P15731 (UBC4_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Ubiquitin-conjugating enzyme E2 4
EC=6.3.2.19

Alternative name(s):
Ubiquitin carrier protein 4
Ubiquitin-protein ligase 4

Gene names

Name:	UBC4
Ordered Locus Names:	YBR082C
ORF Names:	YBR0745

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	148 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the covalent attachment of ubiquitin to other proteins. Mediates the selective degradation of short-lived and abnormal proteins. Mediates ubiquitination of PEX5. Ref.7
Catalytic activity	ATP + ubiquitin + protein lysine = AMP + diphosphate + protein N-ubiquityllysine.
Pathway	Protein modification; protein ubiquitination.
Subunit structure	Interacts with TUL1. Ref.5
Induction	By heat shock and cadmium.
Post-translational modification	The N-terminus is blocked.
Miscellaneous	Present with 13500 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the ubiquitin-conjugating enzyme family.

Ontologies

Keywords
Biological process	Stress response Ubl conjugation pathway
Ligand	ATP-binding Nucleotide-binding
Molecular function	Ligase
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	protein monoubiquitination Inferred from direct assay PubMed 8391479. Source: SGD protein polyubiquitination Inferred from mutant phenotype Ref.7. Source: UniProtKB response to stress Inferred from direct assay Ref.1. Source: SGD ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway Inferred from mutant phenotype Ref.5. Source: SGD
Cellular_component	proteasome complex Inferred from physical interaction PubMed 10848595. Source: SGD
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW ubiquitin binding Inferred from mutant phenotype PubMed 21357418. Source: SGD ubiquitin-protein ligase activity Inferred from mutant phenotype Ref.7. Source: UniProtKB
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
EGD2	P38879	2	EBI-19735,EBI-6379

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 148

148

Ubiquitin-conjugating enzyme E2 4

PRO_0000082545

Sites

Active site

86

1

Glycyl thioester intermediate

Amino acid modifications

Modified residue

12

1

Phosphoserine Ref.8

Secondary structure

1

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148

Helix Strand Turn

Details...

Helix

2 – 14

13

Beta strand

20 – 27

8

Beta strand

30 – 40

11

Beta strand

50 – 56

7

Turn

59 – 62

4

Beta strand

67 – 70

4

Helix

88 – 90

3

Turn

91 – 93

3

Helix

100 – 112

13

Helix

122 – 130

9

Helix

132 – 146

15

Sequences

	Sequence		Length	Mass (Da)
	P15731 [UniParc]. Last modified April 1, 1990. Version 1. Checksum: 8E96137D3EB20F80	FASTA	148	16,456
	10 20 30 40 50 60 MSSSKRIAKE LSDLERDPPT SCSAGPVGDD LYHWQASIMG PADSPYAGGV FFLSIHFPTD 70 80 90 100 110 120 YPFKPPKISF TTKIYHPNIN ANGNICLDIL KDQWSPALTL SKVLLSICSL LTDANPDDPL 130 140 VPEIAHIYKT DRPKYEATAR EWTKKYAV

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Ubiquitin-conjugating enzymes UBC4 and UBC5 mediate selective degradation of short-lived and abnormal proteins." Seufert W., Jentsch S. EMBO J. 9:543-550(1990) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 40-64 AND 119-125.
[2]	"Sequence analysis of a 31 kb DNA fragment from the right arm of Saccharomyces cerevisiae chromosome II." van der Aart Q.J.M., Barthe C., Doignon F., Aigle M., Crouzet M., Steensma H.Y. Yeast 10:959-964(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[3]	"Complete DNA sequence of yeast chromosome II." Feldmann H., Aigle M., Aljinovic G., Andre B., Baclet M.C., Barthe C., Baur A., Becam A.-M., Biteau N., Boles E., Brandt T., Brendel M., Brueckner M., Bussereau F., Christiansen C., Contreras R., Crouzet M., Cziepluch C. , Demolis N., Delaveau T., Doignon F., Domdey H., Duesterhus S., Dubois E., Dujon B., El Bakkoury M., Entian K.-D., Feuermann M., Fiers W., Fobo G.M., Fritz C., Gassenhuber J., Glansdorff N., Goffeau A., Grivell L.A., de Haan M., Hein C., Herbert C.J., Hollenberg C.P., Holmstroem K., Jacq C., Jacquet M., Jauniaux J.-C., Jonniaux J.-L., Kallesoee T., Kiesau P., Kirchrath L., Koetter P., Korol S., Liebl S., Logghe M., Lohan A.J.E., Louis E.J., Li Z.Y., Maat M.J., Mallet L., Mannhaupt G., Messenguy F., Miosga T., Molemans F., Mueller S., Nasr F., Obermaier B., Perea J., Pierard A., Piravandi E., Pohl F.M., Pohl T.M., Potier S., Proft M., Purnelle B., Ramezani Rad M., Rieger M., Rose M., Schaaff-Gerstenschlaeger I., Scherens B., Schwarzlose C., Skala J., Slonimski P.P., Smits P.H.M., Souciet J.-L., Steensma H.Y., Stucka R., Urrestarazu L.A., van der Aart Q.J.M., Van Dyck L., Vassarotti A., Vetter I., Vierendeels F., Vissers S., Wagner G., de Wergifosse P., Wolfe K.H., Zagulski M., Zimmermann F.K., Mewes H.-W., Kleine K. EMBO J. 13:5795-5809(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[4]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[5]	"A transmembrane ubiquitin ligase required to sort membrane proteins into multivesicular bodies." Reggiori F., Pelham H.R.B. Nat. Cell Biol. 4:117-123(2002) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH TUL1.
[6]	"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] [Europe PMC] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[7]	"A conserved cysteine is essential for Pex4p-dependent ubiquitination of the peroxisomal import receptor Pex5p." Williams C., van den Berg M., Sprenger R.R., Distel B. J. Biol. Chem. 282:22534-22543(2007) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[8]	"A multidimensional chromatography technology for in-depth phosphoproteome analysis." Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H. Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-12, MASS SPECTROMETRY.
[9]	"Tertiary structures of class I ubiquitin-conjugating enzymes are highly conserved: crystal structure of yeast Ubc4." Cook W.J., Jeffrey L.C., Xu Y., Chau V. Biochemistry 32:13809-13817(1993) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X17493 Genomic DNA. Translation: CAA35528.1.
X76294 Genomic DNA. Translation: CAA53942.1.
Z35951 Genomic DNA. Translation: CAA85027.1.
BK006936 Genomic DNA. Translation: DAA07201.1.

PIR

S22857.

RefSeq

NP_009638.1. NM_001178430.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1QCQ	X-ray	2.70	A	1-148	[»]

ProteinModelPortal

P15731.

SMR

P15731. Positions 1-148.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-6596N.

IntAct

P15731. 5 interactions.

MINT

MINT-677321.

STRING

4932.YBR082C.

Proteomic databases

PeptideAtlas

P15731.

PRIDE

P15731.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YBR082C; YBR082C; YBR082C.

GeneID

852376.

KEGG

sce:YBR082C.

Organism-specific databases

CYGD

YBR082c.

SGD

S000000286. UBC4.

Phylogenomic databases

GeneTree

ENSGT00700000104033.

HOGENOM

HOG000233455.

KO

K06689.

OMA

KVNFTTR.

OrthoDB

EOG4KM2CF.

Enzyme and pathway databases

UniPathway

UPA00143.

Gene expression databases

Genevestigator

P15731.

GermOnline

YBR082C. Saccharomyces cerevisiae.

Family and domain databases

Gene3D

3.10.110.10. 1 hit.

InterPro

IPR000608. UBQ-conjugat_E2.
IPR023313. UBQ-conjugating_AS.
IPR016135. UBQ-conjugating_enzyme/RWD.
[Graphical view]

Pfam

PF00179. UQ_con. 1 hit.
[Graphical view]

SUPFAM

SSF54495. UBQ-conjugat/RWD-like. 1 hit.

PROSITE

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

ProtoNet

Search...

Other

EvolutionaryTrace

P15731.

NextBio

971168.

Entry information

Entry name

UBC4_YEAST

Accession

Primary (citable) accession number: P15731
Secondary accession number(s): D6VQ81

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 1, 1990
Last sequence update:	April 1, 1990
Last modified:	May 1, 2013
This is version 137 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program