PIB1_YEAST
ID PIB1_YEAST Reviewed; 286 AA.
AC Q06651; D6VSU2; Q6Q5S5;
DT 11-JUL-2006, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 157.
DE RecName: Full=E3 ubiquitin-protein ligase PIB1;
DE EC=2.3.2.27;
DE AltName: Full=Phosphatidylinositol 3-phosphate-binding protein 1;
DE AltName: Full=RING-type E3 ubiquitin transferase PIB1 {ECO:0000305};
GN Name=PIB1; OrderedLocusNames=YDR313C;
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 [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169867;
RA Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G.,
RA Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C.,
RA Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F.,
RA Delaveau T., del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M.,
RA Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T.,
RA Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C.,
RA Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S.,
RA Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L.,
RA Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H.,
RA Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M.,
RA Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M.,
RA Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A.,
RA Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G.,
RA Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E.,
RA Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S.,
RA Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D.,
RA Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V.,
RA Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E.,
RA Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M.,
RA Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D.,
RA Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X.,
RA Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A.,
RA Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R.,
RA Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T.,
RA Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L.,
RA Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E.,
RA Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L.,
RA Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M.,
RA Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K.,
RA Mewes H.-W., Zollner A., Zaccaria P.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV.";
RL Nature 387:75-78(1997).
RN [2]
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 [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=17322287; DOI=10.1101/gr.6037607;
RA Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
RA Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J.,
RA Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J.,
RA Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D.,
RA LaBaer J.;
RT "Approaching a complete repository of sequence-verified protein-encoding
RT clones for Saccharomyces cerevisiae.";
RL Genome Res. 17:536-543(2007).
RN [4]
RP FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=9702203; DOI=10.1016/s1097-2765(00)80125-2;
RA Burd C.G., Emr S.D.;
RT "Phosphatidylinositol(3)-phosphate signaling mediated by specific binding
RT to RING FYVE domains.";
RL Mol. Cell 2:157-162(1998).
RN [5]
RP FUNCTION, SUBCELLULAR LOCATION, AND MUTAGENESIS OF CYS-23 AND CYS-225.
RX PubMed=11526110; DOI=10.1074/jbc.m105665200;
RA Shin M.E., Ogburn K.D., Varban O.A., Gilbert P.M., Burd C.G.;
RT "FYVE domain targets Pib1p ubiquitin ligase to endosome and vacuolar
RT membranes.";
RL J. Biol. Chem. 276:41388-41393(2001).
RN [6]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=14562095; DOI=10.1038/nature02026;
RA Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA Weissman J.S., O'Shea E.K.;
RT "Global analysis of protein localization in budding yeast.";
RL Nature 425:686-691(2003).
RN [7]
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 [8]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22814378; DOI=10.1073/pnas.1210303109;
RA Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
RA Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E.,
RA Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.;
RT "N-terminal acetylome analyses and functional insights of the N-terminal
RT acetyltransferase NatB.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
CC -!- FUNCTION: Functions as an E3 ubiquitin-protein ligase. Binds
CC phospholipid vesicles containing phosphatidylinositol 3-phosphate.
CC {ECO:0000269|PubMed:11526110, ECO:0000269|PubMed:9702203}.
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;
CC -!- PATHWAY: Protein modification; protein ubiquitination.
CC -!- SUBCELLULAR LOCATION: Endosome membrane; Peripheral membrane protein.
CC Vacuole membrane; Peripheral membrane protein.
CC -!- DOMAIN: The FYVE domain mediates phosphatidylinositol 3-phosphate
CC binding and is necessary and sufficient for targeting to endosome and
CC vacuole membranes.
CC -!- MISCELLANEOUS: Present with 195 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
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DR EMBL; U28374; AAB64749.1; -; Genomic_DNA.
DR EMBL; AY557742; AAS56068.1; -; Genomic_DNA.
DR EMBL; BK006938; DAA12152.1; -; Genomic_DNA.
DR PIR; S61199; S61199.
DR RefSeq; NP_010599.1; NM_001180621.1.
DR AlphaFoldDB; Q06651; -.
DR BioGRID; 32366; 94.
DR DIP; DIP-1514N; -.
DR IntAct; Q06651; 3.
DR MINT; Q06651; -.
DR STRING; 4932.YDR313C; -.
DR iPTMnet; Q06651; -.
DR MaxQB; Q06651; -.
DR PaxDb; Q06651; -.
DR PRIDE; Q06651; -.
DR EnsemblFungi; YDR313C_mRNA; YDR313C; YDR313C.
DR GeneID; 851908; -.
DR KEGG; sce:YDR313C; -.
DR SGD; S000002721; PIB1.
DR VEuPathDB; FungiDB:YDR313C; -.
DR eggNOG; KOG1729; Eukaryota.
DR HOGENOM; CLU_069851_0_0_1; -.
DR InParanoid; Q06651; -.
DR OMA; FCPLHDA; -.
DR BioCyc; YEAST:G3O-29872-MON; -.
DR UniPathway; UPA00143; -.
DR PRO; PR:Q06651; -.
DR Proteomes; UP000002311; Chromosome IV.
DR RNAct; Q06651; protein.
DR GO; GO:0010008; C:endosome membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0000329; C:fungal-type vacuole membrane; IDA:SGD.
DR GO; GO:0005770; C:late endosome; IDA:SGD.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0032266; F:phosphatidylinositol-3-phosphate binding; IDA:SGD.
DR GO; GO:0004842; F:ubiquitin-protein transferase activity; IDA:SGD.
DR GO; GO:0045721; P:negative regulation of gluconeogenesis; IMP:SGD.
DR GO; GO:0016567; P:protein ubiquitination; IDA:SGD.
DR GO; GO:0042176; P:regulation of protein catabolic process; IMP:SGD.
DR GO; GO:0031647; P:regulation of protein stability; IMP:SGD.
DR Gene3D; 3.30.40.10; -; 2.
DR InterPro; IPR000306; Znf_FYVE.
DR InterPro; IPR017455; Znf_FYVE-rel.
DR InterPro; IPR011011; Znf_FYVE_PHD.
DR InterPro; IPR001841; Znf_RING.
DR InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR Pfam; PF01363; FYVE; 1.
DR Pfam; PF13639; zf-RING_2; 1.
DR SMART; SM00064; FYVE; 1.
DR SMART; SM00184; RING; 2.
DR SUPFAM; SSF57903; SSF57903; 1.
DR PROSITE; PS50178; ZF_FYVE; 1.
DR PROSITE; PS50089; ZF_RING_2; 1.
PE 1: Evidence at protein level;
KW Endosome; Membrane; Metal-binding; Reference proteome; Transferase;
KW Ubl conjugation pathway; Vacuole; Zinc; Zinc-finger.
FT CHAIN 1..286
FT /note="E3 ubiquitin-protein ligase PIB1"
FT /id="PRO_0000245839"
FT ZN_FING 17..88
FT /note="FYVE-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00091"
FT ZN_FING 225..283
FT /note="RING-type; atypical"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00175"
FT BINDING 23
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00091"
FT BINDING 26
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00091"
FT BINDING 39
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00091"
FT BINDING 42
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00091"
FT BINDING 47
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00091"
FT BINDING 50
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00091"
FT BINDING 80
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00091"
FT BINDING 83
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00091"
FT MUTAGEN 23
FT /note="C->S: Abolishes endosomal targeting."
FT /evidence="ECO:0000269|PubMed:11526110"
FT MUTAGEN 225
FT /note="C->S: Abolishes E3 activity, strongly reduces zinc
FT binding and destabilizes the protein, but no effect on
FT subcellular location."
FT /evidence="ECO:0000269|PubMed:11526110"
FT CONFLICT 166
FT /note="D -> G (in Ref. 3; AAS56068)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 286 AA; 32675 MW; E7E9DCDEC9BAA183 CRC64;
MVIKEDCINN LARWQADEEA HSCFQCKTNF SFLVRRHHCR CCGRIFCSSC TENFVNYNKK
RVHALQKKNS DVESPPYRTC NECYDNLLHL NLLVSSTNRD VRLSQTSVPP NALALSAPDS
NTDEDAEILE DSVDQSGTAC RSEESSQNEE DHFCPICNSD LTQFPDEEET RKHVEDCIQR
AENAQQHTNT SDAADDSVKE SPAFQNRMLV YKISPNTTDN AIKECPICFE NMEPGEKVGR
LECLCVFHYK CIKNWFHKRA QMTAAQKGNG HAFVKRNFCP FHDAVF
