UBC12_YEAST
ID UBC12_YEAST Reviewed; 188 AA.
AC P52491; D6VYU9;
DT 01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1996, sequence version 1.
DT 03-AUG-2022, entry version 178.
DE RecName: Full=NEDD8-conjugating enzyme UBC12;
DE EC=2.3.2.34;
DE AltName: Full=RUB1-conjugating enzyme;
DE AltName: Full=Ubiquitin carrier protein 12;
GN Name=UBC12; OrderedLocusNames=YLR306W; ORFNames=L2142.3;
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.
RC STRAIN=ATCC 200912 / DF5;
RX PubMed=9545234; DOI=10.1093/emboj/17.8.2208;
RA Liakopoulos D., Doenges G., Matuschewski K., Jentsch S.;
RT "A novel protein modification pathway related to the ubiquitin system.";
RL EMBO J. 17:2208-2214(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169871;
RA Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W.,
RA Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A.,
RA Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K.,
RA Heuss-Neitzel D., Hilbert H., Hilger F., Kleine K., Koetter P., Louis E.J.,
RA Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S.,
RA Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D.,
RA Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M.,
RA Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P.,
RA Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M.,
RA Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K.,
RA Zollner A., Hani J., Hoheisel J.D.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XII.";
RL Nature 387:87-90(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 X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 2-24 IN COMPLEX WITH DCN1, AND
RP ACETYLATION AT MET-1.
RX PubMed=21940857; DOI=10.1126/science.1209307;
RA Scott D.C., Monda J.K., Bennett E.J., Harper J.W., Schulman B.A.;
RT "N-terminal acetylation acts as an avidity enhancer within an
RT interconnected multiprotein complex.";
RL Science 334:674-678(2011).
CC -!- FUNCTION: Accepts the ubiquitin-like protein NEDD8/RUB1 from the UBA3-
CC ULA1 E1 complex and catalyzes its covalent attachment to other
CC proteins. The major substrate is CDC53/Cullin.
CC {ECO:0000269|PubMed:9545234}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=[E1 NEDD8-activating enzyme]-S-[NEDD8 protein]-yl-L-cysteine +
CC [E2 NEDD8-conjugating enzyme]-L-cysteine = [E1 NEDD8-activating
CC enzyme]-L-cysteine + [E2 NEDD8-conjugating enzyme]-S-[NEDD8-protein]-
CC yl-L-cysteine.; EC=2.3.2.34;
CC -!- PATHWAY: Protein modification; protein neddylation.
CC -!- SUBUNIT: Interacts with DCN1. {ECO:0000269|PubMed:21940857}.
CC -!- INTERACTION:
CC P52491; Q13616: CUL1; Xeno; NbExp=2; IntAct=EBI-19772, EBI-359390;
CC -!- PTM: The acetylation of Met-1 is cotranslational, and not regulatory.
CC The N-acetylmethionine increases affinity for DCUN1D1 by about 2 orders
CC of magnitude and is crucial for NEDD8 transfer to cullins.
CC {ECO:0000269|PubMed:21940857}.
CC -!- SIMILARITY: Belongs to the ubiquitin-conjugating enzyme family. UBC12
CC subfamily. {ECO:0000255|PROSITE-ProRule:PRU00388}.
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DR EMBL; X99442; CAA67805.1; -; Genomic_DNA.
DR EMBL; U17247; AAB67357.1; -; Genomic_DNA.
DR EMBL; BK006945; DAA09615.1; -; Genomic_DNA.
DR PIR; S51438; S51438.
DR RefSeq; NP_013409.1; NM_001182194.1.
DR PDB; 3O2U; X-ray; 2.00 A; A/B=1-188.
DR PDB; 3TDI; X-ray; 2.30 A; C/D=1-24.
DR PDBsum; 3O2U; -.
DR PDBsum; 3TDI; -.
DR AlphaFoldDB; P52491; -.
DR SMR; P52491; -.
DR BioGRID; 31571; 135.
DR DIP; DIP-2051N; -.
DR IntAct; P52491; 7.
DR MINT; P52491; -.
DR STRING; 4932.YLR306W; -.
DR iPTMnet; P52491; -.
DR MaxQB; P52491; -.
DR PaxDb; P52491; -.
DR PRIDE; P52491; -.
DR EnsemblFungi; YLR306W_mRNA; YLR306W; YLR306W.
DR GeneID; 851015; -.
DR KEGG; sce:YLR306W; -.
DR SGD; S000004297; UBC12.
DR VEuPathDB; FungiDB:YLR306W; -.
DR eggNOG; KOG0420; Eukaryota.
DR GeneTree; ENSGT00940000163935; -.
DR HOGENOM; CLU_030988_6_0_1; -.
DR InParanoid; P52491; -.
DR OMA; KESYFRG; -.
DR BioCyc; YEAST:G3O-32394-MON; -.
DR Reactome; R-SCE-8951664; Neddylation.
DR Reactome; R-SCE-983168; Antigen processing: Ubiquitination & Proteasome degradation.
DR UniPathway; UPA00885; -.
DR EvolutionaryTrace; P52491; -.
DR PRO; PR:P52491; -.
DR Proteomes; UP000002311; Chromosome XII.
DR RNAct; P52491; protein.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0019788; F:NEDD8 transferase activity; IDA:SGD.
DR GO; GO:0045116; P:protein neddylation; 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; Acetylation; ATP-binding; Nucleotide-binding;
KW Reference proteome; Transferase; Ubl conjugation pathway.
FT CHAIN 1..188
FT /note="NEDD8-conjugating enzyme UBC12"
FT /id="PRO_0000082501"
FT DOMAIN 27..177
FT /note="UBC core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00388"
FT REGION 1..23
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 115
FT /note="Glycyl thioester intermediate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00388,
FT ECO:0000255|PROSITE-ProRule:PRU10133"
FT MOD_RES 1
FT /note="N-acetylmethionine"
FT /evidence="ECO:0000269|PubMed:21940857"
FT HELIX 1..19
FT /evidence="ECO:0007829|PDB:3O2U"
FT STRAND 20..22
FT /evidence="ECO:0007829|PDB:3O2U"
FT HELIX 27..37
FT /evidence="ECO:0007829|PDB:3O2U"
FT STRAND 45..51
FT /evidence="ECO:0007829|PDB:3O2U"
FT STRAND 63..68
FT /evidence="ECO:0007829|PDB:3O2U"
FT STRAND 71..73
FT /evidence="ECO:0007829|PDB:3O2U"
FT TURN 74..77
FT /evidence="ECO:0007829|PDB:3O2U"
FT STRAND 80..85
FT /evidence="ECO:0007829|PDB:3O2U"
FT TURN 88..92
FT /evidence="ECO:0007829|PDB:3O2U"
FT STRAND 96..99
FT /evidence="ECO:0007829|PDB:3O2U"
FT STRAND 112..114
FT /evidence="ECO:0007829|PDB:3O2U"
FT HELIX 117..119
FT /evidence="ECO:0007829|PDB:3O2U"
FT TURN 120..122
FT /evidence="ECO:0007829|PDB:3O2U"
FT HELIX 129..141
FT /evidence="ECO:0007829|PDB:3O2U"
FT HELIX 151..158
FT /evidence="ECO:0007829|PDB:3O2U"
FT HELIX 161..172
FT /evidence="ECO:0007829|PDB:3O2U"
SQ SEQUENCE 188 AA; 21203 MW; BEEECF40B82C4BAB CRC64;
MLKLRQLQKK KQKENENSSS IQPNLSAARI RLKRDLDSLD LPPTVTLNVI TSPDSADRSQ
SPKLEVIVRP DEGYYNYGSI NFNLDFNEVY PIEPPKVVCL KKIFHPNIDL KGNVCLNILR
EDWSPALDLQ SIITGLLFLF LEPNPNDPLN KDAAKLLCEG EKEFAEAVRL TMSGGSIEHV
KYDNIVSP
