UniProtKB - P52490 (UBC13_YEAST)

BLAST

>sp|P52490|UBC13_YEAST Ubiquitin-conjugating enzyme E2 13 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=UBC13 PE=1 SV=1
MASLPKRIIKETEKLVSDPVPGITAEPHDDNLRYFQVTIEGPEQSPYEDGIFELELYLPD
DYPMEAPKVRFLTKIYHPNIDRLGRICLDVLKTNWSPALQIRTVLLSIQALLASPNPNDP
LANDVAEDWIKNEQGAKAKAREWTKLYAKKKPE

Align
Format
Add to basket Added to basket
History
Entry version 167 (07 Nov 2018)
Sequence version 1 (01 Oct 1996)
Previous versions | rss
Other tutorials and videos
Help video
Feedback

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 key	Position(s)	DescriptionActions	Graphical view	Length
Active siteⁱ	87	Glycyl thioester intermediate		1

GO - Molecular functionⁱ

ATP binding Source: UniProtKB-KW
ubiquitin conjugating enzyme activity
Source: GO_Central
Inferred from biological aspect of ancestorⁱ
- 21873635

View the complete GO annotation on QuickGO ...

GO - Biological processⁱ

free ubiquitin chain polymerization
Source: SGD
Inferred from direct assayⁱ
- 19706603
postreplication repair
Source: SGD
Inferred from mutant phenotypeⁱ
- 10089880
protein K63-linked ubiquitination
Source: GO_Central
Inferred from biological aspect of ancestorⁱ
- 21873635
protein monoubiquitination
Source: SGD
Traceable author statementⁱ
- 8982460
protein polyubiquitination
Source: SGD
Inferred from direct assayⁱ
- 10089880

View the complete GO annotation on QuickGO ...

Keywordsⁱ

Molecular function	Transferase
Biological process	Ubl conjugation pathway
Ligand	ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCycⁱ	YEAST:G3O-29697-MONOMER
Reactomeⁱ	R-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
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	cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae
Proteomesⁱ	UP000002311 Componentⁱ: Chromosome IV

Organism-specific databases

Saccharomyces Genome Database More...SGDⁱ	S000002499 UBC13

SGDⁱ

S000002499 UBC13

Subcellular locationⁱ

GO - Cellular component

Pathology & Biotechⁱ

Mutagenesis

Feature key	Position(s)	DescriptionActions	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 conjugation

Proteomic databases

PaxDbⁱ	P52490
PRIDEⁱ	P52490
TopDownProteomicsⁱ	P52490

PTM databases

iPTMnetⁱ	P52490

iPTMnetⁱ

P52490

Interactionⁱ

Subunit structureⁱ

Heterodimer with MMS2.1 Publication

Binary interactionsⁱ

With	Entry	#Exp.	IntAct	Notes
MMS2	P53152	10	EBI-19777,EBI-11035

With

Entry

#Exp.

IntAct

Notes

MMS2

P53152

EBI-19777,EBI-11035

Protein-protein interaction databases

BioGridⁱ	32149, 272 interactors
ComplexPortalⁱ	CPX-2541 MMS2-UBC13 ubiquitin ligase complex
Database of interacting proteins More...DIPⁱ	DIP-5486N
IntActⁱ	P52490, 20 interactors
Molecular INTeraction database More...MINTⁱ	P52490
STRINGⁱ	4932.YDR092W

Structureⁱ

Secondary structure

Legend: HelixTurnBeta strandPDB Structure known for this area

Feature key	Position(s)	DescriptionActions	Length
Helixⁱ	6 – 17	Combined sources	12
Beta strandⁱ	23 – 28	Combined sources	6
Beta strandⁱ	31 – 40	Combined sources	10
Turnⁱ	46 – 49	Combined sources	4
Beta strandⁱ	50 – 57	Combined sources	8
Turnⁱ	60 – 64	Combined sources	5
Beta strandⁱ	68 – 71	Combined sources	4
Helixⁱ	89 – 91	Combined sources	3
Turnⁱ	92 – 94	Combined sources	3
Helixⁱ	101 – 113	Combined sources	13
Helixⁱ	126 – 131	Combined sources	6
Helixⁱ	133 – 147	Combined sources	15
Beta strandⁱ	148 – 150	Combined sources	3

Show more details

3D structure databases

ProteinModelPortalⁱ	P52490
SMRⁱ	P52490
ModBaseⁱ	Search...
MobiDBⁱ	Search...

Miscellaneous databases

EvolutionaryTraceⁱ

P52490

Family & Domainsⁱ

Sequence similaritiesⁱ

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

Phylogenomic databases

Ensembl GeneTree More...GeneTreeⁱ	ENSGT00540000070023
HOGENOMⁱ	HOG000233455
InParanoidⁱ	P52490
KEGG Orthology (KO) More...KOⁱ	K10580
OMAⁱ	YFDVTIQ
Database of Orthologous Groups More...OrthoDBⁱ	EOG092C50OL

Family and domain databases

Conserved Domains Database More...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
Pfam protein domain database More...Pfamⁱ	View protein in Pfam PF00179 UQ_con, 1 hit
SUPFAMⁱ	SSF54495 SSF54495, 1 hit
PROSITEⁱ	View protein in PROSITE PS00183 UBIQUITIN_CONJUGAT_1, 1 hit PS50127 UBIQUITIN_CONJUGAT_2, 1 hit

Sequenceⁱ

Sequence statusⁱ: Complete.

P52490-1 [UniParc]FASTA Add 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

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
NCBI Reference Sequences More...RefSeqⁱ	NP_010377.3, NM_001180400.3

Genome annotation databases

EnsemblFungiⁱ	YDR092W; YDR092W; YDR092W
GeneIDⁱ	851666
KEGGⁱ	sce:YDR092W

Protein	Similar proteins		Species	Score	Length	Source
P52490	Ubiquitin-conjugating enzyme E2 13		YEAS1		153	UniRef100_P52490
Ubc13p		YEAS8		153
UBC13p E2 ubiquitin-conjugating enzyme		Saccharomyces sp. 'boulardii'		153
Ubc13p		YEASC		153
Ubiquitin-conjugating enzyme		YEAS7		153
+1

Protein	Similar proteins		Species	Score	Length	Source
P52490	Ubiquitin-conjugating enzyme E2 13		YEAS1		153	UniRef90_P52490
Ubc13p		YEAS8		153
UBC13p E2 ubiquitin-conjugating enzyme		Saccharomyces sp. 'boulardii'		153
Ubc13p		YEASC		153
Ubiquitin-conjugating enzyme		YEAS7		153
+8

Protein	Similar proteins		Species	Score	Length	Source
P52490	Probable ubiquitin-conjugating enzyme E2 N		DICDI		154	UniRef50_P52490
Ubiquitin-conjugating enzyme E2 13		YEAS1		153
Ubc13p		YEAS8		153
UBC13p E2 ubiquitin-conjugating enzyme		Saccharomyces sp. 'boulardii'		153
Ubc13p		YEASC		153
+121

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: Protein Data Bank Europe More...PDBeⁱ Protein Data Bank RCSB More...RCSB PDBⁱ Protein Data Bank Japan More...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	[»]
ProteinModelPortalⁱ	P52490
SMRⁱ	P52490
ModBaseⁱ	Search...
MobiDBⁱ	Search...

Protein-protein interaction databases

BioGridⁱ	32149, 272 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

iPTMnetⁱ

P52490

Proteomic databases

PaxDbⁱ	P52490
PRIDEⁱ	P52490
TopDownProteomicsⁱ	P52490

Protocols and materials databases

Structural Biology Knowledgebase	Search...

Structural Biology Knowledgebase

Search...

Genome annotation databases

EnsemblFungiⁱ	YDR092W; YDR092W; YDR092W
GeneIDⁱ	851666
KEGGⁱ	sce:YDR092W

Organism-specific databases

SGDⁱ	S000002499 UBC13

Phylogenomic databases

GeneTreeⁱ	ENSGT00540000070023
HOGENOMⁱ	HOG000233455
InParanoidⁱ	P52490
KOⁱ	K10580
OMAⁱ	YFDVTIQ
OrthoDBⁱ	EOG092C50OL

Enzyme and pathway databases

UniPathwayⁱ	UPA00143
BioCycⁱ	YEAST:G3O-29697-MONOMER
Reactomeⁱ	R-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

Miscellaneous databases

EvolutionaryTraceⁱ	P52490
Protein Ontology More...PROⁱ	PR:P52490

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 UBIQUITIN_CONJUGAT_1, 1 hit PS50127 UBIQUITIN_CONJUGAT_2, 1 hit
ProtoNetⁱ	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:	November 7, 2018
	This is version 167 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, Complete proteome, Reference proteome

Documents

SIMILARITY comments
Index of protein domains and families
PATHWAY comments
Index of metabolic and biosynthesis pathways
PDB cross-references
Index of Protein Data Bank (PDB) cross-references
Yeast
Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
Yeast chromosome IV
Yeast (Saccharomyces cerevisiae) chromosome IV: entries and gene names

UniProtKB

UniParc

Help

UniRef

Proteomes

Annotation systems

Supporting data

UniProtKB - P52490 (UBC13_YEAST)

Your basket is currently empty. i <p>When browsing through different UniProt proteins, you can use the ‘basket’ to save them, so that you can back to find or analyse them later.<p><a href='/help/basket' target='_top'>More...</a></p>

Ubiquitin-conjugating enzyme E2 13

UBC13

Select a section on the left to see content.

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Miscellaneous

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>Pathwayi: protein ubiquitination

Sites

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

Enzyme and pathway databases

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

Organism-specific databases

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Nucleus

Other locations

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

Mutagenesis

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Amino acid modifications

Keywords - PTMi

Proteomic databases

PTM databases

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

Protein-protein interaction databases

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

3D structure databases

Miscellaneous databases

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

<p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Phylogenomic databases

Family and domain databases

Sequence databases

Genome annotation databases

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

3D structure databases

Protein-protein interaction databases

PTM databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Miscellaneous databases

Family and domain databases

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

Documents

UniProt is an ELIXIR core data resource

Your basket is currently empty. ⁱ

Functionⁱ

Pathwayⁱ: protein ubiquitination

GO - Molecular functionⁱ

GO - Biological processⁱ

Names & Taxonomyⁱ

Subcellular locationⁱ

Pathology & Biotechⁱ

PTM / Processingⁱ

Keywords - PTMⁱ

Interactionⁱ

Structureⁱ

Family & Domainsⁱ

Sequence similaritiesⁱ

Cross-referencesⁱ

Entry informationⁱ

Miscellaneousⁱ

Keywords - Technical termⁱ