UBC13_YEAST
ID UBC13_YEAST Reviewed; 153 AA.
AC P52490; D6VS79;
DT 01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1996, sequence version 1.
DT 03-AUG-2022, entry version 187.
DE RecName: Full=Ubiquitin-conjugating enzyme E2 13;
DE EC=2.3.2.23;
DE AltName: Full=E2 ubiquitin-conjugating enzyme 13;
DE AltName: Full=Ubiquitin carrier protein 13;
DE AltName: Full=Ubiquitin-protein ligase 13;
GN Name=UBC13; OrderedLocusNames=YDR092W; ORFNames=YD6652.04;
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].
RC STRAIN=ATCC 200912 / DF5;
RX PubMed=8576256; DOI=10.1074/jbc.271.5.2789;
RA Matuschewski K., Hauser H.P., Treier M., Jentsch S.;
RT "Identification of a novel family of ubiquitin-conjugating enzymes with
RT distinct amino-terminal extensions.";
RL J. Biol. Chem. 271:2789-2794(1996).
RN [2]
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 [3]
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 [4]
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 [5]
RP UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-92, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22106047; DOI=10.1002/pmic.201100166;
RA Starita L.M., Lo R.S., Eng J.K., von Haller P.D., Fields S.;
RT "Sites of ubiquitin attachment in Saccharomyces cerevisiae.";
RL Proteomics 12:236-240(2012).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) IN COMPLEX WITH MMS2, AND MUTAGENESIS
RP OF GLU-55.
RX PubMed=11440714; DOI=10.1016/s0092-8674(01)00387-7;
RA VanDemark A.P., Hofmann R.M., Tsui C., Pickart C.M., Wolberger C.;
RT "Molecular insights into polyubiquitin chain assembly: crystal structure of
RT the Mms2/Ubc13 heterodimer.";
RL Cell 105:711-720(2001).
CC -!- FUNCTION: Has a role in the DNA error-free postreplication repair (PRR)
CC pathway. The UBC13/MMS2 heterodimer catalyzes the synthesis of non-
CC canonical poly-ubiquitin chains that are linked through 'Lys-63'.
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: Heterodimer with MMS2. {ECO:0000269|PubMed:11440714}.
CC -!- INTERACTION:
CC P52490; P53152: MMS2; NbExp=10; IntAct=EBI-19777, EBI-11035;
CC -!- MISCELLANEOUS: Present with 8970 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; X99443; CAA67806.1; -; Genomic_DNA.
DR EMBL; Z50111; CAA90451.1; -; Genomic_DNA.
DR EMBL; BK006938; DAA11939.1; -; Genomic_DNA.
DR PIR; S58092; S58092.
DR RefSeq; NP_010377.3; NM_001180400.3.
DR PDB; 1JAT; X-ray; 1.60 A; A=2-153.
DR PDB; 1JBB; X-ray; 2.00 A; A/B=1-153.
DR PDB; 2GMI; X-ray; 2.50 A; A=1-152.
DR PDB; 4FH1; X-ray; 2.61 A; A=1-152.
DR PDB; 5OJW; X-ray; 2.00 A; A=1-152.
DR PDB; 6ZHS; X-ray; 2.35 A; B/C=1-153.
DR PDB; 6ZHT; X-ray; 2.30 A; B=1-152.
DR PDBsum; 1JAT; -.
DR PDBsum; 1JBB; -.
DR PDBsum; 2GMI; -.
DR PDBsum; 4FH1; -.
DR PDBsum; 5OJW; -.
DR PDBsum; 6ZHS; -.
DR PDBsum; 6ZHT; -.
DR AlphaFoldDB; P52490; -.
DR SMR; P52490; -.
DR BioGRID; 32149; 276.
DR ComplexPortal; CPX-2541; MMS2-UBC13 ubiquitin ligase complex.
DR DIP; DIP-5486N; -.
DR IntAct; P52490; 20.
DR MINT; P52490; -.
DR STRING; 4932.YDR092W; -.
DR iPTMnet; P52490; -.
DR PaxDb; P52490; -.
DR PRIDE; P52490; -.
DR TopDownProteomics; P52490; -.
DR EnsemblFungi; YDR092W_mRNA; YDR092W; YDR092W.
DR GeneID; 851666; -.
DR KEGG; sce:YDR092W; -.
DR SGD; S000002499; UBC13.
DR VEuPathDB; FungiDB:YDR092W; -.
DR eggNOG; KOG0417; Eukaryota.
DR GeneTree; ENSGT00940000166520; -.
DR HOGENOM; CLU_030988_13_2_1; -.
DR InParanoid; P52490; -.
DR OMA; PDDYPME; -.
DR BioCyc; YEAST:G3O-29697-MON; -.
DR Reactome; R-SCE-5693565; Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks.
DR Reactome; R-SCE-9020702; Interleukin-1 signaling.
DR Reactome; R-SCE-9646399; Aggrephagy.
DR Reactome; R-SCE-983168; Antigen processing: Ubiquitination & Proteasome degradation.
DR UniPathway; UPA00143; -.
DR EvolutionaryTrace; P52490; -.
DR PRO; PR:P52490; -.
DR Proteomes; UP000002311; Chromosome IV.
DR RNAct; P52490; protein.
DR GO; GO:0005737; C:cytoplasm; IDA:SGD.
DR GO; GO:0005829; C:cytosol; TAS:Reactome.
DR GO; GO:0000329; C:fungal-type vacuole membrane; IDA:SGD.
DR GO; GO:0005634; C:nucleus; IDA:SGD.
DR GO; GO:0031372; C:UBC13-MMS2 complex; IPI:ComplexPortal.
DR GO; GO:0031371; C:ubiquitin conjugating enzyme complex; IPI: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:0010994; P:free ubiquitin chain polymerization; IDA:SGD.
DR GO; GO:0006301; P:postreplication repair; IMP:SGD.
DR GO; GO:0070534; P:protein K63-linked ubiquitination; IBA:GO_Central.
DR GO; GO:0000209; P:protein polyubiquitination; IDA:SGD.
DR GO; GO:0044395; P:protein targeting to vacuolar membrane; IMP: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; Isopeptide bond; Nucleotide-binding;
KW Reference proteome; Transferase; Ubl conjugation; Ubl conjugation pathway.
FT CHAIN 1..153
FT /note="Ubiquitin-conjugating enzyme E2 13"
FT /id="PRO_0000082565"
FT DOMAIN 3..149
FT /note="UBC core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00388"
FT ACT_SITE 87
FT /note="Glycyl thioester intermediate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00388"
FT CROSSLNK 92
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in ubiquitin)"
FT /evidence="ECO:0007744|PubMed:22106047"
FT MUTAGEN 55
FT /note="E->A: Strongly reduces MMS2 binding and interferes
FT with error-free DNA repair."
FT /evidence="ECO:0000269|PubMed:11440714"
FT MUTAGEN 81
FT /note="D->R: Abolishes ubiquitin chain elongation. No
FT effect on thioester formation at the active site."
FT MUTAGEN 110
FT /note="A->R: Lowers rate of ubiquitin chain elongation. No
FT effect on thioester formation at the active site."
FT HELIX 6..17
FT /evidence="ECO:0007829|PDB:1JAT"
FT STRAND 23..28
FT /evidence="ECO:0007829|PDB:1JAT"
FT STRAND 31..40
FT /evidence="ECO:0007829|PDB:1JAT"
FT TURN 46..49
FT /evidence="ECO:0007829|PDB:1JAT"
FT STRAND 50..57
FT /evidence="ECO:0007829|PDB:1JAT"
FT TURN 60..64
FT /evidence="ECO:0007829|PDB:1JAT"
FT STRAND 68..71
FT /evidence="ECO:0007829|PDB:1JAT"
FT HELIX 89..91
FT /evidence="ECO:0007829|PDB:1JAT"
FT TURN 92..94
FT /evidence="ECO:0007829|PDB:1JAT"
FT HELIX 101..113
FT /evidence="ECO:0007829|PDB:1JAT"
FT HELIX 126..131
FT /evidence="ECO:0007829|PDB:1JAT"
FT HELIX 133..147
FT /evidence="ECO:0007829|PDB:1JAT"
FT STRAND 148..150
FT /evidence="ECO:0007829|PDB:1JAT"
SQ SEQUENCE 153 AA; 17468 MW; 445558F8F193275B CRC64;
MASLPKRIIK ETEKLVSDPV PGITAEPHDD NLRYFQVTIE GPEQSPYEDG IFELELYLPD
DYPMEAPKVR FLTKIYHPNI DRLGRICLDV LKTNWSPALQ IRTVLLSIQA LLASPNPNDP
LANDVAEDWI KNEQGAKAKA REWTKLYAKK KPE
