Histone-lysine N-methyltransferase, H3 lysine-36 specific - Saccharomyces cerevisiae (Baker's yeast)

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Reviewed, UniProtKB/Swiss-Prot P46995 (SET2_YEAST)

Last modified November 3, 2009. Version 92. History...

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein names

Recommended name:
    Histone-lysine N-methyltransferase, H3 lysine-36 specific
    EC=2.1.1.43
Alternative name(s):
    SET domain-containing protein 2
    Lysine N-methyltransferase 3

Gene names

Name:	SET2
Synonyms:	EZL1, KMT3
Ordered Locus Names:	YJL168C
ORF Names:	J0520

Organism

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

Taxonomic identifier

4932 [NCBI]

Taxonomic lineage

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

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Protein attributes

Sequence length	733 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

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General annotation (Comments)

Function	Histone methyltransferase that methylates histone H3 to form H3K36me. Involved in transcription elongation as well as in transcription repression. The methyltransferase activity requires the recruitment to the RNA polymerase II, which is CTK1 dependent. Ref.3 Ref.4 Ref.6 Ref.7 Ref.8 Ref.10 Ref.11
Catalytic activity	S-adenosyl-L-methionine + histone L-lysine = S-adenosyl-L-homocysteine + histone N(6)-methyl-L-lysine.
Subunit structure	Interacts with the RNA polymerase II hyperphosphorylated CTD. Interacts with CYC8. Ref.4 Ref.6 Ref.8 Ref.10 Ref.2 Ref.5 Ref.12
Subcellular location	Nucleus.
Domain	The AWS and SET domains are necessary for transcription repression. Ref.7 Ref.10
Miscellaneous	Present with 217 molecules/cell in log phase SD medium. Ref.9
Sequence similarities	Belongs to the histone-lysine methyltransferase family. SET2 subfamily. Contains 1 AWS domain. Contains 1 post-SET domain. Contains 1 SET domain. Contains 1 WW domain.

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Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Chromosomal protein Nucleus
Domain	Coiled coil
Molecular function	Methyltransferase Repressor Transferase
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	RNA elongation Ref.8 Inferred from direct assay. Source: SGD ascospore formation Inferred from mutant phenotype. Source: SGD histone methylation Ref.3 Inferred from direct assay. Source: SGD regulation of transcription, DNA-dependent Ref.3 Inferred from direct assay. Source: SGD
Cellular component	chromosome Inferred from electronic annotation. Source: UniProtKB-KW nucleus Ref.3 Inferred from physical interaction. Source: SGD
Molecular function	histone methyltransferase activity (H3-K36 specific) Ref.3 Inferred from direct assay. Source: SGD protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

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Binary interactions

With	Entry	#Exp.	IntAct
	O13550	1	EBI-16985,EBI-35936
	P25561	1	EBI-16985,EBI-21696
	P38081	1	EBI-16985,EBI-21453
	P47137	1	EBI-16985,EBI-25572
	P53089	1	EBI-16985,EBI-24133
	P53265	1	EBI-16985,EBI-23264
	P53857	1	EBI-16985,EBI-29204
	P53864	1	EBI-16985,EBI-29179
ACR2	Q06597	1	EBI-16985,EBI-2117
ADE12	P80210	1	EBI-16985,EBI-14267
ARP2	P32381	1	EBI-16985,EBI-2927
ATP17	Q06405	1	EBI-16985,EBI-3285
CMD1	P06787	1	EBI-16985,EBI-3976
DPS1	P04802	1	EBI-16985,EBI-18655
ENO2	P00925	1	EBI-16985,EBI-6475
GON7	P46984	1	EBI-16985,EBI-26178
HCR1	Q05775	1	EBI-16985,EBI-8944
HEM13	P11353	1	EBI-16985,EBI-8257
HHT1	P61830	1	EBI-16985,EBI-8098
LYS21	Q12122	1	EBI-16985,EBI-8508
OPT2	Q06593	1	EBI-16985,EBI-37672
OYE3	P41816	1	EBI-16985,EBI-12734
PAI3	P01094	1	EBI-16985,EBI-9305
PCK1	P10963	1	EBI-16985,EBI-13770
PRE10	P21242	1	EBI-16985,EBI-13963
RNR4	P49723	1	EBI-16985,EBI-15251
RPS14A	P06367	1	EBI-16985,EBI-14460
RUB1	Q03919	1	EBI-16985,EBI-37695
SIP2	P34164	1	EBI-16985,EBI-17187
STM1	P39015	1	EBI-16985,EBI-11238
TKL1	P23254	1	EBI-16985,EBI-19291
UBP10	P53874	1	EBI-16985,EBI-19873
YDL086W	Q07505	1	EBI-16985,EBI-5951
YEL047C	P32614	1	EBI-16985,EBI-22366
YPT11	P48559	1	EBI-16985,EBI-29362

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 733

733

Histone-lysine N-methyltransferase, H3 lysine-36 specific

PRO_0000186087

Regions

Domain

63 – 118

AWS

Domain

119 – 241

123

SET

Domain

244 – 260

Post-SET

Domain

475 – 507

Region

619 – 718

100

Binding to RNA polymerase II CTD

Coiled coil

548 – 630

Potential

Amino acid modifications

Modified residue

522

Phosphoserine Ref.13

Experimental info

Mutagenesis

195

R → G: Reduces dramatically histone methyltransferase activity toward nucleosomes. Ref.3

Mutagenesis

201

C → A: Reduces dramatically histone methyltransferase activity toward nucleosomes. Ref.3

Secondary structure

733

Helix Strand Turn

Details...

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Sequences

Sequence

Length

Mass (Da)

Tools

P46995-1 [UniParc].

Last modified February 1, 1996. Version 1.
Checksum: 0BF8A80BC5DE2C95
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FASTA

733

84,540

        10         20         30         40         50         60 
MSKNQSVSAS EDEKEILNNN AEGHKPQRLF DQEPDLTEEA LTKFENLDDC IYANKRIGTF 

        70         80         90        100        110        120 
KNNDFMECDC YEEFSDGVNH ACDEDSDCIN RLTLIECVND LCSSCGNDCQ NQRFQKKQYA 

       130        140        150        160        170        180 
PIAIFKTKHK GYGVRAEQDI EANQFIYEYK GEVIEEMEFR DRLIDYDQRH FKHFYFMMLQ 

       190        200        210        220        230        240 
NGEFIDATIK GSLARFCNHS CSPNAYVNKW VVKDKLRMGI FAQRKILKGE EITFDYNVDR 

       250        260        270        280        290        300 
YGAQAQKCYC EEPNCIGFLG GKTQTDAASL LPQNIADALG VTVSMEKKWL KLKKLSGEPI 

       310        320        330        340        350        360 
IKNENENINI EFLQSLEVQP IDSPVDVTKI MSVLLQQDNK IIASKLLKRL FTIDDDSLRH 

       370        380        390        400        410        420 
QAIKLHGYTC FSKMLKLFIT EQPQVDGKGN ETEEDDIKFI KGILDFLLEL PKTTRNGIES 

       430        440        450        460        470        480 
SQIDNVVKTL PAKFPFLKPN CDELLEKWSK FETYKRITKK DINVAASKMI DLRRVRLPPG 

       490        500        510        520        530        540 
WEIIHENGRP LYYNAEQKTK LHYPPSGSSK VFSSRSNTQV NSPSSSGIPK TPGALDSKKH 

       550        560        570        580        590        600 
KLSDEEYERK KQKRLEYERI ALERAKQEEL ESLKQKLKLE NERKSVLEDI IAEFNKQKEL 

       610        620        630        640        650        660 
QKEESKKLVE AKEAKRLKRK TVSQSQRLEH NWNKFFASFV PNLIKKNPQS KQFDHENIKQ 

       670        680        690        700        710        720 
CAKDIVKILT TKELKKDSSR APPDDLTKGK RHKVKEFINS YMDKIILKKK QKKALGLSSA 

       730 
STRMSSPPPS TSS

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References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Complete nucleotide sequence of Saccharomyces cerevisiae chromosome X." Galibert F., Alexandraki D., Baur A., Boles E., Chalwatzis N., Chuat J.-C., Coster F., Cziepluch C., de Haan M., Domdey H., Durand P., Entian K.-D., Gatius M., Goffeau A., Grivell L.A., Hennemann A., Herbert C.J., Heumann K. Karpfinger-Hartl L. EMBO J. 15:2031-2049(1996) [PubMed: 8641269] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[2]	"Association of the histone methyltransferase Set2 with RNA polymerase II plays a role in transcription elongation." Li J., Moazed D., Gygi S.P. J. Biol. Chem. 277:49383-49388(2002) [PubMed: 12381723] [Abstract] Cited for: INTERACTION WITH RBP1 AND RBP2.
[3]	"Set2 is a nucleosomal histone H3-selective methyltransferase that mediates transcriptional repression." Strahl B.D., Grant P.A., Briggs S.D., Sun Z.-W., Bone J.R., Caldwell J.A., Mollah S., Cook R.G., Shabanowitz J., Hunt D.F., Allis C.D. Mol. Cell. Biol. 22:1298-1306(2002) [PubMed: 11839797] [Abstract] Cited for: FUNCTION, MUTAGENESIS OF ARG-195 AND CYS-201.
[4]	"Phosphorylation of RNA polymerase II CTD regulates H3 methylation in yeast." Xiao T., Hall H., Kizer K.O., Shibata Y., Hall M.C., Borchers C.H., Strahl B.D. Genes Dev. 17:654-663(2003) [PubMed: 12629047] [Abstract] Cited for: INTERACTION WITH RNA POLYMERASE II, FUNCTION.
[5]	"The Set2 histone methyltransferase functions through the phosphorylated carboxyl-terminal domain of RNA polymerase II." Li B., Howe L., Anderson S., Yates J.R. III, Workman J.L. J. Biol. Chem. 278:8897-8903(2003) [PubMed: 12511561] [Abstract] Cited for: INTERACTION WITH RNA POLYMERASE II.
[6]	"Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II." Krogan N.J., Kim M., Tong A., Golshani A., Cagney G., Canadien V., Richards D.P., Beattie B.K., Emili A., Boone C., Shilatifard A., Buratowski S., Greenblatt J. Mol. Cell. Biol. 23:4207-4218(2003) [PubMed: 12773564] [Abstract] Cited for: FUNCTION, INTERACTION WITH RNA POLYMERASE II.
[7]	"Set2-catalyzed methylation of histone H3 represses basal expression of GAL4 in Saccharomyces cerevisiae." Landry J., Sutton A., Hesman T., Min J., Xu R.-M., Johnston M., Sternglanz R. Mol. Cell. Biol. 23:5972-5978(2003) [PubMed: 12917322] [Abstract] Cited for: FUNCTION, DOMAINS.
[8]	"The histone 3 lysine 36 methyltransferase, SET2, is involved in transcriptional elongation." Schaft D., Roguev A., Kotovic K.M., Shevchenko A., Sarov M., Shevchenko A., Neugebauer K.M., Stewart A.F. Nucleic Acids Res. 31:2475-2482(2003) [PubMed: 12736296] [Abstract] Cited for: FUNCTION, INTERACTION WITH RNA POLYMERASE II.
[9]	"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].
[10]	"A novel domain in Set2 mediates RNA polymerase II interaction and couples histone H3 K36 methylation with transcript elongation." Kizer K.O., Phatnani H.P., Shibata Y., Hall H., Greenleaf A.L., Strahl B.D. Mol. Cell. Biol. 25:3305-3316(2005) [PubMed: 15798214] [Abstract] Cited for: FUNCTION, DOMAIN, INTERACTION WITH RNA POLYMERASE II CTD.
[11]	"Dimethylation of histone H3 at lysine 36 demarcates regulatory and nonregulatory chromatin genome-wide." Rao B., Shibata Y., Strahl B.D., Lieb J.D. Mol. Cell. Biol. 25:9447-9459(2005) [PubMed: 16227595] [Abstract] Cited for: FUNCTION.
[12]	"The Set2 methyltransferase associates with Ssn6 yet Tup1-Ssn6 repression is independent of histone methylation." Tripic T., Edmondson D.G., Davie J.K., Strahl B.D., Dent S.Y.R. Biochem. Biophys. Res. Commun. 339:905-914(2006) [PubMed: 16329992] [Abstract] Cited for: INTERACTION WITH CYC8.
[13]	"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-522, MASS SPECTROMETRY.
[14]	"Structural analysis of WW domains and design of a WW prototype." Macias M.J., Gervais V., Civera C., Oschkinat H. Nat. Struct. Biol. 7:375-379(2000) [PubMed: 10802733] [Abstract] Cited for: STRUCTURE BY NMR OF 7-33.
[15]	"Structure and carboxyl-terminal domain (CTD) binding of the Set2 SRI domain that couples histone H3 Lys36 methylation to transcription." Vojnic E., Simon B., Strahl B.D., Sattler M., Cramer P. J. Biol. Chem. 281:13-15(2006) [PubMed: 16286474] [Abstract] Cited for: STRUCTURE BY NMR OF 619-718.
+	Additional computationally mapped references.

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Cross-references

Sequence databases

Z49444 Genomic DNA. Translation: CAA89464.1.

PIR

S56951.

RefSeq

NP_012367.1.

3D structure databases

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1E0N	NMR	-	A	479-505	[»]
2C5Z	NMR	-	A	620-719	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:2150N.

IntAct

P46995. 59 interactions.

STRING

P46995.

Proteomic databases

PeptideAtlas

P46995.

PRIDE

P46995.

Genome annotation databases

Ensembl

YJL168C; YJL168C; YJL168C; Saccharomyces cerevisiae. [Genome view]

GeneID

853271.

GenomeReviews

Gene locus YJL168C in contig Y13136_GR.

KEGG

sce:YJL168C.

NMPDR

fig|4932.3.peg.3331.

Organism-specific databases

CYGD

YJL168c.

SGD

S000003704. SET2.

Phylogenomic databases

HOGENOM

P46995.

OMA

GKTQTDA.

Enzyme and pathway databases

BRENDA

2.1.1.43. 250.

Gene expression databases

ArrayExpress

P46995.

Genevestigator

P46995.

GermOnline

YJL168C. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR006560. AWS.
IPR003616. Post-SET_Zn_bd.
IPR001214. SET.
IPR013257. SRI.
IPR001202. WW_Rsp5_WWP.
[Graphical view]

Pfam

PF00856. SET. 1 hit.
PF08236. SRI. 1 hit.
[Graphical view]

SMART

SM00570. AWS. 1 hit.
SM00508. PostSET. 1 hit.
SM00317. SET. 1 hit.
SM00456. WW. 1 hit.
[Graphical view]

PROSITE

PS51215. AWS. 1 hit.
PS50868. POST_SET. 1 hit.
PS50280. SET. 1 hit.
PS01159. WW_DOMAIN_1. False negative.
PS50020. WW_DOMAIN_2. False negative.
[Graphical view]

ProtoNet

Search...

Other Resources

NextBio

973544.

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Entry information

Entry name

SET2_YEAST

Accession

Primary (citable) accession number: P46995

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1996
Last sequence update:	February 1, 1996
Last modified:	November 3, 2009
This is version 92 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)

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Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

Yeast chromosome X

Yeast (Saccharomyces cerevisiae) chromosome X: entries and gene names

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Regions

Amino acid modifications

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other Resources

Entry information

Relevant documents