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UniProtKB - P52490 (UBC13_YEAST)
Protein
Ubiquitin-conjugating enzyme E2 13
Gene
UBC13
Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
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'.
Miscellaneous
Present with 8970 molecules/cell in log phase SD medium.1 Publication
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 EC:2.3.2.23
: protein ubiquitination Pathwayi
This protein is involved in the pathway protein ubiquitination, which is part of Protein modification.PROSITE-ProRule annotationView all proteins of this organism that are known to be involved in the pathway protein ubiquitination and in Protein modification.
Sites
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Active sitei | 87 | Glycyl thioester intermediatePROSITE-ProRule annotation | 1 |
GO - Molecular functioni
- ATP binding Source: UniProtKB-KW
- ubiquitin conjugating enzyme activity Source: GO_Central
GO - Biological processi
- free ubiquitin chain polymerization Source: SGD
- postreplication repair Source: SGD
- protein K63-linked ubiquitination Source: GO_Central
- protein polyubiquitination Source: SGD
- protein targeting to vacuolar membrane Source: SGD
Keywordsi
Molecular function | Transferase |
Biological process | Ubl conjugation pathway |
Ligand | ATP-binding, Nucleotide-binding |
Enzyme and pathway databases
Reactomei | R-SCE-5693565, Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks R-SCE-9020702, Interleukin-1 signaling R-SCE-9646399, Aggrephagy R-SCE-983168, Antigen processing: Ubiquitination & Proteasome degradation |
UniPathwayi | UPA00143 |
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 |
Organismi | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) |
Taxonomic identifieri | 559292 [NCBI] |
Taxonomic lineagei | Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › |
Proteomesi |
|
Organism-specific databases
SGDi | S000002499, UBC13 |
VEuPathDBi | FungiDB:YDR092W |
Subcellular locationi
Cytosol
- cytosol Source: Reactome
Nucleus
- nucleus Source: SGD
Vacuole
- fungal-type vacuole membrane Source: SGD
Other locations
- cytoplasm Source: SGD
- UBC13-MMS2 complex Source: ComplexPortal
- ubiquitin conjugating enzyme complex Source: SGD
Pathology & Biotechi
Mutagenesis
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Mutagenesisi | 55 | E → A: Strongly reduces MMS2 binding and interferes with error-free DNA repair. 1 Publication | 1 | |
Mutagenesisi | 81 | D → R: Abolishes ubiquitin chain elongation. No effect on thioester formation at the active site. | 1 | |
Mutagenesisi | 110 | A → R: Lowers rate of ubiquitin chain elongation. No effect on thioester formation at the active site. | 1 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000082565 | 1 – 153 | Ubiquitin-conjugating enzyme E2 13Add BLAST | 153 |
Amino acid modifications
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Cross-linki | 92 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources |
Keywords - PTMi
Isopeptide bond, Ubl conjugationProteomic databases
PaxDbi | P52490 |
PRIDEi | P52490 |
TopDownProteomicsi | P52490 |
PTM databases
iPTMneti | P52490 |
Interactioni
Subunit structurei
Heterodimer with MMS2.
1 PublicationBinary interactionsi
P52490
With | #Exp. | IntAct |
---|---|---|
MMS2 [P53152] | 10 | EBI-19777,EBI-11035 |
Protein-protein interaction databases
BioGRIDi | 32149, 276 interactors |
ComplexPortali | CPX-2541, MMS2-UBC13 ubiquitin ligase complex |
DIPi | DIP-5486N |
IntActi | P52490, 20 interactors |
MINTi | P52490 |
STRINGi | 4932.YDR092W |
Miscellaneous databases
RNActi | P52490, protein |
Structurei
Secondary structure
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details3D structure databases
AlphaFoldDBi | P52490 |
SMRi | P52490 |
ModBasei | Search... |
PDBe-KBi | Search... |
Miscellaneous databases
EvolutionaryTracei | P52490 |
Family & Domainsi
Domains and Repeats
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Domaini | 3 – 149 | UBC corePROSITE-ProRule annotationAdd BLAST | 147 |
Sequence similaritiesi
Belongs to the ubiquitin-conjugating enzyme family.PROSITE-ProRule annotation
Phylogenomic databases
eggNOGi | KOG0417, Eukaryota |
GeneTreei | ENSGT00940000166520 |
HOGENOMi | CLU_030988_13_2_1 |
InParanoidi | P52490 |
OMAi | PDDYPME |
Family and domain databases
CDDi | cd00195, UBCc, 1 hit |
Gene3Di | 3.10.110.10, 1 hit |
InterProi | View protein in InterPro IPR000608, UBQ-conjugat_E2 IPR023313, UBQ-conjugating_AS IPR016135, UBQ-conjugating_enzyme/RWD |
Pfami | View protein in Pfam PF00179, UQ_con, 1 hit |
SUPFAMi | SSF54495, SSF54495, 1 hit |
PROSITEi | View protein in PROSITE PS00183, UBC_1, 1 hit PS50127, UBC_2, 1 hit |
i Sequence
Sequence statusi: Complete.
P52490-1 [UniParc]FASTAAdd to basket
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
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 |
Genome annotation databases
EnsemblFungii | YDR092W_mRNA; YDR092W; YDR092W |
GeneIDi | 851666 |
KEGGi | sce:YDR092W |
Similar proteinsi
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 | PDB 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 | [»] | |
5OJW | X-ray | 2.00 | A | 1-152 | [»] | |
6ZHS | X-ray | 2.35 | B/C | 1-153 | [»] | |
6ZHT | X-ray | 2.30 | B | 1-152 | [»] | |
AlphaFoldDBi | P52490 | |||||
SMRi | P52490 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGRIDi | 32149, 276 interactors |
ComplexPortali | CPX-2541, MMS2-UBC13 ubiquitin ligase complex |
DIPi | DIP-5486N |
IntActi | P52490, 20 interactors |
MINTi | P52490 |
STRINGi | 4932.YDR092W |
PTM databases
iPTMneti | P52490 |
Proteomic databases
PaxDbi | P52490 |
PRIDEi | P52490 |
TopDownProteomicsi | P52490 |
Genome annotation databases
EnsemblFungii | YDR092W_mRNA; YDR092W; YDR092W |
GeneIDi | 851666 |
KEGGi | sce:YDR092W |
Organism-specific databases
SGDi | S000002499, UBC13 |
VEuPathDBi | FungiDB:YDR092W |
Phylogenomic databases
eggNOGi | KOG0417, Eukaryota |
GeneTreei | ENSGT00940000166520 |
HOGENOMi | CLU_030988_13_2_1 |
InParanoidi | P52490 |
OMAi | PDDYPME |
Enzyme and pathway databases
UniPathwayi | UPA00143 |
Reactomei | R-SCE-5693565, Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks R-SCE-9020702, Interleukin-1 signaling R-SCE-9646399, Aggrephagy R-SCE-983168, Antigen processing: Ubiquitination & Proteasome degradation |
Miscellaneous databases
EvolutionaryTracei | P52490 |
PROi | PR:P52490 |
RNActi | P52490, protein |
Family and domain databases
CDDi | cd00195, UBCc, 1 hit |
Gene3Di | 3.10.110.10, 1 hit |
InterProi | View protein in InterPro IPR000608, UBQ-conjugat_E2 IPR023313, UBQ-conjugating_AS IPR016135, UBQ-conjugating_enzyme/RWD |
Pfami | View protein in Pfam PF00179, UQ_con, 1 hit |
SUPFAMi | SSF54495, SSF54495, 1 hit |
PROSITEi | View protein in PROSITE PS00183, UBC_1, 1 hit PS50127, UBC_2, 1 hit |
MobiDBi | Search... |
Entry informationi
Entry namei | UBC13_YEAST | |
Accessioni | P52490Primary (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: | May 25, 2022 | |
This is version 186 of the entry and version 1 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Fungal Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
3D-structure, Reference proteomeDocuments
- Yeast
Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD - Yeast chromosome IV
Yeast (Saccharomyces cerevisiae) chromosome IV: entries and gene names - PATHWAY comments
Index of metabolic and biosynthesis pathways - PDB cross-references
Index of Protein Data Bank (PDB) cross-references - SIMILARITY comments
Index of protein domains and families