Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.

P52490

- UBC13_YEAST

UniProt

P52490 - UBC13_YEAST

(max 400 entries)x

Your basket is currently empty.

Select item(s) and click on "Add to basket" to create your own collection here
(400 entries max)

Protein

Ubiquitin-conjugating enzyme E2 13

Gene

UBC13

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.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. 138 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.
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

        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 .
PIRi S58092.
RefSeqi NP_010377.3. NM_001180400.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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. 138 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.
InParanoidi P52490.
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: October 29, 2014
This is version 132 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