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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

Miscellaneous

Present with 1200 molecules/cell in log phase SD medium.1 Publication

Catalytic activityi

S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N6-ubiquitinyl-[acceptor protein]-L-lysine.1 Publication

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri928 – 973RING-typePROSITE-ProRule annotationAdd BLAST46

GO - Molecular functioni

GO - Biological processi

  • endosome organization Source: GO_Central
  • Golgi to endosome transport Source: SGD
  • histone catabolic process Source: SGD
  • histone ubiquitination Source: SGD
  • intracellular protein transport Source: InterPro
  • late endosome to vacuole transport Source: SGD
  • lysosome organization Source: GO_Central
  • regulation of SNARE complex assembly Source: SGD
  • regulation of vacuole fusion, non-autophagic Source: SGD
  • vacuole fusion, non-autophagic Source: SGD
  • vesicle docking involved in exocytosis Source: GO_Central
  • vesicle tethering Source: SGD

Keywordsi

Molecular functionTransferase
Biological processProtein transport, Transport, Ubl conjugation pathway
LigandMetal-binding, Zinc

Enzyme and pathway databases

BioCyciYEAST:G3O-32912-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
E3 ubiquitin-protein ligase PEP51 Publication (EC:2.3.2.271 Publication)
Alternative name(s):
Carboxypeptidase Y-deficient protein 51 Publication
Histone E3 ligase PEP51 Publication
RING-type E3 ubiquitin transferase PEP5Curated
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
Proteomesi
  • UP000002311 Componenti: Chromosome XIII

Organism-specific databases

EuPathDBiFungiDB:YMR231W.
SGDiS000004844. PEP5.

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Membrane, Vacuole

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000559951 – 1029E3 ubiquitin-protein ligase PEP5Add BLAST1029

Proteomic databases

MaxQBiP12868.
PRIDEiP12868.

PTM databases

iPTMnetiP12868.

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

Show more details

GO - Molecular functioni

Protein-protein interaction databases

BioGridi35409. 75 interactors.
DIPiDIP-4409N.
IntActiP12868. 14 interactors.
MINTiMINT-545862.
STRINGi4932.YMR231W.

Structurei

3D structure databases

ProteinModelPortaliP12868.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati406 – 583CHCRPROSITE-ProRule annotationAdd BLAST178

Sequence similaritiesi

Belongs to the VPS11 family.Curated

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri928 – 973RING-typePROSITE-ProRule annotationAdd BLAST46

Keywords - Domaini

Zinc-finger

Phylogenomic databases

GeneTreeiENSGT00390000015058.
HOGENOMiHOG000074719.
InParanoidiP12868.
KOiK20179.
OMAiVLCQMHN.
OrthoDBiEOG092C0IPS.

Family and domain databases

Gene3Di1.25.40.10. 2 hits.
2.130.10.10. 1 hit.
3.30.40.10. 1 hit.
InterProiView protein in InterPro
IPR000547. Clathrin_H-chain/VPS_repeat.
IPR011990. TPR-like_helical_dom.
IPR016528. VPS11.
IPR024763. VPS11_C.
IPR015943. WD40/YVTN_repeat-like_dom.
IPR036322. WD40_repeat_dom_sf.
IPR001965. Znf_PHD.
IPR001841. Znf_RING.
IPR013083. Znf_RING/FYVE/PHD.
PANTHERiPTHR23323:SF24. PTHR23323:SF24. 1 hit.
PfamiView protein in Pfam
PF12451. VPS11_C. 1 hit.
PIRSFiPIRSF007860. VPS11. 1 hit.
SMARTiView protein in SMART
SM00249. PHD. 1 hit.
SM00184. RING. 1 hit.
SUPFAMiSSF50978. SSF50978. 1 hit.
PROSITEiView protein in PROSITE
PS50236. CHCR. 1 hit.
PS50089. ZF_RING_2. 1 hit.

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)DescriptionActionsGraphical viewLength
Sequence conflicti37A → R in CAA33413 (PubMed:2670552).Curated1
Sequence conflicti619 – 625VFYSYKT → MFFTVTKH in CAA33413 (PubMed:2670552).Curated7
Sequence conflicti769 – 770TK → KQ in CAA33413 (PubMed:2670552).Curated2

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.

Similar proteinsi

Entry informationi

Entry nameiPEP5_YEAST
AccessioniPrimary (citable) accession number: P12868
Secondary accession number(s): D6W057
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1989
Last sequence update: August 1, 1991
Last modified: October 25, 2017
This is version 167 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

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