UBC13 E2 ubiquitin-conjugating protein UBC13 [Saccharomyces cerevisiae S288C] - Gene

Summary

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Official Symbol: UBC13
Official Full Name: E2 ubiquitin-conjugating protein UBC13
Primary source: SGD:S000002499
Locus tag: YDR092W
See related: AllianceGenome:SGD:S000002499; FungiDB:YDR092W; VEuPathDB:YDR092W
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Saccharomyces cerevisiae S288C (strain: S288C)
Lineage: Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
Summary: Contributes to ubiquitin-protein transferase activity. Involved in several processes, including free ubiquitin chain polymerization; postreplication repair; and protein targeting to vacuolar membrane. Located in fungal-type vacuole membrane and nucleus. Part of ubiquitin conjugating enzyme complex. Orthologous to human UBE2N (ubiquitin conjugating enzyme E2 N) and UBE2NL (ubiquitin conjugating enzyme E2 N like (gene/pseudogene)). [provided by Alliance of Genome Resources, Dec 2024]
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Genomic context

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See UBC13 in Genome Data Viewer

Location:: chromosome: IV

Exon count:: 2

Sequence:: Chromosome: IV; NC_001136.10 (629876..630605)

Chromosome IV - NC_001136.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001136.10

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Ubc13-Mms2 cooperates with a family of RING E3 proteins in budding yeast membrane protein sorting.
Title: Ubc13-Mms2 cooperates with a family of RING E3 proteins in budding yeast membrane protein sorting.
Knockdown or conditional knockout of RNF8 or UBC13 in rodent cerebellar granule neurons robustly increases the number of parallel fiber presynaptic boutons and functional parallel fiber/Purkinje cell synapses. In contrast to the role of nuclear RNF8 in proliferating cells, RNF8 operates in the cytoplasm in neurons to suppress synapse differentiation.
Title: RNF8/UBC13 ubiquitin signaling suppresses synapse formation in the mammalian brain.
The authors demonstrate that in the absence of PCNA SUMOylation, Mms2-Ubc13 and Rad5 may, independently of each other, function in the stimulation of translesion DNA synthesis.
Title: The roles of PCNA SUMOylation, Mms2-Ubc13 and Rad5 in translesion DNA synthesis in Saccharomyces cerevisiae.
Ubc13 appears to be essential for epidermal integrity in mice.
Title: E2 Polyubiquitin-conjugating enzyme Ubc13 in keratinocytes is essential for epidermal integrity.
Rad6-Rad18 and Ubc13-Mms2-Rad5 act sequentially and mediate proliferating cell nuclear antigen poly-ubiquitylation by stepwise addition of ubiquitin monomers.
Title: Mechanistic analysis of PCNA poly-ubiquitylation by the ubiquitin protein ligases Rad18 and Rad5.
Rad5 acts both to align monoUb-PCNA with Ub-charged Ubc13 and to stimulate Ub transfer onto Lys(63) of a Ub acceptor.
Title: Synthesis of free and proliferating cell nuclear antigen-bound polyubiquitin chains by the RING E3 ubiquitin ligase Rad5.
Ubc13 is required for G(2) delay and does not contribute to protein turnover.
Title: Yeast Chfr homologs retard cell cycle at G1 and G2/M via Ubc4 and Ubc13/Mms2-dependent ubiquitination.
Data demonstrate that divergent activities of Ubc13 rely on its pairing with either of two Uevs, Uev1A or Mms2.
Title: Distinct regulation of Ubc13 functions by the two ubiquitin-conjugating enzyme variants Mms2 and Uev1A.
The structure reveals the key role of Mms2 in allowing selective insertion of Lys63 into the Ubc13 active site and suggests a molecular model for polyubiquitin chain elongation.
Title: Mms2-Ubc13 covalently bound to ubiquitin reveals the structural basis of linkage-specific polyubiquitin chain formation.
In contrast to the role of Rad5 in postreplicational repair, however, where its function is coupled with that of Mms2-Ubc13, Rad5 function in translesion synthesis would be largely independent of this ubiquitin-conjugating enzyme complex
Title: Mms2-Ubc13-dependent and -independent roles of Rad5 ubiquitin ligase in postreplication repair and translesion DNA synthesis in Saccharomyces cerevisiae.

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Pathways from PubChem

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

Orthologs from OrthoDB

Gene Ontology Provided by SGD

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transferase activity	IEA Inferred from Electronic Annotation more info
enables ubiquitin conjugating enzyme activity	IBA Inferred from Biological aspect of Ancestor more info
enables ubiquitin conjugating enzyme activity	IEA Inferred from Electronic Annotation more info
contributes_to ubiquitin-protein transferase activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in free ubiquitin chain polymerization	IDA Inferred from Direct Assay more info	PubMed
involved_in postreplication repair	IBA Inferred from Biological aspect of Ancestor more info
involved_in postreplication repair	IGI Inferred from Genetic Interaction more info	PubMed
involved_in postreplication repair	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein K63-linked ubiquitination	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein polyubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in protein targeting to vacuolar membrane	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein ubiquitination	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in fungal-type vacuole membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
part_of ubiquitin conjugating enzyme complex	IPI Inferred from Physical Interaction more info	PubMed

General protein information

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Preferred Names: E2 ubiquitin-conjugating protein UBC13

NP_010377.3

EC 2.3.2.23

E2 ubiquitin-conjugating enzyme; involved in the error-free DNA postreplication repair pathway; interacts with Mms2p to assemble ubiquitin chains at the Ub Lys-63 residue; DNA damage triggers redistribution from the cytoplasm to the nucleus

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

NC_001136.10 Reference assembly

Range

629876..630605

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001180400.3 → NP_010377.3 TPA: E2 ubiquitin-conjugating protein UBC13 [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_010377.3

Status: REVIEWED

UniProtKB/Swiss-Prot

D6VS79, P52490

UniProtKB/TrEMBL

A6ZY58, B3LGH9, C8Z510, G2WAJ7, N1P6A4

Conserved Domains (1) summary

cl00154
Location:3 → 152

UBCc; Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin ...