PEP5_YEAST
ID PEP5_YEAST Reviewed; 1029 AA.
AC P12868; D6W057;
DT 01-OCT-1989, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1991, sequence version 2.
DT 03-AUG-2022, entry version 196.
DE RecName: Full=E3 ubiquitin-protein ligase PEP5 {ECO:0000305|PubMed:22570702};
DE EC=2.3.2.27 {ECO:0000269|PubMed:22570702};
DE AltName: Full=Carboxypeptidase Y-deficient protein 5 {ECO:0000303|PubMed:3062374};
DE AltName: Full=Histone E3 ligase PEP5 {ECO:0000303|PubMed:22570702};
DE AltName: Full=RING-type E3 ubiquitin transferase PEP5 {ECO:0000305};
DE AltName: Full=Vacuolar biogenesis protein END1 {ECO:0000303|PubMed:3524852};
DE AltName: Full=Vacuolar morphogenesis protein 1 {ECO:0000303|PubMed:1526998};
DE AltName: Full=Vacuolar protein sorting-associated protein 11 {ECO:0000303|PubMed:3062374};
DE AltName: Full=Vacuolar protein-targeting protein 11 {ECO:0000303|PubMed:3062374};
GN Name=PEP5 {ECO:0000303|PubMed:3062374};
GN Synonyms=END1 {ECO:0000303|PubMed:3524852},
GN VAM1 {ECO:0000303|PubMed:1526998}, VPL9 {ECO:0000303|PubMed:2676511},
GN VPS11 {ECO:0000303|PubMed:3062374}, VPT11 {ECO:0000303|PubMed:3062374};
GN OrderedLocusNames=YMR231W; ORFNames=YM9959.13;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=2204580; DOI=10.1093/genetics/125.4.739;
RA Woolford C.A., Dixon C.K., Manolson M.F., Wright R., Jones E.W.;
RT "Isolation and characterization of PEP5, a gene essential for vacuolar
RT biogenesis in Saccharomyces cerevisiae.";
RL Genetics 125:739-752(1990).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=2670552; DOI=10.1002/j.1460-2075.1989.tb03515.x;
RA Dulic V., Riezman H.;
RT "Characterization of the END1 gene required for vacuole biogenesis and
RT gluconeogenic growth of budding yeast.";
RL EMBO J. 8:1349-1359(1989).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169872;
RA Bowman S., Churcher C.M., Badcock K., Brown D., Chillingworth T.,
RA Connor R., Dedman K., Devlin K., Gentles S., Hamlin N., Hunt S., Jagels K.,
RA Lye G., Moule S., Odell C., Pearson D., Rajandream M.A., Rice P.,
RA Skelton J., Walsh S.V., Whitehead S., Barrell B.G.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XIII.";
RL Nature 387:90-93(1997).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [5]
RP IDENTIFICATION.
RX PubMed=320092; DOI=10.1093/genetics/85.1.23;
RA Jones E.W.;
RT "Proteinase mutants of Saccharomyces cerevisiae.";
RL Genetics 85:23-33(1977).
RN [6]
RP IDENTIFICATION.
RX PubMed=3524852; DOI=10.1016/0092-8674(86)90656-2;
RA Chvatchko Y., Howald I., Riezman H.;
RT "Two yeast mutants defective in endocytosis are defective in pheromone
RT response.";
RL Cell 46:355-364(1986).
RN [7]
RP FUNCTION.
RX PubMed=3062374; DOI=10.1128/mcb.8.11.4936-4948.1988;
RA Robinson J.S., Klionsky D.J., Banta L.M., Emr S.D.;
RT "Protein sorting in Saccharomyces cerevisiae: isolation of mutants
RT defective in the delivery and processing of multiple vacuolar hydrolases.";
RL Mol. Cell. Biol. 8:4936-4948(1988).
RN [8]
RP IDENTIFICATION.
RX PubMed=2676511; DOI=10.1002/j.1460-2075.1989.tb03614.x;
RA Rothman J.H., Howald I., Stevens T.H.;
RT "Characterization of genes required for protein sorting and vacuolar
RT function in the yeast Saccharomyces cerevisiae.";
RL EMBO J. 8:2057-2065(1989).
RN [9]
RP IDENTIFICATION.
RX PubMed=1526998; DOI=10.1016/s0021-9258(19)37012-7;
RA Wada Y., Ohsumi Y., Anraku Y.;
RT "Genes for directing vacuolar morphogenesis in Saccharomyces cerevisiae. I.
RT Isolation and characterization of two classes of vam mutants.";
RL J. Biol. Chem. 267:18665-18670(1992).
RN [10]
RP FUNCTION, AND INTERACTION WITH PEP3 AND PEP7.
RX PubMed=10978279; DOI=10.1093/genetics/156.1.105;
RA Srivastava A., Woolford C.A., Jones E.W.;
RT "Pep3p/Pep5p complex: a putative docking factor at multiple steps of
RT vesicular transport to the vacuole of Saccharomyces cerevisiae.";
RL Genetics 156:105-122(2000).
RN [11]
RP IDENTIFICATION IN THE HOPS COMPLEX, AND SUBCELLULAR LOCATION.
RX PubMed=10944212; DOI=10.1073/pnas.97.17.9402;
RA Seals D.F., Eitzen G., Margolis N., Wickner W.T., Price A.;
RT "A Ypt/Rab effector complex containing the Sec1 homolog Vps33p is required
RT for homotypic vacuole fusion.";
RL Proc. Natl. Acad. Sci. U.S.A. 97:9402-9407(2000).
RN [12]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [13]
RP IDENTIFICATION IN THE HOPS COMPLEX, FUNCTION OF THE HOPS COMPLEX, AND
RP INTERACTION WITH VAM7.
RX PubMed=16601699; DOI=10.1038/sj.emboj.7601051;
RA Stroupe C., Collins K.M., Fratti R.A., Wickner W.;
RT "Purification of active HOPS complex reveals its affinities for
RT phosphoinositides and the SNARE Vam7p.";
RL EMBO J. 25:1579-1589(2006).
RN [14]
RP IDENTIFICATION IN THE CORVET COMPLEX.
RX PubMed=17488625; DOI=10.1016/j.devcel.2007.03.006;
RA Peplowska K., Markgraf D.F., Ostrowicz C.W., Bange G., Ungermann C.;
RT "The CORVET tethering complex interacts with the yeast Rab5 homolog Vps21
RT and is involved in endo-lysosomal biogenesis.";
RL Dev. Cell 12:739-750(2007).
RN [15]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ADR376;
RX PubMed=17330950; DOI=10.1021/pr060559j;
RA Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
RA Elias J.E., Gygi S.P.;
RT "Large-scale phosphorylation analysis of alpha-factor-arrested
RT Saccharomyces cerevisiae.";
RL J. Proteome Res. 6:1190-1197(2007).
RN [16]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT "A multidimensional chromatography technology for in-depth phosphoproteome
RT analysis.";
RL Mol. Cell. Proteomics 7:1389-1396(2008).
RN [17]
RP FUNCTION, INTERACTION WITH UBC4, AND INTERACTION WITH HISTONES H3 AND H4.
RX PubMed=22570702; DOI=10.1371/journal.pone.0036295;
RA Singh R.K., Gonzalez M., Kabbaj M.H., Gunjan A.;
RT "Novel E3 ubiquitin ligases that regulate histone protein levels in the
RT budding yeast Saccharomyces cerevisiae.";
RL PLoS ONE 7:E36295-E36295(2012).
CC -!- FUNCTION: Required for vacuolar biogenesis and for trafficking of
CC hydrolase precursors to the vacuole. Mediates transport at the vacuolar
CC membrane where it may be responsible for tethering transport vesicles
CC on the target membranes. It is required for gluconeogenic growth of
CC yeast. Acts as component of the HOPS complex that acts during the
CC docking stage of vacuole fusion. HOPS is an effector for the vacuolar
CC Rab GTPase YPT7 and is required for vacuolar SNARE complex assembly. It
CC remains bound to SNARE complexes after vacuole fusion (PubMed:3062374,
CC PubMed:10978279, PubMed:10944212, PubMed:16601699). Acts as component
CC of the CORVET complex that is required for transport between endosome
CC and vacuole. CORVET is an effector for the endosomal Rab GTPase VPS21
CC (PubMed:17488625). Probable ubiquitin-protein ligase involved in the
CC degradation-related ubiquitination of histones. Contributes to the
CC post-translational regulation of histone protein levels by
CC polyubiquitination of excess histones for subsequent degradation
CC (PubMed:22570702). {ECO:0000269|PubMed:10944212,
CC ECO:0000269|PubMed:10978279, ECO:0000269|PubMed:16601699,
CC ECO:0000269|PubMed:17488625, ECO:0000269|PubMed:22570702,
CC ECO:0000269|PubMed:3062374}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine +
CC [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-
CC cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine.;
CC EC=2.3.2.27; Evidence={ECO:0000269|PubMed:22570702};
CC -!- SUBUNIT: Component of the homotypic vacuole fusion and vacuole protein
CC sorting (HOPS) complex, which is composed of a core of the 4 class C
CC Vps proteins PEP5/VPS11, PEP3/VPS18, VPS16, VPS33 associated to
CC VAM6/VPS39 and VPS41/VAM2. HOPS associates with phosphoinositides and
CC the PX domain of VAM7. Component of the class C core vacuole/endosome
CC tethering (CORVET) complex, which is composed of a core of the 4 class
CC C Vps proteins PEP5/VPS11, PEP3/VPS18, VPS16, VPS33 associated to
CC VPS3/PEP6 and VPS8. Interacts with PEP3, PEP7 and VAM7. Interacts with
CC the E2 ubiquitin-conjugating enzyme UBC4 and histones H3 and H4.
CC {ECO:0000269|PubMed:10944212, ECO:0000269|PubMed:10978279,
CC ECO:0000269|PubMed:16601699, ECO:0000269|PubMed:17488625,
CC ECO:0000269|PubMed:22570702}.
CC -!- INTERACTION:
CC P12868; P27801: PEP3; NbExp=6; IntAct=EBI-6450, EBI-13130;
CC P12868; P20795: VPS33; NbExp=5; IntAct=EBI-6450, EBI-20395;
CC -!- SUBCELLULAR LOCATION: Vacuole membrane {ECO:0000269|PubMed:10944212};
CC Peripheral membrane protein {ECO:0000269|PubMed:10944212}; Cytoplasmic
CC side {ECO:0000269|PubMed:10944212}.
CC -!- MISCELLANEOUS: Present with 1200 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the VPS11 family. {ECO:0000305}.
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DR EMBL; X54466; CAA38348.1; -; Genomic_DNA.
DR EMBL; X15355; CAA33413.1; -; Genomic_DNA.
DR EMBL; Z49939; CAA90202.1; -; Genomic_DNA.
DR EMBL; BK006946; DAA10131.1; -; Genomic_DNA.
DR PIR; S57598; S57598.
DR RefSeq; NP_013958.1; NM_001182738.1.
DR AlphaFoldDB; P12868; -.
DR BioGRID; 35409; 86.
DR ComplexPortal; CPX-1625; HOPS complex.
DR ComplexPortal; CPX-1626; CORVET complex.
DR DIP; DIP-4409N; -.
DR IntAct; P12868; 14.
DR MINT; P12868; -.
DR STRING; 4932.YMR231W; -.
DR iPTMnet; P12868; -.
DR MaxQB; P12868; -.
DR PaxDb; P12868; -.
DR PRIDE; P12868; -.
DR EnsemblFungi; YMR231W_mRNA; YMR231W; YMR231W.
DR GeneID; 855271; -.
DR KEGG; sce:YMR231W; -.
DR SGD; S000004844; PEP5.
DR VEuPathDB; FungiDB:YMR231W; -.
DR eggNOG; KOG2114; Eukaryota.
DR GeneTree; ENSGT00940000153635; -.
DR HOGENOM; CLU_001287_0_0_1; -.
DR InParanoid; P12868; -.
DR OMA; MRPQSTM; -.
DR BioCyc; YEAST:G3O-32912-MON; -.
DR PRO; PR:P12868; -.
DR Proteomes; UP000002311; Chromosome XIII.
DR RNAct; P12868; protein.
DR GO; GO:0033263; C:CORVET complex; IDA:SGD.
DR GO; GO:0005829; C:cytosol; IEA:GOC.
DR GO; GO:0031901; C:early endosome membrane; IDA:ComplexPortal.
DR GO; GO:0005768; C:endosome; IBA:GO_Central.
DR GO; GO:0000329; C:fungal-type vacuole membrane; IDA:SGD.
DR GO; GO:0030897; C:HOPS complex; IPI:SGD.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0030674; F:protein-macromolecule adaptor activity; IBA:GO_Central.
DR GO; GO:0061630; F:ubiquitin protein ligase activity; IDA:SGD.
DR GO; GO:0007032; P:endosome organization; IBA:GO_Central.
DR GO; GO:0006895; P:Golgi to endosome transport; IGI:SGD.
DR GO; GO:0036205; P:histone catabolic process; IMP:SGD.
DR GO; GO:0016574; P:histone ubiquitination; IDA:SGD.
DR GO; GO:0006886; P:intracellular protein transport; IEA:InterPro.
DR GO; GO:0045324; P:late endosome to vacuole transport; IGI:SGD.
DR GO; GO:0048284; P:organelle fusion; IBA:GO_Central.
DR GO; GO:0035542; P:regulation of SNARE complex assembly; IDA:SGD.
DR GO; GO:0032889; P:regulation of vacuole fusion, non-autophagic; IDA:ComplexPortal.
DR GO; GO:0042144; P:vacuole fusion, non-autophagic; IDA:SGD.
DR GO; GO:0007033; P:vacuole organization; IBA:GO_Central.
DR GO; GO:0006904; P:vesicle docking involved in exocytosis; IBA:GO_Central.
DR GO; GO:0099022; P:vesicle tethering; IDA:SGD.
DR Gene3D; 2.130.10.10; -; 1.
DR Gene3D; 3.30.40.10; -; 1.
DR InterPro; IPR000547; Clathrin_H-chain/VPS_repeat.
DR InterPro; IPR016528; VPS11.
DR InterPro; IPR024763; VPS11_C.
DR InterPro; IPR015943; WD40/YVTN_repeat-like_dom_sf.
DR InterPro; IPR036322; WD40_repeat_dom_sf.
DR InterPro; IPR001965; Znf_PHD.
DR InterPro; IPR001841; Znf_RING.
DR InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR PANTHER; PTHR23323:SF24; PTHR23323:SF24; 1.
DR Pfam; PF12451; VPS11_C; 1.
DR PIRSF; PIRSF007860; VPS11; 1.
DR SMART; SM00249; PHD; 1.
DR SMART; SM00184; RING; 1.
DR SUPFAM; SSF50978; SSF50978; 1.
DR PROSITE; PS50236; CHCR; 1.
DR PROSITE; PS50089; ZF_RING_2; 1.
PE 1: Evidence at protein level;
KW Membrane; Metal-binding; Protein transport; Reference proteome;
KW Transferase; Transport; Ubl conjugation pathway; Vacuole; Zinc;
KW Zinc-finger.
FT CHAIN 1..1029
FT /note="E3 ubiquitin-protein ligase PEP5"
FT /id="PRO_0000055995"
FT REPEAT 406..583
FT /note="CHCR"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01006"
FT ZN_FING 928..973
FT /note="RING-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00175"
FT REGION 637..656
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT CONFLICT 37
FT /note="A -> R (in Ref. 2; CAA33413)"
FT /evidence="ECO:0000305"
FT CONFLICT 619..625
FT /note="VFYSYKT -> MFFTVTKH (in Ref. 2; CAA33413)"
FT /evidence="ECO:0000305"
FT CONFLICT 769..770
FT /note="TK -> KQ (in Ref. 2; CAA33413)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1029 AA; 117478 MW; E5216AD3C285CF34 CRC64;
MSLSSWRQFQ LFENIPIRDP NFGGDSLLYS DPTLCAATIV DPQTLIIAVN SNIIKVVKLN
QSQVIHEFQS FPHDFQITFL KVINGEFLVA LAESIGKPSL IRVYKLEKLP NREQLYHSQV
ELKNGNNTYP ISVVSISNDL SCIVVGFING KIILIRGDIS RDRGSQQRII YEDPSKEPIT
ALFLNNDATA CFAATTSRIL LFNTTGRNRG RPSLVLNSKN GLDLNCGSFN PATNEFICCL
SNFIEFFSSS GKKHQFAFDL SLRKRIFCVD KDHILIVTEE TGVPTTSISV NELSPTIINR
IFIIDAKNKI ISLNFVVSSA IIDIFSTSQS GKNITYLLTS EGVMHRITPK SLENQINIII
QKELYPFALQ LAKQHSLSPL DVQEIHKKYG DYLFKKGLRK EATDQYIQCL DVVETSEIIS
KFGVKEVPDP ESMRNLADYL WSLIKNSISQ RDHVTLLLIV LIKLKDVEGI DTFIQHFDRK
GIWNEGVVMD DMDDVTFFYS DNDFFDLDLI LELMKESDFK RLSYRLAKKY SKDSLIIVDI
LLNLLHNPVK AIKYIKSLPI DETLRCLVTY SKKLLEESPN ETNALLIEVF TGKFKPSTFE
VDLDRRDTTG DFSENIRTVF YSYKTFFNYM NSNGTSDAMS ESSEASHEHE EPTYHPPKPS
IVFSSFVTKP FEFVVFLEAC LACYQQYEGF DEDRQVILTT LYDLYLNLAQ NDVPERIDDW
RSRATGVLRE SNKLVYSAAS NNTSKRVDNS IMLLISHMDQ SSASAKDKTK IDIASFANDN
PEMDLLSTFR AMTLNEEPST CLKFLEKYGT EEPKLLQVAL SYFVSNKLIF KEMGGNEVLK
EKVLRPIIEG ERMPLLDIIK ALSRTNVAHF GLIQDIIIDH VKTEDTEIKR NEKLIESYDK
ELKEKNKKLK NTINSDQPLH VPLKNQTCFM CRLTLDIPVV FFKCGHIYHQ HCLNEEEDTL
ESERKLFKCP KCLVDLETSN KLFEAQHEVV EKNDLLNFAL NSEEGSRDRF KVITEFLGRG
AISYSDITI
