Histone-lysine N-methyltransferase, H3 lysine-4 specific - Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

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P38827 (SET1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 124. History...

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

Documents (4) |

Third-party data

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

Names and origin

Protein names

Recommended name:
Histone-lysine N-methyltransferase, H3 lysine-4 specific
EC=2.1.1.43

Alternative name(s):
COMPASS component SET1
Lysine N-methyltransferase 2
SET domain-containing protein 1

Gene names

Name:	SET1
Synonyms:	KMT2, YTX1
Ordered Locus Names:	YHR119W

Organism

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

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	1080 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalytic component of the COMPASS (Set1C) complex that specifically mono-, di- and trimethylates histone H3 to form H3K4me1/2/3, which subsequently plays a role in telomere length maintenance and transcription elongation regulation. Ref.3 Ref.4 Ref.5 Ref.6 Ref.8 Ref.9 Ref.10 Ref.11 Ref.12 Ref.13 Ref.15 Ref.16
Catalytic activity	S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone]. Ref.9
Subunit structure	Component of the COMPASS (Set1C) complex which consists of SET1₂, BRE2₂, SPP1₂, SDC1₁, SHG1₁, SWD1₁, SWD2₁, and SWD3₁. Interacts with MEC3. Ref.4 Ref.5 Ref.7 Ref.11
Subcellular location	Nucleus Probable. Chromosome Probable.
Miscellaneous	Present with 172 molecules/cell in log phase SD medium.
Sequence similarities	Contains 1 post-SET domain. Contains 1 SET domain.

Ontologies

Keywords
Cellular component	Chromosome Nucleus
Ligand	S-adenosyl-L-methionine
Molecular function	Chromatin regulator Methyltransferase Transferase
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	ascospore formation Inferred from mutant phenotype PubMed 17150765. Source: SGD chromatin silencing at rDNA Traceable author statement PubMed 15340082. Source: SGD chromatin silencing at silent mating-type cassette Inferred from mutant phenotype Ref.3. Source: SGD chromatin silencing at telomere Inferred from mutant phenotype Ref.11 Ref.9 Ref.3 Ref.4. Source: SGD histone H3-K4 methylation Inferred from direct assay Ref.5 Ref.11 Ref.9. Source: SGD peptidyl-lysine dimethylation Inferred from mutant phenotype PubMed 16143104. Source: SGD positive regulation of histone acetylation Inferred from genetic interaction PubMed 19822662. Source: SGD regulation of transcription from RNA polymerase II promoter in response to stress Inferred from mutant phenotype PubMed 16959218. Source: SGD telomere maintenance Inferred from mutant phenotype Ref.5 Ref.3. Source: SGD
Cellular_component	Set1C/COMPASS complex Inferred from physical interaction Ref.7 Ref.5 Ref.11. Source: SGD chromosome Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	RNA binding Inferred from mutant phenotype PubMed 16787775. Source: SGD histone methyltransferase activity Inferred from sequence or structural similarity Ref.15. Source: SGD histone-lysine N-methyltransferase activity Inferred from electronic annotation. Source: EC protein-lysine N-methyltransferase activity Inferred from mutant phenotype PubMed 16143104. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct
BRE2	P43132	7	EBI-16977,EBI-27115
MEC3	Q02574	3	EBI-16977,EBI-10658
SWD2	P36104	6	EBI-16977,EBI-26608

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 1080

1080

Histone-lysine N-methyltransferase, H3 lysine-4 specific

PRO_0000186086

Regions

Domain

936 – 1059

124

SET

Domain

1064 – 1080

Post-SET

Amino acid modifications

Modified residue

625

Phosphoserine Ref.17 Ref.18

Modified residue

655

Phosphoserine Ref.19

Modified residue

785

Phosphothreonine Ref.19

Modified residue

875

Phosphothreonine Ref.19

Secondary structure

1080

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P38827 [UniParc].

Last modified February 1, 1995. Version 1.
Checksum: B7FA5D60F71063FD
Show »

FASTA

1,080

123,912

        10         20         30         40         50         60 
MSNYYRRAHA SSGSYRQPQE QPQYSRSGHY QYSNGHSHQQ YSSQYNQRRR YNHNDGTRRR 

        70         80         90        100        110        120 
YNDDRPHSSN NASTRQYYAT NNSQSGPYVN KKSDISSRRG MSQSRYSNSN VHNTLASSSG 

       130        140        150        160        170        180 
SLPTESALLL QQRPPSVLRY NTDNLKSKFH YFDPIKGEFF NKDKMLSWKA TDKEFSETGY 

       190        200        210        220        230        240 
YVVKELQDGQ FKFKIKHRHP EIKASDPRNE NGIMTSGKVA THRKCRNSLI LLPRISYDRY 

       250        260        270        280        290        300 
SLGPPPSCEI VVYPAQDSTT TNIQDISIKN YFKKYGEISH FEAFNDPNSA LPLHVYLIKY 

       310        320        330        340        350        360 
ASSDGKINDA AKAAFSAVRK HESSGCFIMG FKFEVILNKH SILNNIISKF VEINVKKLQK 

       370        380        390        400        410        420 
LQENLKKAKE KEAENEKAKE LQGKDITLPK EPKVDTLSHS SGSEKRIPYD LLGVVNNRPV 

       430        440        450        460        470        480 
LHVSKIFVAK HRFCVEDFKY KLRGYRCAKF IDHPTGIYII FNDIAHAQTC SNAESGNLTI 

       490        500        510        520        530        540 
MSRSRRIPIL IKFHLILPRF QNRTRFNKSS SSSNSTNVPI KYESKEEFIE ATAKQILKDL 

       550        560        570        580        590        600 
EKTLHVDIKK RLIGPTVFDA LDHANFPELL AKRELKEKEK RQQIASKIAE DELKRKEEAK 

       610        620        630        640        650        660 
RDFDLFGLYG GYAKSNKRNL KRHNSLALDH TSLKRKKLSN GIKPMAHLLN EETDSKETTP 

       670        680        690        700        710        720 
LNDEGITRVS KEHDEEDENM TSSSSEEEEE EAPDKKFKSE SEPTTPESDH LHGIKPLVPD 

       730        740        750        760        770        780 
QNGSSDVLDA SSMYKPTATE IPEPVYPPEE YDLKYSQTLS SMDLQNAIKD EEDMLILKQL 

       790        800        810        820        830        840 
LSTYTPTVTP ETSAALEYKI WQSRRKVLEE EKASDWQIEL NGTLFDSELQ PGSSFKAEGF 

       850        860        870        880        890        900 
RKIADKLKIN YLPHRRRVHQ PLNTVNIHNE RNEYTPELCQ REESSNKEPS DSVPQEVSSS 

       910        920        930        940        950        960 
RDNRASNRRF QQDIEAQKAA IGTESELLSL NQLNKRKKPV MFARSAIHNW GLYALDSIAA 

       970        980        990       1000       1010       1020 
KEMIIEYVGE RIRQPVAEMR EKRYLKNGIG SSYLFRVDEN TVIDATKKGG IARFINHCCD 

      1030       1040       1050       1060       1070       1080 
PNCTAKIIKV GGRRRIVIYA LRDIAASEEL TYDYKFEREK DDEERLPCLC GAPNCKGFLN

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Complete nucleotide sequence of Saccharomyces cerevisiae chromosome VIII." Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Dover J., Du Z., Favello A., Fulton L., Gattung S., Geisel C., Kirsten J., Kucaba T., Hillier L.W., Jier M., Johnston L., Langston Y., Latreille P. Vaudin M. Science 265:2077-2082(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[2]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[3]	"SET1, a yeast member of the Trithorax family, functions in transcriptional silencing and diverse cellular processes." Nislow C., Ray E., Pillus L. Mol. Biol. Cell 8:2421-2436(1997) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[4]	"Interaction between Set1p and checkpoint protein Mec3p in DNA repair and telomere functions." Corda Y., Schramke V., Longhese M.P., Smokvina T., Paciotti V., Brevet V., Gilson E., Geli V. Nat. Genet. 21:204-208(1999) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, INTERACTION WITH MEC3.
[5]	"The Saccharomyces cerevisiae Set1 complex includes an Ash2 homologue and methylates histone 3 lysine 4." Roguev A., Schaft D., Shevchenko A., Pijnappel W.W.M.P., Wilm M., Aasland R., Stewart A.F. EMBO J. 20:7137-7148(2001) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION IN THE SET1 COMPLEX, FUNCTION OF THE SET1 COMPLEX.
[6]	"Histone H3 lysine 4 methylation is mediated by Set1 and required for cell growth and rDNA silencing in Saccharomyces cerevisiae." Briggs S.D., Bryk M., Strahl B.D., Cheung W.L., Davie J.K., Dent S.Y.R., Winston F., Allis C.D. Genes Dev. 15:3286-3295(2001) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[7]	"COMPASS: a complex of proteins associated with a trithorax-related SET domain protein." Miller T., Krogan N.J., Dover J., Erdjument-Bromage H., Tempst P., Johnston M., Greenblatt J.F., Shilatifard A. Proc. Natl. Acad. Sci. U.S.A. 98:12902-12907(2001) [PubMed] [Europe PMC] [Abstract] Cited for: SUBUNIT.
[8]	"Evidence that Set1, a factor required for methylation of histone H3, regulates rDNA silencing in S. cerevisiae by a Sir2-independent mechanism." Bryk M., Briggs S.D., Strahl B.D., Curcio M.J., Allis C.D., Winston F. Curr. Biol. 12:165-170(2002) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[9]	"COMPASS, a histone H3 (Lysine 4) methyltransferase required for telomeric silencing of gene expression." Krogan N.J., Dover J., Khorrami S., Greenblatt J.F., Schneider J., Johnston M., Shilatifard A. J. Biol. Chem. 277:10753-10755(2002) [PubMed] [Europe PMC] [Abstract] Cited for: ENZYME ACTIVITY, FUNCTION.
[10]	"Active genes are tri-methylated at K4 of histone H3." Santos-Rosa H., Schneider R., Bannister A.J., Sherriff J., Bernstein B.E., Emre N.C.T., Schreiber S.L., Mellor J., Kouzarides T. Nature 419:407-411(2002) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[11]	"A trithorax-group complex purified from Saccharomyces cerevisiae is required for methylation of histone H3." Nagy P.L., Griesenbeck J., Kornberg R.D., Cleary M.L. Proc. Natl. Acad. Sci. U.S.A. 99:90-94(2002) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION IN THE SET1 COMPLEX, FUNCTION OF THE SET1 COMPLEX.
[12]	"Methylation of histone H3 Lys 4 in coding regions of active genes." Bernstein B.E., Humphrey E.L., Erlich R.L., Schneider R., Bouman P., Liu J.S., Kouzarides T., Schreiber S.L. Proc. Natl. Acad. Sci. U.S.A. 99:8695-8700(2002) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[13]	"Methylation of histone H3 K4 mediates association of the Isw1p ATPase with chromatin." Santos-Rosa H., Schneider R., Bernstein B.E., Karabetsou N., Morillon A., Weise C., Schreiber S.L., Mellor J., Kouzarides T. Mol. Cell 12:1325-1332(2003) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[14]	"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].
[15]	"Saccharomyces cerevisiae Set1p is a methyltransferase specific for lysine 4 of histone H3 and is required for efficient gene expression." Boa S., Coert C., Patterton H.-G. Yeast 20:827-835(2003) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[16]	"Dynamic lysine methylation on histone H3 defines the regulatory phase of gene transcription." Morillon A., Karabetsou N., Nair A., Mellor J. Mol. Cell 18:723-734(2005) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION OF THE COMPASS COMPLEX.
[17]	"Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae." Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P. J. Proteome Res. 6:1190-1197(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-625, MASS SPECTROMETRY. Strain: ADR376.
[18]	"Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry." Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L., Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F. Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-625, MASS SPECTROMETRY.
[19]	"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-655; THR-785 AND THR-875, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U00059 Genomic DNA. Translation: AAB68867.1.
BK006934 Genomic DNA. Translation: DAA06813.1.

PIR

S48961.

RefSeq

NP_011987.1. NM_001179249.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2J8A	X-ray	3.00	A	247-375	[»]

ProteinModelPortal

P38827.

SMR

P38827. Positions 247-366, 907-1080.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-4616N.

IntAct

P38827. 29 interactions.

MINT

MINT-552558.

STRING

4932.YHR119W.

Proteomic databases

PaxDb

P38827.

PRIDE

P38827.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YHR119W; YHR119W; YHR119W.

GeneID

856519.

KEGG

sce:YHR119W.

Organism-specific databases

CYGD

YHR119w.

SGD

S000001161. SET1.

Phylogenomic databases

eggNOG

COG2940.

GeneTree

ENSGT00700000104213.

HOGENOM

HOG000066111.

K11422.

OMA

ERIRCLC.

OrthoDB

EOG4ZW8K8.

Gene expression databases

Genevestigator

P38827.

GermOnline

YHR119W. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR024657. COMPASS_Set1_N-SET.
IPR017111. Hist_H3-K4_MeTrfase_1_fun.
IPR015722. Histone-lysine_MeTfrase.
IPR003616. Post-SET_dom.
IPR024636. SET_assoc.
IPR001214. SET_dom.
[Graphical view]

PANTHER

PTHR22884:SF10. PTHR22884:SF10. 1 hit.

Pfam

PF11764. N-SET. 1 hit.
PF00856. SET. 1 hit.
PF11767. SET_assoc. 1 hit.
[Graphical view]

PIRSF

PIRSF037104. Histone_H3-K4_mtfrase_Set1_fun. 1 hit.

SMART

SM00508. PostSET. 1 hit.
SM00317. SET. 1 hit.
[Graphical view]

PROSITE

PS50868. POST_SET. 1 hit.
PS50280. SET. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P38827.

NextBio

982275.

Entry information

Entry name

SET1_YEAST

Accession

Primary (citable) accession number: P38827
Secondary accession number(s): D3DL69

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1995
Last sequence update:	February 1, 1995
Last modified:	May 1, 2013
This is version 124 of the entry and version 1 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 VIII

Yeast (Saccharomyces cerevisiae) chromosome VIII: 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·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

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

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