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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: -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'.

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

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

Keywordsi

Molecular functionTransferase
Biological processUbl conjugation pathway
LigandATP-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
R-SCE-8866654 E3 ubiquitin ligases ubiquitinate target proteins
R-SCE-983168 Antigen processing: Ubiquitination & Proteasome degradation
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

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

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

PaxDbiP52490
PRIDEiP52490
TopDownProteomicsiP52490

PTM databases

iPTMnetiP52490

Interactioni

Subunit structurei

Heterodimer with MMS2.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
MMS2P5315210EBI-19777,EBI-11035

GO - Molecular functioni

Protein-protein interaction databases

BioGridi32149, 264 interactors
ComplexPortaliCPX-2541 MMS2-UBC13 ubiquitin ligase complex
DIPiDIP-5486N
IntActiP52490, 20 interactors
MINTiP52490
STRINGi4932.YDR092W

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[»]
5OJWX-ray2.00A1-152[»]
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
OMAiYFDVTIQ
OrthoDBiEOG092C50OL

Family and domain databases

CDDicd00195 UBCc, 1 hit
Gene3Di3.10.110.10, 1 hit
InterProiView protein in InterPro
IPR000608 UBQ-conjugat_E2
IPR023313 UBQ-conjugating_AS
IPR016135 UBQ-conjugating_enzyme/RWD
PfamiView protein in Pfam
PF00179 UQ_con, 1 hit
SUPFAMiSSF54495 SSF54495, 1 hit
PROSITEiView protein in PROSITE
PS00183 UBIQUITIN_CONJUGAT_1, 1 hit
PS50127 UBIQUITIN_CONJUGAT_2, 1 hit

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

Similar proteinsi

Entry informationi

Entry nameiUBC13_YEAST
AccessioniPrimary (citable) accession number: P52490
Secondary accession number(s): D6VS79
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: October 1, 1996
Last modified: June 20, 2018
This is version 164 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

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

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