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Protein

Ubiquitin-conjugating enzyme E2 13

Gene

UBC13

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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 activityi

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

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei87 – 871Glycyl thioester intermediate

GO - Molecular functioni

  1. acid-amino acid ligase activity Source: InterPro
  2. ATP binding Source: UniProtKB-KW

GO - Biological processi

  1. free ubiquitin chain polymerization Source: SGD
  2. postreplication repair Source: SGD
  3. protein monoubiquitination Source: SGD
  4. protein polyubiquitination Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

Ubl conjugation pathway

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-29697-MONOMER.
UniPathwayiUPA00143.

Names & Taxonomyi

Protein namesi
Recommended name:
Ubiquitin-conjugating enzyme E2 13 (EC:6.3.2.19)
Alternative name(s):
Ubiquitin carrier protein 13
Ubiquitin-protein ligase 13
Gene namesi
Name:UBC13
Ordered Locus Names:YDR092W
ORF Names:YD6652.04
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome IV

Organism-specific databases

CYGDiYDR092w.
SGDiS000002499. UBC13.

Subcellular locationi

GO - Cellular componenti

  1. cytoplasm Source: SGD
  2. nucleus Source: SGD
  3. ubiquitin conjugating enzyme complex Source: SGD
Complete GO annotation...

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi55 – 551E → A: Strongly reduces MMS2 binding and interferes with error-free DNA repair. 1 Publication
Mutagenesisi81 – 811D → R: Abolishes ubiquitin chain elongation. No effect on thioester formation at the active site.
Mutagenesisi110 – 1101A → R: Lowers rate of ubiquitin chain elongation. No effect on thioester formation at the active site.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 153153Ubiquitin-conjugating enzyme E2 13PRO_0000082565Add
BLAST

Proteomic databases

PaxDbiP52490.
PeptideAtlasiP52490.

Expressioni

Gene expression databases

GenevestigatoriP52490.

Interactioni

Subunit structurei

Heterodimer with MMS2.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
MMS2P531524EBI-19777,EBI-11035

Protein-protein interaction databases

BioGridi32149. 142 interactions.
DIPiDIP-5486N.
IntActiP52490. 6 interactions.
MINTiMINT-533850.
STRINGi4932.YDR092W.

Structurei

Secondary structure

1
153
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi6 – 1712Combined sources
Beta strandi23 – 286Combined sources
Beta strandi31 – 4010Combined sources
Turni46 – 494Combined sources
Beta strandi50 – 578Combined sources
Turni60 – 645Combined sources
Beta strandi68 – 714Combined sources
Helixi89 – 913Combined sources
Turni92 – 943Combined sources
Helixi101 – 11313Combined sources
Helixi126 – 1316Combined sources
Helixi133 – 14715Combined sources
Beta strandi148 – 1503Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1JATX-ray1.60A2-153[»]
1JBBX-ray2.00A/B1-153[»]
2GMIX-ray2.50A1-152[»]
4FH1X-ray2.61A1-152[»]
ProteinModelPortaliP52490.
SMRiP52490. Positions 2-152.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP52490.

Family & Domainsi

Sequence similaritiesi

Belongs to the ubiquitin-conjugating enzyme family.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiCOG5078.
GeneTreeiENSGT00540000070023.
HOGENOMiHOG000233455.
InParanoidiP52490.
KOiK10580.
OMAiYFDVEIH.
OrthoDBiEOG7SBP18.

Family and domain databases

Gene3Di3.10.110.10. 1 hit.
InterProiIPR000608. UBQ-conjugat_E2.
IPR023313. UBQ-conjugating_AS.
IPR016135. UBQ-conjugating_enzyme/RWD.
[Graphical view]
PfamiPF00179. UQ_con. 1 hit.
[Graphical view]
SUPFAMiSSF54495. SSF54495. 1 hit.
PROSITEiPS00183. UBIQUITIN_CONJUGAT_1. 1 hit.
PS50127. UBIQUITIN_CONJUGAT_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P52490-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MASLPKRIIK ETEKLVSDPV PGITAEPHDD NLRYFQVTIE GPEQSPYEDG
60 70 80 90 100
IFELELYLPD DYPMEAPKVR FLTKIYHPNI DRLGRICLDV LKTNWSPALQ
110 120 130 140 150
IRTVLLSIQA LLASPNPNDP LANDVAEDWI KNEQGAKAKA REWTKLYAKK

KPE
Length:153
Mass (Da):17,468
Last modified:October 1, 1996 - v1
Checksum:i445558F8F193275B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X99443 Genomic DNA. Translation: CAA67806.1.
Z50111 Genomic DNA. Translation: CAA90451.1.
BK006938 Genomic DNA. Translation: DAA11939.1.
PIRiS58092.
RefSeqiNP_010377.3. NM_001180400.3.

Genome annotation databases

EnsemblFungiiYDR092W; YDR092W; YDR092W.
GeneIDi851666.
KEGGisce:YDR092W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X99443 Genomic DNA. Translation: CAA67806.1.
Z50111 Genomic DNA. Translation: CAA90451.1.
BK006938 Genomic DNA. Translation: DAA11939.1.
PIRiS58092.
RefSeqiNP_010377.3. NM_001180400.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1JATX-ray1.60A2-153[»]
1JBBX-ray2.00A/B1-153[»]
2GMIX-ray2.50A1-152[»]
4FH1X-ray2.61A1-152[»]
ProteinModelPortaliP52490.
SMRiP52490. Positions 2-152.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi32149. 142 interactions.
DIPiDIP-5486N.
IntActiP52490. 6 interactions.
MINTiMINT-533850.
STRINGi4932.YDR092W.

Proteomic databases

PaxDbiP52490.
PeptideAtlasiP52490.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYDR092W; YDR092W; YDR092W.
GeneIDi851666.
KEGGisce:YDR092W.

Organism-specific databases

CYGDiYDR092w.
SGDiS000002499. UBC13.

Phylogenomic databases

eggNOGiCOG5078.
GeneTreeiENSGT00540000070023.
HOGENOMiHOG000233455.
InParanoidiP52490.
KOiK10580.
OMAiYFDVEIH.
OrthoDBiEOG7SBP18.

Enzyme and pathway databases

UniPathwayiUPA00143.
BioCyciYEAST:G3O-29697-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP52490.
NextBioi969283.
PROiP52490.

Gene expression databases

GenevestigatoriP52490.

Family and domain databases

Gene3Di3.10.110.10. 1 hit.
InterProiIPR000608. UBQ-conjugat_E2.
IPR023313. UBQ-conjugating_AS.
IPR016135. UBQ-conjugating_enzyme/RWD.
[Graphical view]
PfamiPF00179. UQ_con. 1 hit.
[Graphical view]
SUPFAMiSSF54495. SSF54495. 1 hit.
PROSITEiPS00183. UBIQUITIN_CONJUGAT_1. 1 hit.
PS50127. UBIQUITIN_CONJUGAT_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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.
    , 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. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  4. 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.

Entry informationi

Entry nameiUBC13_YEAST
AccessioniPrimary (citable) accession number: P52490
Secondary accession number(s): D6VS79
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: October 1, 1996
Last modified: February 4, 2015
This is version 134 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 8970 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families
  4. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  5. Yeast chromosome IV
    Yeast (Saccharomyces cerevisiae) chromosome IV: entries and gene names

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.