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Protein

Vacuolar membrane protein PEP3

Gene

PEP3

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. 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.2 Publications

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri826 – 85126RING-type; atypicalAdd
BLAST

GO - Molecular functioni

  • protein binding, bridging Source: SGD
  • zinc ion binding Source: InterPro

GO - Biological processi

  • Golgi to endosome transport Source: SGD
  • intracellular protein transport Source: InterPro
  • late endosome to vacuole transport Source: SGD
  • 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: SGD
Complete GO annotation...

Keywords - Biological processi

Protein transport, Transport

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

BioCyciYEAST:G3O-32284-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Vacuolar membrane protein PEP3
Alternative name(s):
Carboxypeptidase Y-deficient protein 3
Vacuolar morphogenesis protein 8
Vacuolar protein sorting-associated protein 18
Vacuolar protein-targeting protein 18
Gene namesi
Name:PEP3
Synonyms:VAM8, VPS18, VPT18
Ordered Locus Names:YLR148W
ORF Names:L9634.2
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311 Componenti: Chromosome XII

Organism-specific databases

CYGDiYLR148w.
EuPathDBiFungiDB:YLR148W.
SGDiS000004138. PEP3.

Subcellular locationi

GO - Cellular componenti

  • CORVET complex Source: SGD
  • extrinsic component of vacuolar membrane Source: SGD
  • fungal-type vacuole membrane Source: SGD
  • HOPS complex Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Membrane, Vacuole

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 918918Vacuolar membrane protein PEP3PRO_0000055993Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei907 – 9071Phosphoserine2 Publications

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP27801.
PaxDbiP27801.
PRIDEiP27801.

Interactioni

Subunit structurei

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 PEP5, PEP7 and VAM7.2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
PEP5P128687EBI-13130,EBI-6450
VPS33P207957EBI-13130,EBI-20395

Protein-protein interaction databases

BioGridi31417. 70 interactions.
DIPiDIP-5912N.
IntActiP27801. 15 interactions.
MINTiMINT-615177.

Structurei

Secondary structure

1
918
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 97Combined sources
Turni15 – 173Combined sources
Beta strandi22 – 265Combined sources
Beta strandi29 – 335Combined sources
Beta strandi35 – 428Combined sources
Beta strandi49 – 535Combined sources
Beta strandi58 – 603Combined sources
Beta strandi63 – 686Combined sources
Beta strandi75 – 795Combined sources
Beta strandi84 – 885Combined sources
Beta strandi91 – 944Combined sources
Helixi96 – 983Combined sources
Beta strandi103 – 11816Combined sources
Beta strandi123 – 1297Combined sources
Beta strandi134 – 1418Combined sources
Beta strandi149 – 1557Combined sources
Beta strandi158 – 1636Combined sources
Beta strandi166 – 1716Combined sources
Beta strandi178 – 1803Combined sources
Beta strandi184 – 1885Combined sources
Beta strandi199 – 2035Combined sources
Beta strandi206 – 21914Combined sources
Turni237 – 2404Combined sources
Beta strandi242 – 2454Combined sources
Helixi246 – 2483Combined sources
Beta strandi260 – 2656Combined sources
Beta strandi267 – 2748Combined sources
Beta strandi277 – 2826Combined sources
Turni283 – 2853Combined sources
Beta strandi288 – 2936Combined sources
Beta strandi310 – 3167Combined sources
Turni317 – 3204Combined sources
Beta strandi321 – 3288Combined sources
Beta strandi330 – 3378Combined sources
Helixi338 – 3469Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4UUYX-ray2.14A/B2-348[»]
ProteinModelPortaliP27801.
SMRiP27801. Positions 2-347, 820-856.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Repeati585 – 741157CHCRAdd
BLAST

Sequence similaritiesi

Belongs to the VPS18 family.Curated
Contains 1 CHCR (clathrin heavy-chain) repeat.PROSITE-ProRule annotation
Contains 1 RING-type zinc finger.Curated

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri826 – 85126RING-type; atypicalAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiNOG246118.
GeneTreeiENSGT00390000015233.
HOGENOMiHOG000001125.
InParanoidiP27801.
OMAiQIARTRV.
OrthoDBiEOG7673K5.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR000547. Clathrin_H-chain/VPS_repeat.
IPR007810. Pep3_Vps18.
IPR019453. VPS39/TGF_beta_rcpt-assoc_2.
IPR001841. Znf_RING.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamiPF00637. Clathrin. 1 hit.
PF05131. Pep3_Vps18. 1 hit.
PF10367. Vps39_2. 1 hit.
[Graphical view]
SMARTiSM00299. CLH. 1 hit.
SM00184. RING. 1 hit.
[Graphical view]
PROSITEiPS50236. CHCR. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P27801-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MIKTRIEEVQ LQFLTGNTEL THLKVSNDQL IVTTQRTIYR INLQDPAIVN
60 70 80 90 100
HFDCPLSKEL ETIMNVHVSP MGSVILIRTN FGRYMLLKDG EFTQLNKIKN
110 120 130 140 150
LDLSSLHWIN ETTFLMGIKK TPKLYRVELT GKDITTKLWY ENKKLSGGID
160 170 180 190 200
GIAYWEGSLL LTIKDNILYW RDVTNMKFPL VLPDESEQFE RLKHHAIKKF
210 220 230 240 250
DSYNGLFAWV TSNGIVFGDL KEKQMEKDPA SNNFGKFLSS SKVLLNFELP
260 270 280 290 300
DYQNDKDHLI KDIVLTAFHI LLLRKNTVTM VSQLNNDVVF HETIPRHQLT
310 320 330 340 350
GSNTDSNEKF LGLVRDSVKE TFWCFSNINV FEIIIENEPN SVWNLLVRDN
360 370 380 390 400
KFDKALSLKG LTVREIESVK LSKAMYLFHT AKDFHSAAQT LGSMKDLSHF
410 420 430 440 450
GEIALNFLQI KDYNDLNVIL IKQLDNVPWK STQVVLSSWI IWNFMKQLND
460 470 480 490 500
IELKINTTKP ASTDEDNLLN WNLNLKEKSN ELTKFLESHL EKLDNETVYQ
510 520 530 540 550
IMSKQNRQNE LLIFASLIND MKFLLSFWID QGNWYESLKI LLTINNHDLV
560 570 580 590 600
YKYSLILLLN SPEATVSTWM KIKDLDPNKL IPTILKFFTN WQNNSKLITN
610 620 630 640 650
ISEYPENYSL TYLKWCVREV PKMCNPIVYN SILYMMITDP RNDMILENDI
660 670 680 690 700
IKFMKSNENK YDLNFQLRLS LKFKKTKTSI FLLTRLNLFE DAIDLALKNN
710 720 730 740 750
LIDDCKVIVN DEILIEDYKL RKRLWLKIAK HLLLSMKDID IKQLIRTILN
760 770 780 790 800
DSNEILTIKD LLPFFNEYTT IANLKEELIK FLENHNMKMN EISEDIINSK
810 820 830 840 850
NLKVEINTEI SKFNEIYRIL EPGKSCDECG KFLQIKKFIV FPCGHCFHWN
860 870 880 890 900
CIIRVILNSN DYNLRQKTEN FLKAKSKHNL NDLENIIVEK CGLCSDININ
910
KIDQPISIDE TELAKWNE
Length:918
Mass (Da):107,398
Last modified:August 1, 1992 - v1
Checksum:i37AE3C34AE0470B8
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M65144 Genomic DNA. Translation: AAA34852.1.
Z73320 Genomic DNA. Translation: CAA97720.1.
U53879 Genomic DNA. Translation: AAB82382.1.
BK006945 Genomic DNA. Translation: DAA09459.1.
PIRiA41943.
RefSeqiNP_013249.1. NM_001182035.1.

Genome annotation databases

EnsemblFungiiYLR148W; YLR148W; YLR148W.
GeneIDi850840.
KEGGisce:YLR148W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M65144 Genomic DNA. Translation: AAA34852.1.
Z73320 Genomic DNA. Translation: CAA97720.1.
U53879 Genomic DNA. Translation: AAB82382.1.
BK006945 Genomic DNA. Translation: DAA09459.1.
PIRiA41943.
RefSeqiNP_013249.1. NM_001182035.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4UUYX-ray2.14A/B2-348[»]
ProteinModelPortaliP27801.
SMRiP27801. Positions 2-347, 820-856.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi31417. 70 interactions.
DIPiDIP-5912N.
IntActiP27801. 15 interactions.
MINTiMINT-615177.

Proteomic databases

MaxQBiP27801.
PaxDbiP27801.
PRIDEiP27801.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYLR148W; YLR148W; YLR148W.
GeneIDi850840.
KEGGisce:YLR148W.

Organism-specific databases

CYGDiYLR148w.
EuPathDBiFungiDB:YLR148W.
SGDiS000004138. PEP3.

Phylogenomic databases

eggNOGiNOG246118.
GeneTreeiENSGT00390000015233.
HOGENOMiHOG000001125.
InParanoidiP27801.
OMAiQIARTRV.
OrthoDBiEOG7673K5.

Enzyme and pathway databases

BioCyciYEAST:G3O-32284-MONOMER.

Miscellaneous databases

NextBioi967123.
PROiP27801.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR000547. Clathrin_H-chain/VPS_repeat.
IPR007810. Pep3_Vps18.
IPR019453. VPS39/TGF_beta_rcpt-assoc_2.
IPR001841. Znf_RING.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamiPF00637. Clathrin. 1 hit.
PF05131. Pep3_Vps18. 1 hit.
PF10367. Vps39_2. 1 hit.
[Graphical view]
SMARTiSM00299. CLH. 1 hit.
SM00184. RING. 1 hit.
[Graphical view]
PROSITEiPS50236. CHCR. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Isolation and characterization of PEP3, a gene required for vacuolar biogenesis in Saccharomyces cerevisiae."
    Preston R., Manolson M.F., Becherer K., Weindnhammer E., Kirkpatrick D., Wright R., Jones E.W.
    Mol. Cell. Biol. 11:5801-5812(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "A putative zinc finger protein, Saccharomyces cerevisiae Vps18p, affects late Golgi functions required for vacuolar protein sorting and efficient alpha-factor prohormone maturation."
    Robinson J.S., Graham T.R., Emr S.D.
    Mol. Cell. Biol. 11:5813-5824(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XII."
    Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W., Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A., Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K., Heuss-Neitzel D., Hilbert H.
    , Hilger F., Kleine K., Koetter P., Louis E.J., Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S., Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D., Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M., Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P., Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M., Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K., Zollner A., Hani J., Hoheisel J.D.
    Nature 387:87-90(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  4. 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 PEP5 AND PEP7.
  6. 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. "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-907, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  9. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
    Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
    Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-907, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiPEP3_YEAST
AccessioniPrimary (citable) accession number: P27801
Secondary accession number(s): D6VYE3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1992
Last sequence update: August 1, 1992
Last modified: July 22, 2015
This is version 139 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 2020 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 XII
    Yeast (Saccharomyces cerevisiae) chromosome XII: 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.