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P52490 (UBC13_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 129. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Ubiquitin-conjugating enzyme E2 13

EC=6.3.2.19
Alternative name(s):
Ubiquitin carrier protein 13
Ubiquitin-protein ligase 13
Gene names
Name:UBC13
Ordered Locus Names:YDR092W
ORF Names:YD6652.04
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length153 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Has a role in the DNA error-free postreplication repair (PRR) pathway. The UBC13/MMS2 heterodimer catalyzes the synthesis of non-canonical poly-ubiquitin chains that are linked through 'Lys-63'.

Catalytic activity

ATP + ubiquitin + protein lysine = AMP + diphosphate + protein N-ubiquityllysine.

Pathway

Protein modification; protein ubiquitination.

Subunit structure

Heterodimer with MMS2.

Miscellaneous

Present with 8970 molecules/cell in log phase SD medium.

Sequence similarities

Belongs to the ubiquitin-conjugating enzyme family.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

MMS2P531524EBI-19777,EBI-11035

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 153153Ubiquitin-conjugating enzyme E2 13
PRO_0000082565

Sites

Active site871Glycyl thioester intermediate

Experimental info

Mutagenesis551E → A: Strongly reduces MMS2 binding and interferes with error-free DNA repair. Ref.6
Mutagenesis811D → R: Abolishes ubiquitin chain elongation. No effect on thioester formation at the active site.
Mutagenesis1101A → R: Lowers rate of ubiquitin chain elongation. No effect on thioester formation at the active site.

Secondary structure

........................ 153
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P52490 [UniParc].

Last modified October 1, 1996. Version 1.
Checksum: 445558F8F193275B

FASTA15317,468
        10         20         30         40         50         60 
MASLPKRIIK ETEKLVSDPV PGITAEPHDD NLRYFQVTIE GPEQSPYEDG IFELELYLPD 

        70         80         90        100        110        120 
DYPMEAPKVR FLTKIYHPNI DRLGRICLDV LKTNWSPALQ IRTVLLSIQA LLASPNPNDP 

       130        140        150 
LANDVAEDWI KNEQGAKAKA REWTKLYAKK KPE 

« Hide

References

« Hide 'large scale' references
[1]"Identification of a novel family of ubiquitin-conjugating enzymes with distinct amino-terminal extensions."
Matuschewski K., Hauser H.P., Treier M., Jentsch S.
J. Biol. Chem. 271:2789-2794(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: ATCC 200912 / DF5.
[2]"The nucleotide sequence of Saccharomyces cerevisiae chromosome IV."
Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T. expand/collapse author list , del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P.
Nature 387:75-78(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[3]"The reference genome sequence of Saccharomyces cerevisiae: Then and now."
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R., Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S., Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.
G3 (Bethesda) 4:389-398(2014) [PubMed] [Europe PMC] [Abstract]
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[4]"Global analysis of protein expression in yeast."
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S.
Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[5]"Sites of ubiquitin attachment in Saccharomyces cerevisiae."
Starita L.M., Lo R.S., Eng J.K., von Haller P.D., Fields S.
Proteomics 12:236-240(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[6]"Molecular insights into polyubiquitin chain assembly: crystal structure of the Mms2/Ubc13 heterodimer."
VanDemark A.P., Hofmann R.M., Tsui C., Pickart C.M., Wolberger C.
Cell 105:711-720(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) IN COMPLEX WITH MMS2, MUTAGENESIS OF GLU-55.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X99443 Genomic DNA. Translation: CAA67806.1.
Z50111 Genomic DNA. Translation: CAA90451.1.
BK006938 Genomic DNA. Translation: DAA11939.1.
PIRS58092.
RefSeqNP_010377.3. NM_001180400.3.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1JATX-ray1.60A2-153[»]
1JBBX-ray2.00A/B1-153[»]
2GMIX-ray2.50A1-152[»]
4FH1X-ray2.61A1-152[»]
ProteinModelPortalP52490.
SMRP52490. Positions 2-152.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid32149. 133 interactions.
DIPDIP-5486N.
IntActP52490. 6 interactions.
MINTMINT-533850.
STRING4932.YDR092W.

Proteomic databases

PaxDbP52490.
PeptideAtlasP52490.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYDR092W; YDR092W; YDR092W.
GeneID851666.
KEGGsce:YDR092W.

Organism-specific databases

CYGDYDR092w.
SGDS000002499. UBC13.

Phylogenomic databases

eggNOGCOG5078.
GeneTreeENSGT00540000070023.
HOGENOMHOG000233455.
KOK10580.
OMADVAKHYK.
OrthoDBEOG7SBP18.

Enzyme and pathway databases

BioCycYEAST:G3O-29697-MONOMER.
UniPathwayUPA00143.

Gene expression databases

GenevestigatorP52490.

Family and domain databases

Gene3D3.10.110.10. 1 hit.
InterProIPR000608. UBQ-conjugat_E2.
IPR023313. UBQ-conjugating_AS.
IPR016135. UBQ-conjugating_enzyme/RWD.
[Graphical view]
PfamPF00179. UQ_con. 1 hit.
[Graphical view]
SUPFAMSSF54495. SSF54495. 1 hit.
PROSITEPS00183. UBIQUITIN_CONJUGAT_1. 1 hit.
PS50127. UBIQUITIN_CONJUGAT_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP52490.
NextBio969283.
PROP52490.

Entry information

Entry nameUBC13_YEAST
AccessionPrimary (citable) accession number: P52490
Secondary accession number(s): D6VS79
Entry history
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: October 1, 1996
Last modified: July 9, 2014
This is version 129 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome IV

Yeast (Saccharomyces cerevisiae) chromosome IV: entries and gene names

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways