Reviewed, UniProtKB/Swiss-Prot P06104 (UBC2_YEAST)

Names and origin

Protein names

Recommended name:
    Ubiquitin-conjugating enzyme E2 2
    EC=6.3.2.19
Alternative name(s):
    Ubiquitin-protein ligase UBC2
    Ubiquitin carrier protein UBC2
    Radiation sensitivity protein 6

Gene names

Name:	RAD6
Synonyms:	UBC2
Ordered Locus Names:	YGL058W

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	172 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
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.4 Ref.5 Ref.7 Ref.8 Ref.9 Ref.10 Ref.11 Ref.12 Ref.13 Ref.15 Ref.16 Ref.17 Ref.20 Ref.21 Ref.22 Ref.23 Ref.24
Catalytic activity	ATP + ubiquitin + protein lysine = AMP + diphosphate + protein N-ubiquityllysine.
Pathway	Protein modification; protein ubiquitination.
Subunit structure	Forms 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.8 Ref.10 Ref.11 Ref.12 Ref.23 Ref.14
Subcellular location	Cytoplasm. Nucleus. Ref.10 Ref.15 Ref.18
Induction	Up-regulated by UV radiations and during meiosis. Ref.6
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. Ref.19
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
Gene Ontology (GO)
Biological process	histone ubiquitination Ref.4 Inferred from direct assay. Source: SGD postreplication repair Inferred from mutant phenotype. Source: SGD protein monoubiquitination Inferred from mutant phenotype. Source: SGD regulation of protein metabolic process Inferred from electronic annotation. Source: InterPro regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW sporulation resulting in formation of a cellular spore Inferred from electronic annotation. Source: UniProtKB-KW transcription Inferred from electronic annotation. Source: UniProtKB-KW ubiquitin-dependent protein catabolic process Ref.7 Inferred from mutant phenotype. Source: SGD
Cellular component	cytoplasm Ref.15 Inferred from direct assay. Source: SGD nucleus Ref.11 Ref.15 Inferred from direct assay. Source: SGD proteasome complex Inferred from physical interaction. Source: SGD
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW protein binding Ref.8 Inferred from physical interaction. Source: IntAct ubiquitin-protein ligase activity Ref.4 Ref.7 Ref.12 Inferred from direct assay. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
RAD18	P10862	2	EBI-19722,EBI-14659
UBR1	P19812	1	EBI-19722,EBI-19909

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.22 Ref.25

Experimental info

Mutagenesis

1 – 9

9

Missing: Prevents H3K4me3 formation. Ref.10 Ref.16

Mutagenesis

88

1

C → A or V: Loss of activity. Ref.7 Ref.16

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)
	P06104-1 [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: 3881753] [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: 9234674] [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: 9169869] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[4]	"The yeast DNA repair gene RAD6 encodes a ubiquitin-conjugating enzyme." Jentsch S., McGrath J.P., Varshavsky A. Nature 329:131-134(1987) [PubMed: 3306404] [Abstract] Cited for: PROTEIN SEQUENCE OF 77-91, FUNCTION.
[5]	"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: 7038392] [Abstract] Cited for: FUNCTION.
[6]	"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: 2179869] [Abstract] Cited for: INDUCTION.
[7]	"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: 2157209] [Abstract] Cited for: FUNCTION, MUTAGENESIS OF CYS-88.
[8]	"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: 1651502] [Abstract] Cited for: FUNCTION, INTERACTION WITH UBR1.
[9]	"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: 2065660] [Abstract] Cited for: FUNCTION.
[10]	"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: 8436296] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH UBR1, MUTAGENESIS OF 1-MET--LEU-9.
[11]	"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: 7926769] [Abstract] Cited for: FUNCTION, INTERACTION WITH RAD18 AND UBR1.
[12]	"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: 9287349] [Abstract] Cited for: FUNCTION, INTERACTION WITH RAD18.
[13]	"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: 9343433] [Abstract] Cited for: FUNCTION.
[14]	"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: 10581257] [Abstract] Cited for: INTERACTION WITH UBR1 AND UBR2.
[15]	"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: 10880451] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION.
[16]	"Ubiquitination of histone H2B regulates H3 methylation and gene silencing in yeast." Sun Z.-W., Allis C.D. Nature 418:104-108(2002) [PubMed: 12077605] [Abstract] Cited for: FUNCTION, MUTAGENESIS OF CYS-88 AND 1-MET--LEU-9.
[17]	"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: 12226657] [Abstract] Cited for: FUNCTION.
[18]	"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: 14562095] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[19]	"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].
[20]	"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: 14752010] [Abstract] Cited for: FUNCTION.
[21]	"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: 15388802] [Abstract] Cited for: FUNCTION.
[22]	"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: 16307922] [Abstract] Cited for: FUNCTION, PHOSPHORYLATION AT SER-120.
[23]	"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: 15632065] [Abstract] Cited for: FUNCTION, INTERACTION WITH RTF1; PAF1 AND THE RNA POLYMERASE II HYPERPHOSPHORYLATED FORM.
[24]	"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: 16247017] [Abstract] Cited for: FUNCTION.
[25]	"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: 18407956] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-120, MASS SPECTROMETRY.
[26]	"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: 9497353] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

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

PIR

A21906.

RefSeq

NP_011457.1.

3D structure databases

PDBPDBe

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

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:1555N.

IntAct

P06104. 7 interactions.

Proteomic databases

PeptideAtlas

P06104.

Genome annotation databases

Ensembl

YGL058W. Saccharomyces cerevisiae. [Contig view]

GeneID

852822.

GenomeReviews

Gene locus YGL058W in contig Y13135_GR.

KEGG

sce:YGL058W.

NMPDR

fig|4932.3.peg.2563.

Organism-specific databases

CYGD

YGL058w.

SGD

S000003026. RAD6.

Yeast-GFP

Search...

Phylogenomic databases

HOGENOM

P06104.

OMA

P06104. YANGEIC.

Enzyme and pathway databases

BRENDA

6.3.2.19. 250.

Gene expression databases

GermOnline

YGL058W. 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.

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

NextBio

972372.

Entry information

Entry name

UBC2_YEAST

Accession

Primary (citable) accession number: P06104

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 1, 1988
Last sequence update:	January 1, 1988
Last modified:	June 16, 2009
This is version 101 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)