UBC3_YEAST
ID UBC3_YEAST Reviewed; 295 AA.
AC P14682; D6VS40;
DT 01-APR-1990, integrated into UniProtKB/Swiss-Prot.
DT 01-APR-1990, sequence version 1.
DT 03-AUG-2022, entry version 217.
DE RecName: Full=Ubiquitin-conjugating enzyme E2-34 kDa;
DE EC=2.3.2.23;
DE AltName: Full=Cell division control protein 34;
DE AltName: Full=E2 ubiquitin-conjugating enzyme 3;
DE AltName: Full=E3 ubiquitin ligase complex SCF subunit CDC34;
DE AltName: Full=Ubiquitin carrier protein;
DE AltName: Full=Ubiquitin-protein ligase;
GN Name=CDC34; Synonyms=DNA6, UBC3; OrderedLocusNames=YDR054C;
GN ORFNames=D4211, YD9609.08C;
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], AND FUNCTION.
RX PubMed=2842867; DOI=10.1126/science.2842867;
RA Goebl M.G., Yochem J., Jentsch S., McGrath J.P., Varshavsky A., Byers B.;
RT "The yeast cell cycle gene CDC34 encodes a ubiquitin-conjugating enzyme.";
RL Science 241:1331-1335(1988).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=8789263;
RX DOI=10.1002/(sici)1097-0061(199601)12:1<85::aid-yea890>3.0.co;2-u;
RA Brandt P., Ramlow S., Otto B., Bloecker H.;
RT "Nucleotide sequence analysis of a 32,500 bp region of the right arm of
RT Saccharomyces cerevisiae chromosome IV.";
RL Yeast 12:85-90(1996).
RN [3]
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 [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 FUNCTION.
RX PubMed=9312054; DOI=10.1093/emboj/16.19.5966;
RA Drury L.S., Perkins G., Diffley J.F.;
RT "The Cdc4/34/53 pathway targets Cdc6p for proteolysis in budding yeast.";
RL EMBO J. 16:5966-5976(1997).
RN [6]
RP FUNCTION, AND SUBUNIT.
RX PubMed=9499404; DOI=10.1101/gad.12.5.692;
RA Patton E.E., Willems A.R., Sa D., Kuras L., Thomas D., Craig K.L.,
RA Tyers M.;
RT "Cdc53 is a scaffold protein for multiple Cdc34/Skp1/F-box protein
RT complexes that regulate cell division and methionine biosynthesis in
RT yeast.";
RL Genes Dev. 12:692-705(1998).
RN [7]
RP INTERACTION WITH HRT1.
RX PubMed=10385629; DOI=10.1101/gad.13.12.1614;
RA Seol J.H., Feldman R.M.R., Zachariae W., Shevchenko A., Correll C.C.,
RA Lyapina S., Chi Y., Galova M., Claypool J., Sandmeyer S., Nasmyth K.,
RA Shevchenko A., Deshaies R.J.;
RT "Cdc53/cullin and the essential Hrt1 RING-H2 subunit of SCF define a
RT ubiquitin ligase module that activates the E2 enzyme Cdc34.";
RL Genes Dev. 13:1614-1626(1999).
RN [8]
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 [9]
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 [10]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-186 AND SER-292, AND
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 [11]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-282, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19779198; DOI=10.1126/science.1172867;
RA Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
RT "Global analysis of Cdk1 substrate phosphorylation sites provides insights
RT into evolution.";
RL Science 325:1682-1686(2009).
CC -!- FUNCTION: Catalyzes the covalent attachment of ubiquitin to other
CC proteins. Capable, in vitro, to ubiquitinate histone H2A.
CC -!- FUNCTION: Mediates the initiation of DNA replication (transition of G1
CC to S phase in cell cycle). Essential component of the E3 ubiquitin
CC ligase complex SCF (SKP1-CUL1-F-box protein), which mediates the
CC ubiquitination and subsequent proteasomal degradation of target
CC proteins. Involved in the regulation of methionine biosynthesis genes
CC and in the degradation of CDC6 together with CDC4 and CDC53.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine +
CC [E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-
CC activating enzyme]-L-cysteine + S-ubiquitinyl-[E2 ubiquitin-
CC conjugating enzyme]-L-cysteine.; EC=2.3.2.23;
CC Evidence={ECO:0000255|PROSITE-ProRule:PRU00388, ECO:0000255|PROSITE-
CC ProRule:PRU10133};
CC -!- PATHWAY: Protein modification; protein ubiquitination.
CC {ECO:0000255|PROSITE-ProRule:PRU00388}.
CC -!- SUBUNIT: Interacts with CDC53. Component of the E3 ubiquitin ligase
CC complexes SCF with CDC53, SKP1/CBF3D, HRT1 and some F-box proteins like
CC MET30 and CDC4. {ECO:0000269|PubMed:10385629,
CC ECO:0000269|PubMed:9499404}.
CC -!- INTERACTION:
CC P14682; Q12018: CDC53; NbExp=3; IntAct=EBI-19730, EBI-4321;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}. Nucleus
CC {ECO:0000269|PubMed:14562095}.
CC -!- DOMAIN: The acidic C-terminal extension is essential for the cell cycle
CC function.
CC -!- MISCELLANEOUS: Present with 8170 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the ubiquitin-conjugating enzyme family.
CC {ECO:0000255|PROSITE-ProRule:PRU00388}.
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DR EMBL; M21877; AAA35188.1; -; Genomic_DNA.
DR EMBL; X84162; CAA58970.1; -; Genomic_DNA.
DR EMBL; Z74350; CAA98872.1; -; Genomic_DNA.
DR EMBL; Z49209; CAA89083.1; -; Genomic_DNA.
DR EMBL; BK006938; DAA11900.1; -; Genomic_DNA.
DR PIR; A41241; A41241.
DR RefSeq; NP_010339.1; NM_001180362.1.
DR PDB; 6NYA; X-ray; 2.06 A; C/F=3-195.
DR PDB; 6NYD; X-ray; 1.65 A; C=3-195.
DR PDB; 6ZHU; X-ray; 3.18 A; B/D/F/H=1-295.
DR PDB; 7K5J; X-ray; 3.42 A; B/E/F/H/J/L/T/V=3-195.
DR PDBsum; 6NYA; -.
DR PDBsum; 6NYD; -.
DR PDBsum; 6ZHU; -.
DR PDBsum; 7K5J; -.
DR AlphaFoldDB; P14682; -.
DR SMR; P14682; -.
DR BioGRID; 32107; 458.
DR ComplexPortal; CPX-3234; SCF-Cdc4 ubiquitin ligase complex.
DR ComplexPortal; CPX-3241; SCF-Grr1 ubiquitin ligase complex.
DR ComplexPortal; CPX-3242; SCF-Mdm30 ubiquitin ligase complex.
DR ComplexPortal; CPX-3243; SCF-Ufo1 ubiquitin ligase complex.
DR ComplexPortal; CPX-3244; SCF-Das1 ubiquitin ligase complex.
DR ComplexPortal; CPX-3249; SCF-Met30 ubiquitin ligase complex.
DR ComplexPortal; CPX-3250; SCF-Dia2 ubiquitin ligase complex.
DR ComplexPortal; CPX-3253; SCF-Ylr352w ubiquitin ligase complex.
DR ComplexPortal; CPX-3254; SCF-Saf1 ubiquitin ligase complex.
DR ComplexPortal; CPX-3255; SCF-Hrt3 ubiquitin ligase complex.
DR ComplexPortal; CPX-3681; SCF-Ydr131c ubiquitin ligase complex.
DR DIP; DIP-1618N; -.
DR IntAct; P14682; 6.
DR MINT; P14682; -.
DR STRING; 4932.YDR054C; -.
DR iPTMnet; P14682; -.
DR MaxQB; P14682; -.
DR PaxDb; P14682; -.
DR PRIDE; P14682; -.
DR EnsemblFungi; YDR054C_mRNA; YDR054C; YDR054C.
DR GeneID; 851624; -.
DR KEGG; sce:YDR054C; -.
DR SGD; S000002461; CDC34.
DR VEuPathDB; FungiDB:YDR054C; -.
DR eggNOG; KOG0425; Eukaryota.
DR GeneTree; ENSGT00940000167430; -.
DR HOGENOM; CLU_030988_1_1_1; -.
DR InParanoid; P14682; -.
DR OMA; DEYPYQP; -.
DR BioCyc; YEAST:G3O-29663-MON; -.
DR BRENDA; 2.3.2.23; 984.
DR Reactome; R-SCE-8866652; Synthesis of active ubiquitin: roles of E1 and E2 enzymes.
DR Reactome; R-SCE-983168; Antigen processing: Ubiquitination & Proteasome degradation.
DR UniPathway; UPA00143; -.
DR PRO; PR:P14682; -.
DR Proteomes; UP000002311; Chromosome IV.
DR RNAct; P14682; protein.
DR GO; GO:0005737; C:cytoplasm; IDA:SGD.
DR GO; GO:0005634; C:nucleus; IDA:SGD.
DR GO; GO:0019005; C:SCF ubiquitin ligase complex; IDA:SGD.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0061631; F:ubiquitin conjugating enzyme activity; IBA:GO_Central.
DR GO; GO:0004842; F:ubiquitin-protein transferase activity; IDA:SGD.
DR GO; GO:0051301; P:cell division; IEA:UniProtKB-KW.
DR GO; GO:0071406; P:cellular response to methylmercury; IC:ComplexPortal.
DR GO; GO:0006260; P:DNA replication; IEA:UniProtKB-KW.
DR GO; GO:0000082; P:G1/S transition of mitotic cell cycle; IDA:ComplexPortal.
DR GO; GO:0000086; P:G2/M transition of mitotic cell cycle; IGI:SGD.
DR GO; GO:0008053; P:mitochondrial fusion; IC:ComplexPortal.
DR GO; GO:0031573; P:mitotic intra-S DNA damage checkpoint signaling; IC:ComplexPortal.
DR GO; GO:0010828; P:positive regulation of glucose transmembrane transport; IDA:ComplexPortal.
DR GO; GO:0043161; P:proteasome-mediated ubiquitin-dependent protein catabolic process; IBA:GO_Central.
DR GO; GO:0051865; P:protein autoubiquitination; IDA:SGD.
DR GO; GO:0000209; P:protein polyubiquitination; IDA:SGD.
DR GO; GO:0019222; P:regulation of metabolic process; IC:ComplexPortal.
DR GO; GO:0007346; P:regulation of mitotic cell cycle; IC:ComplexPortal.
DR GO; GO:0031335; P:regulation of sulfur amino acid metabolic process; IC:ComplexPortal.
DR GO; GO:0000409; P:regulation of transcription by galactose; IC:ComplexPortal.
DR GO; GO:0031146; P:SCF-dependent proteasomal ubiquitin-dependent protein catabolic process; IDA:SGD.
DR GO; GO:0030466; P:silent mating-type cassette heterochromatin assembly; IDA:ComplexPortal.
DR GO; GO:0006511; P:ubiquitin-dependent protein catabolic process; IDA:SGD.
DR CDD; cd00195; UBCc; 1.
DR Gene3D; 3.10.110.10; -; 1.
DR InterPro; IPR000608; UBQ-conjugat_E2.
DR InterPro; IPR023313; UBQ-conjugating_AS.
DR InterPro; IPR016135; UBQ-conjugating_enzyme/RWD.
DR Pfam; PF00179; UQ_con; 1.
DR SUPFAM; SSF54495; SSF54495; 1.
DR PROSITE; PS00183; UBC_1; 1.
DR PROSITE; PS50127; UBC_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Cell cycle; Cell division; Cytoplasm;
KW DNA replication; Nucleotide-binding; Nucleus; Phosphoprotein;
KW Reference proteome; Transferase; Ubl conjugation pathway.
FT CHAIN 1..295
FT /note="Ubiquitin-conjugating enzyme E2-34 kDa"
FT /id="PRO_0000082541"
FT DOMAIN 7..169
FT /note="UBC core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00388"
FT REGION 185..295
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 205..220
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 223..237
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 238..265
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 266..295
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 95
FT /note="Glycyl thioester intermediate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00388,
FT ECO:0000255|PROSITE-ProRule:PRU10133"
FT MOD_RES 186
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18407956"
FT MOD_RES 282
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19779198"
FT MOD_RES 292
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18407956"
FT HELIX 4..20
FT /evidence="ECO:0007829|PDB:6NYD"
FT TURN 22..24
FT /evidence="ECO:0007829|PDB:6NYD"
FT STRAND 29..34
FT /evidence="ECO:0007829|PDB:6NYD"
FT TURN 35..37
FT /evidence="ECO:0007829|PDB:6NYD"
FT STRAND 38..46
FT /evidence="ECO:0007829|PDB:6NYD"
FT STRAND 51..53
FT /evidence="ECO:0007829|PDB:6ZHU"
FT TURN 54..57
FT /evidence="ECO:0007829|PDB:6NYD"
FT STRAND 60..65
FT /evidence="ECO:0007829|PDB:6NYD"
FT TURN 68..71
FT /evidence="ECO:0007829|PDB:6NYD"
FT STRAND 76..81
FT /evidence="ECO:0007829|PDB:6NYD"
FT STRAND 92..94
FT /evidence="ECO:0007829|PDB:6NYD"
FT HELIX 97..99
FT /evidence="ECO:0007829|PDB:6NYD"
FT HELIX 121..133
FT /evidence="ECO:0007829|PDB:6NYD"
FT STRAND 137..139
FT /evidence="ECO:0007829|PDB:6ZHU"
FT HELIX 143..151
FT /evidence="ECO:0007829|PDB:6NYD"
FT HELIX 153..167
FT /evidence="ECO:0007829|PDB:6NYD"
FT HELIX 168..170
FT /evidence="ECO:0007829|PDB:6NYD"
FT STRAND 171..175
FT /evidence="ECO:0007829|PDB:6ZHU"
SQ SEQUENCE 295 AA; 34065 MW; 1CE3E0C3AB1436DC CRC64;
MSSRKSTASS LLLRQYRELT DPKKAIPSFH IELEDDSNIF TWNIGVMVLN EDSIYHGGFF
KAQMRFPEDF PFSPPQFRFT PAIYHPNVYR DGRLCISILH QSGDPMTDEP DAETWSPVQT
VESVLISIVS LLEDPNINSP ANVDAAVDYR KNPEQYKQRV KMEVERSKQD IPKGFIMPTS
ESAYISQSKL DEPESNKDMA DNFWYDSDLD DDENGSVILQ DDDYDDGNNH IPFEDDDVYN
YNDNDDDDER IEFEDDDDDD DDSIDNDSVM DRKQPHKAED ESEDVEDVER VSKKI
