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P46995

- SET2_YEAST

UniProt

P46995 - SET2_YEAST

Protein

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

Gene

SET2

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 143 (01 Oct 2014)
      Sequence version 2 (21 Sep 2011)
      Previous versions | rss
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    Functioni

    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.7 Publications

    Catalytic activityi

    S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone].PROSITE-ProRule annotation

    GO - Molecular functioni

    1. histone methyltransferase activity Source: SGD
    2. histone methyltransferase activity (H3-K36 specific) Source: SGD

    GO - Biological processi

    1. ascospore formation Source: SGD
    2. DNA-templated transcription, elongation Source: SGD
    3. DNA-templated transcription, termination Source: SGD
    4. histone deacetylation Source: SGD
    5. histone methylation Source: SGD
    6. negative regulation of antisense RNA transcription Source: SGD
    7. negative regulation of histone H3-K14 acetylation Source: SGD
    8. negative regulation of histone H3-K9 acetylation Source: SGD
    9. negative regulation of reciprocal meiotic recombination Source: SGD
    10. positive regulation of histone acetylation Source: SGD
    11. regulation of DNA-dependent DNA replication initiation Source: SGD
    12. regulation of histone exchange Source: SGD
    13. regulation of transcription, DNA-templated Source: SGD

    Keywords - Molecular functioni

    Methyltransferase, Repressor, Transferase

    Keywords - Biological processi

    Transcription, Transcription regulation

    Keywords - Ligandi

    S-adenosyl-L-methionine

    Enzyme and pathway databases

    BioCyciYEAST:G3O-31606-MONOMER.

    Names & Taxonomyi

    Protein namesi
    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 namesi
    Name:SET2
    Synonyms:EZL1, KMT3
    Ordered Locus Names:YJL168C
    ORF Names:J0520
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome X

    Organism-specific databases

    CYGDiYJL168c.
    SGDiS000003704. SET2.

    Subcellular locationi

    GO - Cellular componenti

    1. chromosome Source: UniProtKB-SubCell
    2. cytosol Source: SGD
    3. nucleus Source: SGD

    Keywords - Cellular componenti

    Chromosome, Nucleus

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi195 – 1951R → G: Reduces dramatically histone methyltransferase activity toward nucleosomes. 1 Publication
    Mutagenesisi201 – 2011C → A: Reduces dramatically histone methyltransferase activity toward nucleosomes. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 733733Histone-lysine N-methyltransferase, H3 lysine-36 specificPRO_0000186087Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei10 – 101Phosphoserine1 Publication
    Modified residuei522 – 5221Phosphoserine1 Publication

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    MaxQBiP46995.
    PaxDbiP46995.
    PeptideAtlasiP46995.

    Expressioni

    Gene expression databases

    GenevestigatoriP46995.

    Interactioni

    Subunit structurei

    Interacts with the RNA polymerase II hyperphosphorylated CTD. Interacts with CYC8.7 Publications

    Protein-protein interaction databases

    BioGridi33591. 392 interactions.
    DIPiDIP-2150N.
    IntActiP46995. 62 interactions.
    MINTiMINT-500810.
    STRINGi4932.YJL168C.

    Structurei

    Secondary structure

    1
    733
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi481 – 49414
    Turni495 – 4984
    Beta strandi499 – 5035
    Helixi624 – 64522
    Turni648 – 6525
    Helixi655 – 67622
    Helixi688 – 71225

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1E0NNMR-A479-505[»]
    2C5ZNMR-A620-719[»]
    ProteinModelPortaliP46995.
    SMRiP46995. Positions 66-261, 479-505, 622-703.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP46995.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini63 – 11856AWSPROSITE-ProRule annotationAdd
    BLAST
    Domaini120 – 237118SETPROSITE-ProRule annotationAdd
    BLAST
    Domaini244 – 26017Post-SETPROSITE-ProRule annotationAdd
    BLAST
    Domaini475 – 50733WWAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni619 – 718100Binding to RNA polymerase II CTDAdd
    BLAST

    Coiled coil

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Coiled coili548 – 63083Sequence AnalysisAdd
    BLAST

    Domaini

    The AWS and SET domains are necessary for transcription repression.2 Publications

    Sequence similaritiesi

    Belongs to the class V-like SAM-binding methyltransferase superfamily. Histone-lysine methyltransferase family. SET2 subfamily.PROSITE-ProRule annotation
    Contains 1 AWS domain.PROSITE-ProRule annotation
    Contains 1 post-SET domain.PROSITE-ProRule annotation
    Contains 1 SET domain.PROSITE-ProRule annotation
    Contains 1 WW domain.Curated

    Keywords - Domaini

    Coiled coil

    Phylogenomic databases

    eggNOGiCOG2940.
    GeneTreeiENSGT00750000117355.
    HOGENOMiHOG000248214.
    KOiK11423.
    OMAiSCNPNAY.
    OrthoDBiEOG7P8PH3.

    Family and domain databases

    InterProiIPR006560. AWS.
    IPR025788. Hist-Lys_N-MeTrfase_SET2_fun.
    IPR003616. Post-SET_dom.
    IPR001214. SET_dom.
    IPR013257. SRI.
    IPR001202. WW_dom.
    [Graphical view]
    PfamiPF00856. SET. 1 hit.
    PF08236. SRI. 1 hit.
    [Graphical view]
    SMARTiSM00570. AWS. 1 hit.
    SM00508. PostSET. 1 hit.
    SM00317. SET. 1 hit.
    SM00456. WW. 1 hit.
    [Graphical view]
    SUPFAMiSSF51045. SSF51045. 1 hit.
    PROSITEiPS51215. AWS. 1 hit.
    PS50868. POST_SET. 1 hit.
    PS51568. SAM_MT43_SET2_1. 1 hit.
    PS50280. SET. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P46995-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSKNQSVSAS EDEKEILNNN AEGHKPQRLF DQEPDLTEEA LTKFENLDDC    50
    IYANKRIGTF KNNDFMECDC YEEFSDGVNH ACDEDSDCIN RLTLIECVND 100
    LCSSCGNDCQ NQRFQKKQYA PIAIFKTKHK GYGVRAEQDI EANQFIYEYK 150
    GEVIEEMEFR DRLIDYDQRH FKHFYFMMLQ NGEFIDATIK GSLARFCNHS 200
    CSPNAYVNKW VVKDKLRMGI FAQRKILKGE EITFDYNVDR YGAQAQKCYC 250
    EEPNCIGFLG GKTQTDAASL LPQNIADALG VTVSMEKKWL KLKKLSGEPI 300
    IKNENENINI EFLQSLEVQP IDSPVDVTKI MSVLLQQDNK IIASKLLKRL 350
    FTIDDDSLRH QAIKLHGYTC FSKMLKLFIT EQPQVDGKGN ETEEDDIKFI 400
    KGILDFLLEL PKTTRNGIES SQIDNVVKTL PAKFPFLKPN CDELLEKWSK 450
    FETYKRITKK DINVAASKMI DLRRVRLPPG WEIIHENGRP LYYNAEQKTK 500
    LHYPPSGSSK VFSSRSNTQV NSPSSSGIPK TPGALDSKKH KLSDEEYERK 550
    KQKRLEYERI ALERAKQEEL ESLKQKLKLE NERKSVLEDI IAEANKQKEL 600
    QKEEAKKLVE AKEAKRLKRK TVSQSQRLEH NWNKFFASFV PNLIKKNPQS 650
    KQFDHENIKQ CAKDIVKILT TKELKKDSSR APPDDLTKGK RHKVKEFINS 700
    YMDKIILKKK QKKALALSSA STRMSSPPPS TSS 733
    Length:733
    Mass (Da):84,461
    Last modified:September 21, 2011 - v2
    Checksum:i05436B181E88EFF5
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti594 – 5941A → F in CAA89464. (PubMed:8641269)Curated
    Sequence conflicti605 – 6051A → S in CAA89464. (PubMed:8641269)Curated
    Sequence conflicti716 – 7161A → G in CAA89464. (PubMed:8641269)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Z49444 Genomic DNA. Translation: CAA89464.1.
    BK006943 Genomic DNA. Translation: DAA08635.2.
    PIRiS56951.
    RefSeqiNP_012367.2. NM_001181601.2.

    Genome annotation databases

    EnsemblFungiiYJL168C; YJL168C; YJL168C.
    GeneIDi853271.
    KEGGisce:YJL168C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Z49444 Genomic DNA. Translation: CAA89464.1 .
    BK006943 Genomic DNA. Translation: DAA08635.2 .
    PIRi S56951.
    RefSeqi NP_012367.2. NM_001181601.2.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1E0N NMR - A 479-505 [» ]
    2C5Z NMR - A 620-719 [» ]
    ProteinModelPortali P46995.
    SMRi P46995. Positions 66-261, 479-505, 622-703.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 33591. 392 interactions.
    DIPi DIP-2150N.
    IntActi P46995. 62 interactions.
    MINTi MINT-500810.
    STRINGi 4932.YJL168C.

    Proteomic databases

    MaxQBi P46995.
    PaxDbi P46995.
    PeptideAtlasi P46995.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YJL168C ; YJL168C ; YJL168C .
    GeneIDi 853271.
    KEGGi sce:YJL168C.

    Organism-specific databases

    CYGDi YJL168c.
    SGDi S000003704. SET2.

    Phylogenomic databases

    eggNOGi COG2940.
    GeneTreei ENSGT00750000117355.
    HOGENOMi HOG000248214.
    KOi K11423.
    OMAi SCNPNAY.
    OrthoDBi EOG7P8PH3.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-31606-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P46995.
    NextBioi 973544.

    Gene expression databases

    Genevestigatori P46995.

    Family and domain databases

    InterProi IPR006560. AWS.
    IPR025788. Hist-Lys_N-MeTrfase_SET2_fun.
    IPR003616. Post-SET_dom.
    IPR001214. SET_dom.
    IPR013257. SRI.
    IPR001202. WW_dom.
    [Graphical view ]
    Pfami PF00856. SET. 1 hit.
    PF08236. SRI. 1 hit.
    [Graphical view ]
    SMARTi SM00570. AWS. 1 hit.
    SM00508. PostSET. 1 hit.
    SM00317. SET. 1 hit.
    SM00456. WW. 1 hit.
    [Graphical view ]
    SUPFAMi SSF51045. SSF51045. 1 hit.
    PROSITEi PS51215. AWS. 1 hit.
    PS50868. POST_SET. 1 hit.
    PS51568. SAM_MT43_SET2_1. 1 hit.
    PS50280. SET. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    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.
      , Hilger F., Hollenberg C.P., Huang M.-E., Jacq C., Jauniaux J.-C., Katsoulou C., Kirchrath L., Kleine K., Kordes E., Koetter P., Liebl S., Louis E.J., Manus V., Mewes H.-W., Miosga T., Obermaier B., Perea J., Pohl T.M., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rasmussen S.W., Rose M., Rossau R., Schaaff-Gerstenschlaeger I., Smits P.H.M., Scarcez T., Soriano N., To Van D., Tzermia M., Van Broekhoven A., Vandenbol M., Wedler H., von Wettstein D., Wambutt R., Zagulski M., Zollner A., Karpfinger-Hartl L.
      EMBO J. 15:2031-2049(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    2. 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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [Abstract]
      Cited for: FUNCTION, INTERACTION WITH RNA POLYMERASE II.
    10. 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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    15. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
      Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
      Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-10 AND SER-522, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    16. "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] [Europe PMC] [Abstract]
      Cited for: STRUCTURE BY NMR OF 7-33.
    17. "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] [Europe PMC] [Abstract]
      Cited for: STRUCTURE BY NMR OF 619-718.

    Entry informationi

    Entry nameiSET2_YEAST
    AccessioniPrimary (citable) accession number: P46995
    Secondary accession number(s): D6VW19
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1996
    Last sequence update: September 21, 2011
    Last modified: October 1, 2014
    This is version 143 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present with 217 molecules/cell in log phase SD medium.1 Publication

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families
    3. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    4. Yeast chromosome X
      Yeast (Saccharomyces cerevisiae) chromosome X: entries and gene names

    External Data

    Dasty 3