ID   UBC4_YEAST              Reviewed;         148 AA.
AC   P15731; D6VQ81;
DT   01-APR-1990, integrated into UniProtKB/Swiss-Prot.
DT   01-APR-1990, sequence version 1.
DT   27-MAR-2024, entry version 218.
DE   RecName: Full=Ubiquitin-conjugating enzyme E2 4;
DE            EC=2.3.2.23 {ECO:0000305|PubMed:2154373};
DE   AltName: Full=E2 ubiquitin-conjugating enzyme 4;
DE   AltName: Full=Ubiquitin carrier protein 4;
DE   AltName: Full=Ubiquitin-protein ligase 4;
GN   Name=UBC4 {ECO:0000303|PubMed:2154373};
GN   OrderedLocusNames=YBR082C {ECO:0000312|SGD:S000000286};
GN   ORFNames=YBR0745;
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], PROTEIN SEQUENCE OF 40-64 AND 119-125,
RP   AND CATALYTIC ACTIVITY.
RX   PubMed=2154373; DOI=10.1002/j.1460-2075.1990.tb08141.x;
RA   Seufert W., Jentsch S.;
RT   "Ubiquitin-conjugating enzymes UBC4 and UBC5 mediate selective degradation
RT   of short-lived and abnormal proteins.";
RL   EMBO J. 9:543-550(1990).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=7985423; DOI=10.1002/yea.320100711;
RA   van der Aart Q.J.M., Barthe C., Doignon F., Aigle M., Crouzet M.,
RA   Steensma H.Y.;
RT   "Sequence analysis of a 31 kb DNA fragment from the right arm of
RT   Saccharomyces cerevisiae chromosome II.";
RL   Yeast 10:959-964(1994).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=7813418; DOI=10.1002/j.1460-2075.1994.tb06923.x;
RA   Feldmann H., Aigle M., Aljinovic G., Andre B., Baclet M.C., Barthe C.,
RA   Baur A., Becam A.-M., Biteau N., Boles E., Brandt T., Brendel M.,
RA   Brueckner M., Bussereau F., Christiansen C., Contreras R., Crouzet M.,
RA   Cziepluch C., Demolis N., Delaveau T., Doignon F., Domdey H.,
RA   Duesterhus S., Dubois E., Dujon B., El Bakkoury M., Entian K.-D.,
RA   Feuermann M., Fiers W., Fobo G.M., Fritz C., Gassenhuber J., Glansdorff N.,
RA   Goffeau A., Grivell L.A., de Haan M., Hein C., Herbert C.J.,
RA   Hollenberg C.P., Holmstroem K., Jacq C., Jacquet M., Jauniaux J.-C.,
RA   Jonniaux J.-L., Kallesoee T., Kiesau P., Kirchrath L., Koetter P.,
RA   Korol S., Liebl S., Logghe M., Lohan A.J.E., Louis E.J., Li Z.Y.,
RA   Maat M.J., Mallet L., Mannhaupt G., Messenguy F., Miosga T., Molemans F.,
RA   Mueller S., Nasr F., Obermaier B., Perea J., Pierard A., Piravandi E.,
RA   Pohl F.M., Pohl T.M., Potier S., Proft M., Purnelle B., Ramezani Rad M.,
RA   Rieger M., Rose M., Schaaff-Gerstenschlaeger I., Scherens B.,
RA   Schwarzlose C., Skala J., Slonimski P.P., Smits P.H.M., Souciet J.-L.,
RA   Steensma H.Y., Stucka R., Urrestarazu L.A., van der Aart Q.J.M.,
RA   Van Dyck L., Vassarotti A., Vetter I., Vierendeels F., Vissers S.,
RA   Wagner G., de Wergifosse P., Wolfe K.H., Zagulski M., Zimmermann F.K.,
RA   Mewes H.-W., Kleine K.;
RT   "Complete DNA sequence of yeast chromosome II.";
RL   EMBO J. 13:5795-5809(1994).
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   INTERACTION WITH TUL1.
RX   PubMed=11788821; DOI=10.1038/ncb743;
RA   Reggiori F., Pelham H.R.B.;
RT   "A transmembrane ubiquitin ligase required to sort membrane proteins into
RT   multivesicular bodies.";
RL   Nat. Cell Biol. 4:117-123(2002).
RN   [6]
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   [7]
RP   FUNCTION.
RX   PubMed=17550898; DOI=10.1074/jbc.m702038200;
RA   Williams C., van den Berg M., Sprenger R.R., Distel B.;
RT   "A conserved cysteine is essential for Pex4p-dependent ubiquitination of
RT   the peroxisomal import receptor Pex5p.";
RL   J. Biol. Chem. 282:22534-22543(2007).
RN   [8]
RP   PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-12, AND IDENTIFICATION BY
RP   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   [9]
RP   UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-91, 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   [10]
RP   DISRUPTION PHENOTYPE.
RX   PubMed=28757607; DOI=10.1038/s41467-017-00188-1;
RA   Matsuo Y., Ikeuchi K., Saeki Y., Iwasaki S., Schmidt C., Udagawa T.,
RA   Sato F., Tsuchiya H., Becker T., Tanaka K., Ingolia N.T., Beckmann R.,
RA   Inada T.;
RT   "Ubiquitination of stalled ribosome triggers ribosome-associated quality
RT   control.";
RL   Nat. Commun. 8:159-159(2017).
RN   [11]
RP   X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS).
RX   PubMed=8268156; DOI=10.1021/bi00213a009;
RA   Cook W.J., Jeffrey L.C., Xu Y., Chau V.;
RT   "Tertiary structures of class I ubiquitin-conjugating enzymes are highly
RT   conserved: crystal structure of yeast Ubc4.";
RL   Biochemistry 32:13809-13817(1993).
CC   -!- FUNCTION: Catalyzes the covalent attachment of ubiquitin to other
CC       proteins (PubMed:17550898). Mediates the selective degradation of
CC       short-lived and abnormal proteins (PubMed:17550898). Mediates
CC       ubiquitination of PEX5 (PubMed:17550898).
CC       {ECO:0000269|PubMed:17550898}.
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, ECO:0000305|PubMed:2154373};
CC   -!- PATHWAY: Protein modification; protein ubiquitination.
CC       {ECO:0000255|PROSITE-ProRule:PRU00388}.
CC   -!- SUBUNIT: Interacts with TUL1. {ECO:0000269|PubMed:11788821}.
CC   -!- INTERACTION:
CC       P15731; P38879: EGD2; NbExp=2; IntAct=EBI-19735, EBI-6379;
CC       P15731; P34909: MOT2; NbExp=2; IntAct=EBI-19735, EBI-12174;
CC   -!- INDUCTION: By heat shock and cadmium.
CC   -!- PTM: The N-terminus is blocked.
CC   -!- DISRUPTION PHENOTYPE: Defective activation of the ribosome quality
CC       control (RQC) pathway. {ECO:0000269|PubMed:28757607}.
CC   -!- MISCELLANEOUS: Present with 13500 molecules/cell in log phase SD
CC       medium. {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; X17493; CAA35528.1; -; Genomic_DNA.
DR   EMBL; X76294; CAA53942.1; -; Genomic_DNA.
DR   EMBL; Z35951; CAA85027.1; -; Genomic_DNA.
DR   EMBL; BK006936; DAA07201.1; -; Genomic_DNA.
DR   PIR; S22857; S22857.
DR   RefSeq; NP_009638.1; NM_001178430.1.
DR   PDB; 1QCQ; X-ray; 2.70 A; A=1-148.
DR   PDB; 5AIE; X-ray; 2.80 A; B=1-148.
DR   PDBsum; 1QCQ; -.
DR   PDBsum; 5AIE; -.
DR   AlphaFoldDB; P15731; -.
DR   SMR; P15731; -.
DR   BioGRID; 32786; 477.
DR   DIP; DIP-6596N; -.
DR   IntAct; P15731; 11.
DR   MINT; P15731; -.
DR   STRING; 4932.YBR082C; -.
DR   iPTMnet; P15731; -.
DR   MaxQB; P15731; -.
DR   PaxDb; 4932-YBR082C; -.
DR   PeptideAtlas; P15731; -.
DR   TopDownProteomics; P15731; -.
DR   EnsemblFungi; YBR082C_mRNA; YBR082C; YBR082C.
DR   GeneID; 852376; -.
DR   KEGG; sce:YBR082C; -.
DR   AGR; SGD:S000000286; -.
DR   SGD; S000000286; UBC4.
DR   VEuPathDB; FungiDB:YBR082C; -.
DR   eggNOG; KOG0417; Eukaryota.
DR   HOGENOM; CLU_030988_13_3_1; -.
DR   InParanoid; P15731; -.
DR   OMA; VHFTTRI; -.
DR   OrthoDB; 5478564at2759; -.
DR   BioCyc; YEAST:G3O-29050-MONOMER; -.
DR   Reactome; R-SCE-9033241; Peroxisomal protein import.
DR   UniPathway; UPA00143; -.
DR   BioGRID-ORCS; 852376; 8 hits in 10 CRISPR screens.
DR   EvolutionaryTrace; P15731; -.
DR   PRO; PR:P15731; -.
DR   Proteomes; UP000002311; Chromosome II.
DR   RNAct; P15731; Protein.
DR   GO; GO:0005737; C:cytoplasm; IDA:SGD.
DR   GO; GO:0005634; C:nucleus; IDA:SGD.
DR   GO; GO:0000151; C:ubiquitin ligase complex; IBA:GO_Central.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR   GO; GO:0070628; F:proteasome binding; IDA:SGD.
DR   GO; GO:0030674; F:protein-macromolecule adaptor activity; IDA:SGD.
DR   GO; GO:0043130; F:ubiquitin binding; IDA:SGD.
DR   GO; GO:0061631; F:ubiquitin conjugating enzyme activity; IDA:UniProtKB.
DR   GO; GO:0031625; F:ubiquitin protein ligase binding; IBA:GO_Central.
DR   GO; GO:0004842; F:ubiquitin-protein transferase activity; IDA:SGD.
DR   GO; GO:0071629; P:cytoplasm protein quality control by the ubiquitin-proteasome system; IMP:SGD.
DR   GO; GO:0072671; P:mitochondria-associated ubiquitin-dependent protein catabolic process; IMP:SGD.
DR   GO; GO:0006513; P:protein monoubiquitination; IDA:SGD.
DR   GO; GO:0000209; P:protein polyubiquitination; IDA:SGD.
DR   GO; GO:0016567; P:protein ubiquitination; IDA:SGD.
DR   GO; GO:0072344; P:rescue of stalled ribosome; IMP:UniProtKB.
DR   GO; GO:1990116; P:ribosome-associated ubiquitin-dependent protein catabolic process; IMP:UniProtKB.
DR   GO; GO:0006511; P:ubiquitin-dependent protein catabolic process; IBA:GO_Central.
DR   GO; GO:0043162; P:ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway; IMP:SGD.
DR   CDD; cd00195; UBCc; 1.
DR   Gene3D; 3.10.110.10; Ubiquitin Conjugating Enzyme; 1.
DR   InterPro; IPR000608; UBQ-conjugat_E2.
DR   InterPro; IPR023313; UBQ-conjugating_AS.
DR   InterPro; IPR016135; UBQ-conjugating_enzyme/RWD.
DR   PANTHER; PTHR24068; UBIQUITIN-CONJUGATING ENZYME E2; 1.
DR   PANTHER; PTHR24068:SF74; UBIQUITIN-CONJUGATING ENZYME E2-17 KDA; 1.
DR   Pfam; PF00179; UQ_con; 1.
DR   SMART; SM00212; UBCc; 1.
DR   SUPFAM; SSF54495; UBC-like; 1.
DR   PROSITE; PS00183; UBC_1; 1.
DR   PROSITE; PS50127; UBC_2; 1.
PE   1: Evidence at protein level;
KW   3D-structure; ATP-binding; Direct protein sequencing; Isopeptide bond;
KW   Nucleotide-binding; Phosphoprotein; Reference proteome; Stress response;
KW   Transferase; Ubl conjugation; Ubl conjugation pathway.
FT   CHAIN           1..148
FT                   /note="Ubiquitin-conjugating enzyme E2 4"
FT                   /id="PRO_0000082545"
FT   DOMAIN          2..148
FT                   /note="UBC core"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00388"
FT   REGION          1..22
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   ACT_SITE        86
FT                   /note="Glycyl thioester intermediate"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00388"
FT   MOD_RES         12
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:18407956"
FT   CROSSLNK        91
FT                   /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT                   G-Cter in ubiquitin)"
FT                   /evidence="ECO:0007744|PubMed:22106047"
FT   HELIX           2..14
FT                   /evidence="ECO:0007829|PDB:1QCQ"
FT   STRAND          20..27
FT                   /evidence="ECO:0007829|PDB:1QCQ"
FT   STRAND          30..40
FT                   /evidence="ECO:0007829|PDB:1QCQ"
FT   STRAND          42..44
FT                   /evidence="ECO:0007829|PDB:5AIE"
FT   TURN            45..48
FT                   /evidence="ECO:0007829|PDB:5AIE"
FT   STRAND          50..56
FT                   /evidence="ECO:0007829|PDB:1QCQ"
FT   TURN            59..62
FT                   /evidence="ECO:0007829|PDB:1QCQ"
FT   STRAND          67..70
FT                   /evidence="ECO:0007829|PDB:1QCQ"
FT   HELIX           88..90
FT                   /evidence="ECO:0007829|PDB:1QCQ"
FT   TURN            91..93
FT                   /evidence="ECO:0007829|PDB:1QCQ"
FT   HELIX           100..112
FT                   /evidence="ECO:0007829|PDB:1QCQ"
FT   HELIX           122..130
FT                   /evidence="ECO:0007829|PDB:1QCQ"
FT   HELIX           132..146
FT                   /evidence="ECO:0007829|PDB:1QCQ"
SQ   SEQUENCE   148 AA;  16456 MW;  8E96137D3EB20F80 CRC64;
     MSSSKRIAKE LSDLERDPPT SCSAGPVGDD LYHWQASIMG PADSPYAGGV FFLSIHFPTD
     YPFKPPKISF TTKIYHPNIN ANGNICLDIL KDQWSPALTL SKVLLSICSL LTDANPDDPL
     VPEIAHIYKT DRPKYEATAR EWTKKYAV
//