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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

S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine.PROSITE-ProRule annotation

Pathwayi: protein ubiquitination

This protein is involved in the pathway protein ubiquitination, which is part of Protein modification.PROSITE-ProRule annotation
View all proteins of this organism that are known to be involved in the pathway protein ubiquitination and in Protein modification.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei87Glycyl thioester intermediate1

GO - Molecular functioni

GO - Biological processi

  • free ubiquitin chain polymerization Source: SGD
  • postreplication repair Source: SGD
  • protein K63-linked ubiquitination Source: GO_Central
  • protein monoubiquitination Source: SGD
  • protein polyubiquitination Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

Ubl conjugation pathway

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-29697-MONOMER.
ReactomeiR-SCE-1169408. ISG15 antiviral mechanism.
R-SCE-5693565. Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks.
R-SCE-8866652. Synthesis of active ubiquitin: roles of E1 and E2 enzymes.
UniPathwayiUPA00143.

Names & Taxonomyi

Protein namesi
Recommended name:
Ubiquitin-conjugating enzyme E2 13 (EC:2.3.2.23)
Alternative name(s):
E2 ubiquitin-conjugating enzyme 13
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
Proteomesi
  • UP000002311 Componenti: Chromosome IV

Organism-specific databases

EuPathDBiFungiDB:YDR092W.
SGDiS000002499. UBC13.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: SGD
  • nucleus Source: SGD
  • ubiquitin conjugating enzyme complex Source: SGD
Complete GO annotation...

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi55E → A: Strongly reduces MMS2 binding and interferes with error-free DNA repair. 1 Publication1
Mutagenesisi81D → R: Abolishes ubiquitin chain elongation. No effect on thioester formation at the active site. 1
Mutagenesisi110A → R: Lowers rate of ubiquitin chain elongation. No effect on thioester formation at the active site. 1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000825651 – 153Ubiquitin-conjugating enzyme E2 13Add BLAST153

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Cross-linki92Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources

Keywords - PTMi

Isopeptide bond, Ubl conjugation

Proteomic databases

PRIDEiP52490.
TopDownProteomicsiP52490.

Interactioni

Subunit structurei

Heterodimer with MMS2.1 Publication

Binary interactionsi

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

GO - Molecular functioni

Protein-protein interaction databases

BioGridi32149. 150 interactors.
DIPiDIP-5486N.
IntActiP52490. 6 interactors.
MINTiMINT-533850.

Structurei

Secondary structure

1153
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi6 – 17Combined sources12
Beta strandi23 – 28Combined sources6
Beta strandi31 – 40Combined sources10
Turni46 – 49Combined sources4
Beta strandi50 – 57Combined sources8
Turni60 – 64Combined sources5
Beta strandi68 – 71Combined sources4
Helixi89 – 91Combined sources3
Turni92 – 94Combined sources3
Helixi101 – 113Combined sources13
Helixi126 – 131Combined sources6
Helixi133 – 147Combined sources15
Beta strandi148 – 150Combined sources3

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiP52490.

Family & Domainsi

Sequence similaritiesi

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

Phylogenomic databases

GeneTreeiENSGT00540000070023.
HOGENOMiHOG000233455.
InParanoidiP52490.
KOiK10580.
OMAiYFDVEIH.
OrthoDBiEOG092C50OL.

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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1JATX-ray1.60A2-153[»]
1JBBX-ray2.00A/B1-153[»]
2GMIX-ray2.50A1-152[»]
4FH1X-ray2.61A1-152[»]
ProteinModelPortaliP52490.
SMRiP52490.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi32149. 150 interactors.
DIPiDIP-5486N.
IntActiP52490. 6 interactors.
MINTiMINT-533850.

Proteomic databases

PRIDEiP52490.
TopDownProteomicsiP52490.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

EuPathDBiFungiDB:YDR092W.
SGDiS000002499. UBC13.

Phylogenomic databases

GeneTreeiENSGT00540000070023.
HOGENOMiHOG000233455.
InParanoidiP52490.
KOiK10580.
OMAiYFDVEIH.
OrthoDBiEOG092C50OL.

Enzyme and pathway databases

UniPathwayiUPA00143.
BioCyciYEAST:G3O-29697-MONOMER.
ReactomeiR-SCE-1169408. ISG15 antiviral mechanism.
R-SCE-5693565. Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks.
R-SCE-8866652. Synthesis of active ubiquitin: roles of E1 and E2 enzymes.

Miscellaneous databases

EvolutionaryTraceiP52490.
PROiP52490.

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...

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: November 30, 2016
This is version 151 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

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 one 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.