P06104 (UBC2_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Ubiquitin-conjugating enzyme E2 2
EC=6.3.2.19

Alternative name(s):
Radiation sensitivity protein 6
Ubiquitin carrier protein UBC2
Ubiquitin-protein ligase UBC2

Gene names

Name:	RAD6
Synonyms:	UBC2
Ordered Locus Names:	YGL058W

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	172 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the covalent attachment of ubiquitin to other proteins. In association with the E3 enzyme BRE1 and LGE1, it plays a role in transcription regulation by catalyzing the monoubiquitination of histone H2B to form H2BK123ub1. H2BK123ub1 gives a specific tag for epigenetic transcriptional activation, elongation by RNA polymerase II, telomeric silencing, and is also a prerequisite for H3K4me and H3K79me formation. In association with the E3 enzyme RAD18, it catalyzes the monoubiquitination of POL30 'Lys-164', involved in postreplication repair of UV-damaged DNA. The RAD6/UBC2-RAD18 complex is also involved in prevention of spontaneous mutations caused by 7,8-dihydro-8-oxoguanine. In association with the E3 enzyme UBR1, is involved in N-end rule-dependent protein degradation. Also involved in sporulation. Ref.5 Ref.6 Ref.8 Ref.9 Ref.10 Ref.11 Ref.12 Ref.13 Ref.14 Ref.16 Ref.17 Ref.18 Ref.21 Ref.22 Ref.23 Ref.24 Ref.25
Catalytic activity	ATP + ubiquitin + protein lysine = AMP + diphosphate + protein N-ubiquityllysine.
Pathway	Protein modification; protein ubiquitination.
Subunit structure	Forms a heterodimer complexes with the E3 enzymes BRE1, RAD18 and UBR1. Interacts also with UBR2, RTF1, PAF1 and the RNA polymerase II hyperphosphorylated form. The interaction with RNA polymerase II is BRE1- and PAF1-dependent. Ref.9 Ref.11 Ref.12 Ref.13 Ref.15 Ref.24
Subcellular location	Cytoplasm. Nucleus Ref.11 Ref.16 Ref.19.
Induction	Up-regulated by UV radiations and during meiosis. Ref.7
Domain	The acidic-tail domain of UBC2 mediates interaction with UBR1 and UBR2, and thus is important for polyubiquitination of histones. This domain is also important for sporulation.
Post-translational modification	The N-terminus is blocked.
Miscellaneous	Present with 2770 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the ubiquitin-conjugating enzyme family.

Ontologies

Keywords
Biological process	DNA damage DNA repair Sporulation Transcription Transcription regulation Ubl conjugation pathway
Cellular component	Cytoplasm Nucleus
Ligand	ATP-binding Nucleotide-binding
Molecular function	Chromatin regulator Ligase
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	chromatin silencing at telomere Inferred from mutant phenotype PubMed 12535539Ref.14. Source: SGD double-strand break repair via homologous recombination Inferred from genetic interaction PubMed 16783014. Source: SGD error-free postreplication DNA repair Inferred from genetic interaction PubMed 9576943. Source: SGD error-free translesion synthesis Inferred from genetic interaction PubMed 9409821. Source: SGD error-prone translesion synthesis Inferred from genetic interaction PubMed 770231. Source: SGD histone monoubiquitination Inferred from mutant phenotype PubMed 12535538PubMed 12535539. Source: SGD meiotic DNA double-strand break formation Inferred from mutant phenotype PubMed 15280549. Source: SGD mitotic G1 DNA damage checkpoint Inferred from mutant phenotype PubMed 15632126PubMed 16166626. Source: SGD protein polyubiquitination Inferred from mutant phenotype Ref.9Ref.11. Source: SGD protein ubiquitination involved in ubiquitin-dependent protein catabolic process Inferred from mutant phenotype Ref.11. Source: SGD regulation of dipeptide transport Inferred from mutant phenotype PubMed 9427760. Source: SGD sporulation resulting in formation of a cellular spore Inferred from electronic annotation. Source: UniProtKB-KW transcription from RNA polymerase II promoter Inferred from physical interaction Ref.24. Source: SGD ubiquitin-dependent protein catabolic process via the N-end rule pathway Inferred from mutant phenotype Ref.9. Source: SGD
Cellular_component	cytoplasm Inferred from direct assay Ref.16. Source: SGD nucleus Inferred from direct assay Ref.16Ref.11. Source: SGD
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW ubiquitin-protein ligase activity Inferred from direct assay Ref.5Ref.13. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
RAD18	P10862	5	EBI-19722,EBI-14659
UBR1	P19812	3	EBI-19722,EBI-19909
UBR2	Q07963	3	EBI-19722,EBI-34338

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 172

172

Ubiquitin-conjugating enzyme E2 2

PRO_0000082540

Regions

Compositional bias

150 – 172

23

Asp/Glu-rich (acidic tail)

Sites

Active site

88

1

Glycyl thioester intermediate

Amino acid modifications

Modified residue

120

1

Phosphoserine; by SGV1 Ref.23 Ref.26

Experimental info

Mutagenesis

1 – 9

9

Missing: Prevents H3K4me3 formation. Ref.11 Ref.17

Mutagenesis

88

1

C → A or V: Loss of activity. Ref.8 Ref.17

Secondary structure

1

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172

Helix Strand Turn

Details...

Helix

4 – 18

15

Beta strand

24 – 29

6

Beta strand

32 – 41

10

Turn

47 – 50

4

Beta strand

52 – 58

7

Turn

61 – 65

5

Beta strand

69 – 74

6

Beta strand

85 – 87

3

Helix

90 – 92

3

Turn

93 – 95

3

Helix

102 – 113

12

Helix

124 – 132

9

Helix

134 – 152

19

Sequences

	Sequence		Length	Mass (Da)
	P06104 [UniParc]. Last modified January 1, 1988. Version 1. Checksum: 5F568DC28ABBD60F	FASTA	172	19,706
	10 20 30 40 50 60 MSTPARRRLM RDFKRMKEDA PPGVSASPLP DNVMVWNAMI IGPADTPYED GTFRLLLEFD 70 80 90 100 110 120 EEYPNKPPHV KFLSEMFHPN VYANGEICLD ILQNRWTPTY DVASILTSIQ SLFNDPNPAS 130 140 150 160 170 PANVEAATLF KDHKSQYVKR VKETVEKSWE DDMDDMDDDD DDDDDDDDDE AD

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"RAD6 gene of Saccharomyces cerevisiae encodes a protein containing a tract of 13 consecutive aspartates." Reynolds P., Weber S., Prakash L. Proc. Natl. Acad. Sci. U.S.A. 82:168-172(1985) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"The characterization of two new clusters of duplicated genes suggests a 'Lego' organization of the yeast Saccharomyces cerevisiae chromosomes." Feuermann M., de Montigny J., Potier S., Souciet J.-L. Yeast 13:861-869(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[3]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome VII." Tettelin H., Agostoni-Carbone M.L., Albermann K., Albers M., Arroyo J., Backes U., Barreiros T., Bertani I., Bjourson A.J., Brueckner M., Bruschi C.V., Carignani G., Castagnoli L., Cerdan E., Clemente M.L., Coblenz A., Coglievina M., Coissac E. , Defoor E., Del Bino S., Delius H., Delneri D., de Wergifosse P., Dujon B., Durand P., Entian K.-D., Eraso P., Escribano V., Fabiani L., Fartmann B., Feroli F., Feuermann M., Frontali L., Garcia-Gonzalez M., Garcia-Saez M.I., Goffeau A., Guerreiro P., Hani J., Hansen M., Hebling U., Hernandez K., Heumann K., Hilger F., Hofmann B., Indge K.J., James C.M., Klima R., Koetter P., Kramer B., Kramer W., Lauquin G., Leuther H., Louis E.J., Maillier E., Marconi A., Martegani E., Mazon M.J., Mazzoni C., McReynolds A.D.K., Melchioretto P., Mewes H.-W., Minenkova O., Mueller-Auer S., Nawrocki A., Netter P., Neu R., Nombela C., Oliver S.G., Panzeri L., Paoluzi S., Plevani P., Portetelle D., Portillo F., Potier S., Purnelle B., Rieger M., Riles L., Rinaldi T., Robben J., Rodrigues-Pousada C., Rodriguez-Belmonte E., Rodriguez-Torres A.M., Rose M., Ruzzi M., Saliola M., Sanchez-Perez M., Schaefer B., Schaefer M., Scharfe M., Schmidheini T., Schreer A., Skala J., Souciet J.-L., Steensma H.Y., Talla E., Thierry A., Vandenbol M., van der Aart Q.J.M., Van Dyck L., Vanoni M., Verhasselt P., Voet M., Volckaert G., Wambutt R., Watson M.D., Weber N., Wedler E., Wedler H., Wipfli P., Wolf K., Wright L.F., Zaccaria P., Zimmermann M., Zollner A., Kleine K. Nature 387:81-84(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[4]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[5]	"The yeast DNA repair gene RAD6 encodes a ubiquitin-conjugating enzyme." Jentsch S., McGrath J.P., Varshavsky A. Nature 329:131-134(1987) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 77-91, FUNCTION.
[6]	"Recombination and mutagenesis in rad6 mutants of Saccharomyces cerevisiae: evidence for multiple functions of the RAD6 gene." Montelone B.A., Prakash S., Prakash L. Mol. Gen. Genet. 184:410-415(1981) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[7]	"Expression of the Saccharomyces cerevisiae DNA repair gene RAD6 that encodes a ubiquitin conjugating enzyme, increases in response to DNA damage and in meiosis but remains constant during the mitotic cell cycle." Madura K., Prakash S., Prakash L. Nucleic Acids Res. 18:771-778(1990) [PubMed] [Europe PMC] [Abstract] Cited for: INDUCTION.
[8]	"Mutation of cysteine-88 in the Saccharomyces cerevisiae RAD6 protein abolishes its ubiquitin-conjugating activity and its various biological functions." Sung P., Prakash S., Prakash L. Proc. Natl. Acad. Sci. U.S.A. 87:2695-2699(1990) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, MUTAGENESIS OF CYS-88.
[9]	"The N-end rule is mediated by the UBC2(RAD6) ubiquitin-conjugating enzyme." Dohmen R.J., Madura K., Bartel B., Varshavsky A. Proc. Natl. Acad. Sci. U.S.A. 88:7351-7355(1991) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, INTERACTION WITH UBR1.
[10]	"Yeast RAD6 encoded ubiquitin conjugating enzyme mediates protein degradation dependent on the N-end-recognizing E3 enzyme." Sung P., Berleth E., Pickart C.M., Prakash S., Prakash L. EMBO J. 10:2187-2193(1991) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[11]	"The extremely conserved amino terminus of RAD6 ubiquitin-conjugating enzyme is essential for amino-end rule-dependent protein degradation." Watkins J.F., Sung P., Prakash S., Prakash L. Genes Dev. 7:250-261(1993) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH UBR1, MUTAGENESIS OF 1-MET--LEU-9.
[12]	"Specific complex formation between yeast RAD6 and RAD18 proteins: a potential mechanism for targeting RAD6 ubiquitin-conjugating activity to DNA damage sites." Bailly V., Lamb J., Sung P., Prakash S., Prakash L. Genes Dev. 8:811-820(1994) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, INTERACTION WITH RAD18 AND UBR1.
[13]	"Yeast DNA repair proteins Rad6 and Rad18 form a heterodimer that has ubiquitin conjugating, DNA binding, and ATP hydrolytic activities." Bailly V., Lauder S., Prakash S., Prakash L. J. Biol. Chem. 272:23360-23365(1997) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, INTERACTION WITH RAD18.
[14]	"The ubiquitin-conjugating enzyme Rad6 (Ubc2) is required for silencing in Saccharomyces cerevisiae." Huang H., Kahana A., Gottschling D.E., Prakash L., Liebman S.W. Mol. Cell. Biol. 17:6693-6699(1997) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[15]	"The E2-E3 interaction in the N-end rule pathway: the RING-H2 finger of E3 is required for the synthesis of multiubiquitin chain." Xie Y., Varshavsky A. EMBO J. 18:6832-6844(1999) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH UBR1 AND UBR2.
[16]	"Two RING finger proteins mediate cooperation between ubiquitin-conjugating enzymes in DNA repair." Ulrich H.D., Jentsch S. EMBO J. 19:3388-3397(2000) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION.
[17]	"Ubiquitination of histone H2B regulates H3 methylation and gene silencing in yeast." Sun Z.-W., Allis C.D. Nature 418:104-108(2002) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, MUTAGENESIS OF CYS-88 AND 1-MET--LEU-9.
[18]	"RAD6-dependent DNA repair is linked to modification of PCNA by ubiquitin and SUMO." Hoege C., Pfander B., Moldovan G.-L., Pyrowolakis G., Jentsch S. Nature 419:135-141(2002) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[19]	"Global analysis of protein localization in budding yeast." Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K. Nature 425:686-691(2003) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[20]	"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].
[21]	"Rad6 plays a role in transcriptional activation through ubiquitylation of histone H2B." Kao C.-F., Hillyer C., Tsukuda T., Henry K.W., Berger S.L., Osley M.A. Genes Dev. 18:184-195(2004) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[22]	"The post-replication repair RAD18 and RAD6 genes are involved in the prevention of spontaneous mutations caused by 7,8-dihydro-8-oxoguanine in Saccharomyces cerevisiae." de Padula M., Slezak G., Auffret van Der Kemp P., Boiteux S. Nucleic Acids Res. 32:5003-5010(2004) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[23]	"The Bur1/Bur2 complex is required for histone H2B monoubiquitination by Rad6/Bre1 and histone methylation by COMPASS." Wood A., Schneider J., Dover J., Johnston M., Shilatifard A. Mol. Cell 20:589-599(2005) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, PHOSPHORYLATION AT SER-120.
[24]	"Histone H2B ubiquitylation is associated with elongating RNA polymerase II." Xiao T., Kao C.-F., Krogan N.J., Sun Z.-W., Greenblatt J.F., Osley M.A., Strahl B.D. Mol. Cell. Biol. 25:637-651(2005) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, INTERACTION WITH RTF1; PAF1 AND THE RNA POLYMERASE II HYPERPHOSPHORYLATED FORM.
[25]	"The error-free component of the RAD6/RAD18 DNA damage tolerance pathway of budding yeast employs sister-strand recombination." Zhang H., Lawrence C.W. Proc. Natl. Acad. Sci. U.S.A. 102:15954-15959(2005) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[26]	"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-120, MASS SPECTROMETRY.
[27]	"Crystal structure of the Saccharomyces cerevisiae ubiquitin-conjugating enzyme Rad6 at 2.6-A resolution." Worthylake D.K., Prakash S., Prakash L., Hill C.P. J. Biol. Chem. 273:6271-6276(1998) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

K02962 Genomic DNA. Translation: AAA34952.1.
Z72580 Genomic DNA. Translation: CAA96761.1.
BK006941 Genomic DNA. Translation: DAA08044.1.

PIR

A21906.

RefSeq

NP_011457.1. NM_001180923.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1AYZ	X-ray	2.60	A/B/C	1-166	[»]

ProteinModelPortal

P06104.

SMR

P06104. Positions 2-154.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-1555N.

IntAct

P06104. 13 interactions.

MINT

MINT-394584.

STRING

4932.YGL058W.

Proteomic databases

PaxDb

P06104.

PeptideAtlas

P06104.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YGL058W; YGL058W; YGL058W.

GeneID

852822.

KEGG

sce:YGL058W.

Organism-specific databases

CYGD

YGL058w.

SGD

S000003026. RAD6.

Phylogenomic databases

eggNOG

COG5078.

GeneTree

ENSGT00680000099547.

HOGENOM

HOG000233454.

KO

K10573.

OMA

YANGEIC.

OrthoDB

EOG4B01ZN.

Enzyme and pathway databases

UniPathway

UPA00143.

Gene expression databases

Genevestigator

P06104.

GermOnline

YGL058W. 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

P06104.

NextBio

972372.

Entry information

Entry name

UBC2_YEAST

Accession

Primary (citable) accession number: P06104
Secondary accession number(s): D6VU83

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 1, 1988
Last sequence update:	January 1, 1988
Last modified:	May 1, 2013
This is version 140 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program