  11. "A Ypt/Rab effector complex containing the Sec1 homolog Vps33p is required for homotypic vacuole fusion."
    Seals D.F., Eitzen G., Margolis N., Wickner W.T., Price A.
    Proc. Natl. Acad. Sci. U.S.A. 97:9402-9407(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN THE HOPS COMPLEX, SUBCELLULAR LOCATION.
  12. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  13. "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(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN THE HOPS COMPLEX, FUNCTION OF THE HOPS COMPLEX, INTERACTION WITH VAM7.
  14. "The CORVET tethering complex interacts with the yeast Rab5 homolog Vps21 and is involved in endo-lysosomal biogenesis."
    Peplowska K., Markgraf D.F., Ostrowicz C.W., Bange G., Ungermann C.
    Dev. Cell 12:739-750(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN THE CORVET COMPLEX.
  15. "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae."
    Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P.
    J. Proteome Res. 6:1190-1197(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Strain: ADR376.
  16. "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(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  17. "Novel E3 ubiquitin ligases that regulate histone protein levels in the budding yeast Saccharomyces cerevisiae."
    Singh R.K., Gonzalez M., Kabbaj M.H., Gunjan A.
    PLoS ONE 7:E36295-E36295(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH UBC4, INTERACTION WITH HISTONES H3 AND H4.

Entry informationi

Entry nameiPEP5_YEAST
AccessioniPrimary (citable) accession number: P12868
Secondary accession number(s): D6W057
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1989
Last sequence update: August 1, 1991
Last modified: April 1, 2015
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 1200 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  3. Yeast chromosome XIII
    Yeast (Saccharomyces cerevisiae) chromosome XIII: entries and gene names

External Data

Dasty 3

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 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.