Reviewed, UniProtKB/Swiss-Prot P52490 (UBC13_YEAST)

Names and origin

Protein names

Recommended name:
    Ubiquitin-conjugating enzyme E2 13
    EC=6.3.2.19
Alternative name(s):
    Ubiquitin-protein ligase 13
    Ubiquitin carrier protein 13

Gene names

Name:	UBC13
Ordered Locus Names:	YDR092W
ORF Names:	YD6652.04

Organism

Saccharomyces cerevisiae (Baker's yeast) [Complete proteome]

Taxonomic identifier

4932 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

Protein attributes

Sequence length	153 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	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 activity	ATP + ubiquitin + protein lysine = AMP + diphosphate + protein N-ubiquityllysine.
Pathway	Protein modification; protein ubiquitination.
Subunit structure	Heterodimer with MMS2.
Miscellaneous	Present with 8970 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the ubiquitin-conjugating enzyme family.

Ontologies

Keywords
Biological process	Ubl conjugation pathway
Molecular function	Ligase
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	postreplication repair Inferred from genetic interaction. Source: SGD protein monoubiquitination Traceable author statement. Source: SGD protein polyubiquitination Inferred from direct assay. Source: SGD regulation of protein metabolic process Inferred from electronic annotation. Source: InterPro ubiquitin-dependent protein catabolic process Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	cytoplasm Inferred from direct assay. Source: SGD nucleus Inferred from direct assay. Source: SGD ubiquitin conjugating enzyme complex Inferred from physical interaction. Source: SGD
Molecular function	protein binding Ref.4 Inferred from physical interaction. Source: IntAct ubiquitin-protein ligase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
MMS2	P53152	1	EBI-19777,EBI-11035

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 153

153

Ubiquitin-conjugating enzyme E2 13

PRO_0000082565

Sites

Active site

87

1

Glycyl thioester intermediate

Experimental info

Mutagenesis

55

1

E → A: Strongly reduces MMS2 binding and interferes with error-free DNA repair

Mutagenesis

81

1

D → R: Abolishes ubiquitin chain elongation. No effect on thioester formation at the active site

Mutagenesis

110

1

A → R: Lowers rate of ubiquitin chain elongation. No effect on thioester formation at the active site

Secondary structure

1

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153

Helix Strand Turn

Details...

Helix

6 – 17

12

Beta strand

23 – 28

6

Beta strand

31 – 40

10

Turn

46 – 49

4

Beta strand

50 – 57

8

Turn

60 – 64

5

Beta strand

68 – 71

4

Helix

89 – 91

3

Turn

92 – 94

3

Helix

101 – 113

13

Helix

126 – 131

6

Helix

133 – 147

15

Beta strand

148 – 150

3

Sequences

	Sequence		Length	Mass (Da)
	P52490-1 [UniParc]. Last modified October 1, 1996. Version 1. Checksum: 445558F8F193275B	FASTA	153	17,468
	10 20 30 40 50 60 MASLPKRIIK ETEKLVSDPV PGITAEPHDD NLRYFQVTIE GPEQSPYEDG IFELELYLPD 70 80 90 100 110 120 DYPMEAPKVR FLTKIYHPNI DRLGRICLDV LKTNWSPALQ IRTVLLSIQA LLASPNPNDP 130 140 150 LANDVAEDWI KNEQGAKAKA REWTKLYAKK KPE

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Identification of a novel family of ubiquitin-conjugating enzymes with distinct amino-terminal extensions." Matuschewski K., Hauser H.P., Treier M., Jentsch S. J. Biol. Chem. 271:2789-2794(1996) [PubMed: 8576256] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 200912 / DF5.
[2]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome IV." Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T. , del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P. Nature 387:75-78(1997) [PubMed: 9169867] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[3]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed: 14562106] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[4]	"Molecular insights into polyubiquitin chain assembly: crystal structure of the Mms2/Ubc13 heterodimer." VanDemark A.P., Hofmann R.M., Tsui C., Pickart C.M., Wolberger C. Cell 105:711-720(2001) [PubMed: 11440714] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) IN COMPLEX WITH MMS2, MUTAGENESIS OF GLU-55.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

X99443 Genomic DNA. Translation: CAA67806.1.
Z50111 Genomic DNA. Translation: CAA90451.1.

PIR

S58092.

RefSeq

NP_010377.1.

3D structure databases

PDBMSD

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	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:5486N.

IntAct

P52490.

Proteomic databases

PeptideAtlas

P52490.

Genome annotation databases

Ensembl

YDR092W. Saccharomyces cerevisiae. [Contig view]

GeneID

851666.

GenomeReviews

Gene locus YDR092W in contig Z71256_GR.

KEGG

sce:YDR092W.

NMPDR

fig|4932.3.peg.1123.

Organism-specific databases

CYGD

YDR092w.

SGD

S000002499. UBC13.

Yeast-GFP

Search...

Phylogenomic databases

HOGENOM

P52490.

Gene expression databases

ArrayExpress

P52490.

GermOnline

YDR092W. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR016135. UBQ-conjugat/RWD-like.
IPR000608. UBQ-conjugat_E2.
[Graphical view]

Gene3D

G3DSA:3.10.110.10. UBQ-conjugat_E2. 1 hit.

PANTHER

PTHR11621. UBQ-conjugat_E2. 1 hit.

Pfam

PF00179. UQ_con. 1 hit.
[Graphical view]

ProDom

PD000461. UBQ_conjugat. 1 hit.
[Graphical view] [Entries sharing at least one domain]

SMART

SM00212. UBCc. 1 hit.
[Graphical view]

PROSITE

PS00183. UBIQUITIN_CONJUGAT_1. 1 hit.
PS50127. UBIQUITIN_CONJUGAT_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other Resources

LinkHub

P52490.

NextBio

969283.

Entry information

Entry name

UBC13_YEAST

Accession

Primary (citable) accession number: P52490

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1996
Last sequence update:	October 1, 1996
Last modified:	November 25, 2008
This is version 78 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)