Histone-lysine N-methyltransferase, H3 lysine-36 specific - Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

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P46995 (SET2_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 118. History...

Clusters with 100%, 90%, 50% identity |

Documents (4) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Histone-lysine N-methyltransferase, H3 lysine-36 specific
EC=2.1.1.43

Alternative name(s):
Lysine N-methyltransferase 3
SET domain-containing protein 2

Gene names

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

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	733 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

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.4 Ref.5 Ref.7 Ref.8 Ref.9 Ref.11 Ref.12
Catalytic activity	S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone].
Subunit structure	Interacts with the RNA polymerase II hyperphosphorylated CTD. Interacts with CYC8. Ref.3 Ref.5 Ref.6 Ref.7 Ref.9 Ref.11 Ref.13
Subcellular location	Nucleus. Chromosome Probable.
Domain	The AWS and SET domains are necessary for transcription repression. Ref.8 Ref.11
Miscellaneous	Present with 217 molecules/cell in log phase SD medium. Ref.10
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.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Chromosome Nucleus
Domain	Coiled coil
Molecular function	Methyltransferase Repressor Transferase
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	ascospore formation Inferred from mutant phenotype. Source: SGD histone deacetylation Inferred from mutant phenotype. Source: SGD negative regulation of antisense RNA transcription Inferred from mutant phenotype. Source: SGD negative regulation of histone H3-K14 acetylation Inferred from mutant phenotype. Source: SGD negative regulation of histone H3-K9 acetylation Inferred from mutant phenotype. Source: SGD negative regulation of reciprocal meiotic recombination Inferred from mutant phenotype. Source: SGD positive regulation of histone acetylation Inferred from genetic interaction. Source: SGD regulation of DNA-dependent DNA replication initiation Inferred from mutant phenotype. Source: SGD transcription elongation, DNA-dependent Inferred from direct assay Ref.9. Source: SGD
Cellular component	chromosome Inferred from electronic annotation. Source: UniProtKB-SubCell nucleus Inferred from physical interaction Ref.4. Source: SGD
Molecular function	histone methyltransferase activity (H3-K36 specific) Inferred from direct assay Ref.4. Source: SGD
Complete GO annotation...

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.14

Experimental info

Mutagenesis

195

R → G: Reduces dramatically histone methyltransferase activity toward nucleosomes. Ref.4

Mutagenesis

201

C → A: Reduces dramatically histone methyltransferase activity toward nucleosomes. Ref.4

Sequence conflict

594

A → F in CAA89464. Ref.1

Sequence conflict

605

A → S in CAA89464. Ref.1

Sequence conflict

716

A → G in CAA89464. Ref.1

Secondary structure

733

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P46995 [UniParc].

Last modified September 21, 2011. Version 2.
Checksum: 05436B181E88EFF5
Show »

FASTA

733

84,461

        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 IAEANKQKEL 

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

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

       730 
STRMSSPPPS TSS

« Hide

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]	Saccharomyces Genome Database Submitted (MAR-2011) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION, SEQUENCE REVISION TO 594; 605 AND 716. Strain: ATCC 204508 / S288c.
[3]	"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.
[4]	"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.
[5]	"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.
[6]	"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.
[7]	"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.
[8]	"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.
[9]	"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.
[10]	"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].
[11]	"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.
[12]	"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.
[13]	"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.
[14]	"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.
[15]	"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.
[16]	"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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

Z49444 Genomic DNA. Translation: CAA89464.1.
BK006943 Genomic DNA. Translation: DAA08635.2.

PIR

S56951.

RefSeq

NP_012367.2. NM_001181601.2.

3D structure databases

PDBe
RCSB PDB
PDBj

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

ProteinModelPortal

P46995.

SMR

P46995. Positions 43-261, 479-505, 622-703.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-2150N.

IntAct

P46995. 65 interactions.

MINT

MINT-500810.

STRING

P46995.

Proteomic databases

PeptideAtlas

P46995.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

853271.

KEGG

sce:YJL168C.

NMPDR

fig|4932.3.peg.3331.

Organism-specific databases

CYGD

YJL168c.

SGD

S000003704. SET2.

Phylogenomic databases

eggNOG

fuNOG06788.

GeneTree

EFGT00050000001847.

HOGENOM

HBG328952.

OMA

GKTQTDA.

OrthoDB

EOG40S3Q4.

Gene expression databases

ArrayExpress

P46995.

Genevestigator

P46995.

GermOnline

YJL168C. Saccharomyces cerevisiae.

Family and domain databases

InterPro

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

K11423.

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]

SUPFAM

SSF51045. WW_Rsp5_WWP. 1 hit.

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

NextBio

973544.

Entry information

Entry name

SET2_YEAST

Accession

Primary (citable) accession number: P46995
Secondary accession number(s): D6VW19

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1996
Last sequence update:	September 21, 2011
Last modified:	January 25, 2012
This is version 118 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program

Relevant documents

Yeast

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

Yeast chromosome X

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

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

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

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents