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P52490

- UBC13_YEAST

UniProt

P52490 - UBC13_YEAST

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Protein
Ubiquitin-conjugating enzyme E2 13
Gene
UBC13, YDR092W, YD6652.04
Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - 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.

Pathwayi

Sites

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

GO - Molecular functioni

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

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 13
PRO_0000082565Add
BLAST

Proteomic databases

PaxDbiP52490.
PeptideAtlasiP52490.

Expressioni

Gene expression databases

GenevestigatoriP52490.

Interactioni

Subunit structurei

Heterodimer with MMS2.

Binary interactionsi

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

Protein-protein interaction databases

BioGridi32149. 137 interactions.
DIPiDIP-5486N.
IntActiP52490. 6 interactions.
MINTiMINT-533850.
STRINGi4932.YDR092W.

Structurei

Secondary structure

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

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
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.

Miscellaneous databases

EvolutionaryTraceiP52490.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG5078.
GeneTreeiENSGT00540000070023.
HOGENOMiHOG000233455.
KOiK10580.
OMAiDVAKHYK.
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

MASLPKRIIK ETEKLVSDPV PGITAEPHDD NLRYFQVTIE GPEQSPYEDG    50
IFELELYLPD DYPMEAPKVR FLTKIYHPNI DRLGRICLDV LKTNWSPALQ 100
IRTVLLSIQA LLASPNPNDP LANDVAEDWI KNEQGAKAKA REWTKLYAKK 150
KPE 153
Length:153
Mass (Da):17,468
Last modified:October 1, 1996 - v1
Checksum:i445558F8F193275B
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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:
EMBL
GenBank
DDBJ
Links Updated
X99443 Genomic DNA. Translation: CAA67806.1 .
Z50111 Genomic DNA. Translation: CAA90451.1 .
BK006938 Genomic DNA. Translation: DAA11939.1 .
PIRi S58092.
RefSeqi NP_010377.3. NM_001180400.3.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1JAT X-ray 1.60 A 2-153 [» ]
1JBB X-ray 2.00 A/B 1-153 [» ]
2GMI X-ray 2.50 A 1-152 [» ]
4FH1 X-ray 2.61 A 1-152 [» ]
ProteinModelPortali P52490.
SMRi P52490. Positions 2-152.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 32149. 137 interactions.
DIPi DIP-5486N.
IntActi P52490. 6 interactions.
MINTi MINT-533850.
STRINGi 4932.YDR092W.

Proteomic databases

PaxDbi P52490.
PeptideAtlasi P52490.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YDR092W ; YDR092W ; YDR092W .
GeneIDi 851666.
KEGGi sce:YDR092W.

Organism-specific databases

CYGDi YDR092w.
SGDi S000002499. UBC13.

Phylogenomic databases

eggNOGi COG5078.
GeneTreei ENSGT00540000070023.
HOGENOMi HOG000233455.
KOi K10580.
OMAi DVAKHYK.
OrthoDBi EOG7SBP18.

Enzyme and pathway databases

UniPathwayi UPA00143 .
BioCyci YEAST:G3O-29697-MONOMER.

Miscellaneous databases

EvolutionaryTracei P52490.
NextBioi 969283.
PROi P52490.

Gene expression databases

Genevestigatori P52490.

Family and domain databases

Gene3Di 3.10.110.10. 1 hit.
InterProi IPR000608. UBQ-conjugat_E2.
IPR023313. UBQ-conjugating_AS.
IPR016135. UBQ-conjugating_enzyme/RWD.
[Graphical view ]
Pfami PF00179. UQ_con. 1 hit.
[Graphical view ]
SUPFAMi SSF54495. SSF54495. 1 hit.
PROSITEi PS00183. UBIQUITIN_CONJUGAT_1. 1 hit.
PS50127. UBIQUITIN_CONJUGAT_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

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: September 3, 2014
This is version 130 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.

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

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