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Histone-lysine N-methyltransferase, H3 lysine-36 specific (EC 2.1.1.43) (Lysine N-methyltransferase 3) (SET domain-containing protein 2)

 SET2_YEAST              Reviewed;         733 AA.
P46995; D6VW19;
01-FEB-1996, integrated into UniProtKB/Swiss-Prot.
21-SEP-2011, sequence version 2.
22-NOV-2017, entry version 171.
RecName: Full=Histone-lysine N-methyltransferase, H3 lysine-36 specific;
EC=2.1.1.43;
AltName: Full=Lysine N-methyltransferase 3;
AltName: Full=SET domain-containing protein 2;
Name=SET2; Synonyms=EZL1, KMT3; OrderedLocusNames=YJL168C;
ORFNames=J0520;
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
NCBI_TaxID=559292;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=8641269;
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.;
"Complete nucleotide sequence of Saccharomyces cerevisiae chromosome
X.";
EMBO J. 15:2031-2049(1996).
[2]
GENOME REANNOTATION, AND SEQUENCE REVISION TO 594; 605 AND 716.
STRAIN=ATCC 204508 / S288c;
PubMed=24374639; DOI=10.1534/g3.113.008995;
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M.,
Cherry J.M.;
"The reference genome sequence of Saccharomyces cerevisiae: Then and
now.";
G3 (Bethesda) 4:389-398(2014).
[3]
INTERACTION WITH RBP1 AND RBP2.
PubMed=12381723; DOI=10.1074/jbc.M209294200;
Li J., Moazed D., Gygi S.P.;
"Association of the histone methyltransferase Set2 with RNA polymerase
II plays a role in transcription elongation.";
J. Biol. Chem. 277:49383-49388(2002).
[4]
FUNCTION, AND MUTAGENESIS OF ARG-195 AND CYS-201.
PubMed=11839797; DOI=10.1128/MCB.22.5.1298-1306.2002;
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.;
"Set2 is a nucleosomal histone H3-selective methyltransferase that
mediates transcriptional repression.";
Mol. Cell. Biol. 22:1298-1306(2002).
[5]
INTERACTION WITH RNA POLYMERASE II, AND FUNCTION.
PubMed=12629047; DOI=10.1101/gad.1055503;
Xiao T., Hall H., Kizer K.O., Shibata Y., Hall M.C., Borchers C.H.,
Strahl B.D.;
"Phosphorylation of RNA polymerase II CTD regulates H3 methylation in
yeast.";
Genes Dev. 17:654-663(2003).
[6]
INTERACTION WITH RNA POLYMERASE II.
PubMed=12511561; DOI=10.1074/jbc.M212134200;
Li B., Howe L., Anderson S., Yates J.R. III, Workman J.L.;
"The Set2 histone methyltransferase functions through the
phosphorylated carboxyl-terminal domain of RNA polymerase II.";
J. Biol. Chem. 278:8897-8903(2003).
[7]
FUNCTION, AND INTERACTION WITH RNA POLYMERASE II.
PubMed=12773564; DOI=10.1128/MCB.23.12.4207-4218.2003;
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.;
"Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is
linked to transcriptional elongation by RNA polymerase II.";
Mol. Cell. Biol. 23:4207-4218(2003).
[8]
FUNCTION, AND DOMAINS.
PubMed=12917322; DOI=10.1128/MCB.23.17.5972-5978.2003;
Landry J., Sutton A., Hesman T., Min J., Xu R.-M., Johnston M.,
Sternglanz R.;
"Set2-catalyzed methylation of histone H3 represses basal expression
of GAL4 in Saccharomyces cerevisiae.";
Mol. Cell. Biol. 23:5972-5978(2003).
[9]
FUNCTION, AND INTERACTION WITH RNA POLYMERASE II.
PubMed=12736296; DOI=10.1093/nar/gkg372;
Schaft D., Roguev A., Kotovic K.M., Shevchenko A., Sarov M.,
Shevchenko A., Neugebauer K.M., Stewart A.F.;
"The histone 3 lysine 36 methyltransferase, SET2, is involved in
transcriptional elongation.";
Nucleic Acids Res. 31:2475-2482(2003).
[10]
LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
PubMed=14562106; DOI=10.1038/nature02046;
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A.,
Dephoure N., O'Shea E.K., Weissman J.S.;
"Global analysis of protein expression in yeast.";
Nature 425:737-741(2003).
[11]
FUNCTION, DOMAIN, AND INTERACTION WITH RNA POLYMERASE II CTD.
PubMed=15798214; DOI=10.1128/MCB.25.8.3305-3316.2005;
Kizer K.O., Phatnani H.P., Shibata Y., Hall H., Greenleaf A.L.,
Strahl B.D.;
"A novel domain in Set2 mediates RNA polymerase II interaction and
couples histone H3 K36 methylation with transcript elongation.";
Mol. Cell. Biol. 25:3305-3316(2005).
[12]
FUNCTION.
PubMed=16227595; DOI=10.1128/MCB.25.21.9447-9459.2005;
Rao B., Shibata Y., Strahl B.D., Lieb J.D.;
"Dimethylation of histone H3 at lysine 36 demarcates regulatory and
nonregulatory chromatin genome-wide.";
Mol. Cell. Biol. 25:9447-9459(2005).
[13]
INTERACTION WITH CYC8.
PubMed=16329992; DOI=10.1016/j.bbrc.2005.11.103;
Tripic T., Edmondson D.G., Davie J.K., Strahl B.D., Dent S.Y.R.;
"The Set2 methyltransferase associates with Ssn6 yet Tup1-Ssn6
repression is independent of histone methylation.";
Biochem. Biophys. Res. Commun. 339:905-914(2006).
[14]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=18407956; DOI=10.1074/mcp.M700468-MCP200;
Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
"A multidimensional chromatography technology for in-depth
phosphoproteome analysis.";
Mol. Cell. Proteomics 7:1389-1396(2008).
[15]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-10 AND SER-522, AND
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=19779198; DOI=10.1126/science.1172867;
Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
"Global analysis of Cdk1 substrate phosphorylation sites provides
insights into evolution.";
Science 325:1682-1686(2009).
[16]
STRUCTURE BY NMR OF 7-33.
PubMed=10802733; DOI=10.1038/75144;
Macias M.J., Gervais V., Civera C., Oschkinat H.;
"Structural analysis of WW domains and design of a WW prototype.";
Nat. Struct. Biol. 7:375-379(2000).
[17]
STRUCTURE BY NMR OF 619-718.
PubMed=16286474; DOI=10.1074/jbc.C500423200;
Vojnic E., Simon B., Strahl B.D., Sattler M., Cramer P.;
"Structure and carboxyl-terminal domain (CTD) binding of the Set2 SRI
domain that couples histone H3 Lys36 methylation to transcription.";
J. Biol. Chem. 281:13-15(2006).
-!- 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.
{ECO:0000269|PubMed:11839797, ECO:0000269|PubMed:12629047,
ECO:0000269|PubMed:12736296, ECO:0000269|PubMed:12773564,
ECO:0000269|PubMed:12917322, ECO:0000269|PubMed:15798214,
ECO:0000269|PubMed:16227595}.
-!- CATALYTIC ACTIVITY: S-adenosyl-L-methionine + L-lysine-[histone] =
S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone].
{ECO:0000255|PROSITE-ProRule:PRU00901}.
-!- SUBUNIT: Interacts with the RNA polymerase II hyperphosphorylated
CTD. Interacts with CYC8. {ECO:0000269|PubMed:12381723,
ECO:0000269|PubMed:12511561, ECO:0000269|PubMed:12629047,
ECO:0000269|PubMed:12736296, ECO:0000269|PubMed:12773564,
ECO:0000269|PubMed:15798214, ECO:0000269|PubMed:16329992}.
-!- INTERACTION:
P61830:HHT2; NbExp=2; IntAct=EBI-16985, EBI-8098;
-!- SUBCELLULAR LOCATION: Nucleus. Chromosome {ECO:0000305}.
-!- DOMAIN: The AWS and SET domains are necessary for transcription
repression. {ECO:0000269|PubMed:12917322,
ECO:0000269|PubMed:15798214}.
-!- MISCELLANEOUS: Present with 217 molecules/cell in log phase SD
medium. {ECO:0000269|PubMed:14562106}.
-!- SIMILARITY: Belongs to the class V-like SAM-binding
methyltransferase superfamily. Histone-lysine methyltransferase
family. SET2 subfamily. {ECO:0000255|PROSITE-ProRule:PRU00901}.
-----------------------------------------------------------------------
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EMBL; Z49444; CAA89464.1; -; Genomic_DNA.
EMBL; BK006943; DAA08635.2; -; Genomic_DNA.
PIR; S56951; S56951.
RefSeq; NP_012367.2; NM_001181601.2.
PDB; 1E0N; NMR; -; A=479-505.
PDB; 2C5Z; NMR; -; A=620-719.
PDBsum; 1E0N; -.
PDBsum; 2C5Z; -.
ProteinModelPortal; P46995; -.
SMR; P46995; -.
BioGrid; 33591; 561.
DIP; DIP-2150N; -.
IntAct; P46995; 62.
MINT; MINT-500810; -.
STRING; 4932.YJL168C; -.
iPTMnet; P46995; -.
MaxQB; P46995; -.
PRIDE; P46995; -.
EnsemblFungi; YJL168C; YJL168C; YJL168C.
GeneID; 853271; -.
KEGG; sce:YJL168C; -.
EuPathDB; FungiDB:YJL168C; -.
SGD; S000003704; SET2.
GeneTree; ENSGT00780000121845; -.
HOGENOM; HOG000248214; -.
InParanoid; P46995; -.
KO; K11423; -.
OMA; YVDKWVV; -.
OrthoDB; EOG092C3T9B; -.
BioCyc; YEAST:G3O-31606-MONOMER; -.
Reactome; R-SCE-2559582; Senescence-Associated Secretory Phenotype (SASP).
Reactome; R-SCE-3214841; PKMTs methylate histone lysines.
Reactome; R-SCE-427359; SIRT1 negatively regulates rRNA expression.
Reactome; R-SCE-5693565; Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks.
EvolutionaryTrace; P46995; -.
PRO; PR:P46995; -.
Proteomes; UP000002311; Chromosome X.
GO; GO:0005694; C:chromosome; IEA:UniProtKB-SubCell.
GO; GO:0005829; C:cytosol; IDA:SGD.
GO; GO:0005634; C:nucleus; IDA:SGD.
GO; GO:0042054; F:histone methyltransferase activity; ISS:SGD.
GO; GO:0046975; F:histone methyltransferase activity (H3-K36 specific); IDA:SGD.
GO; GO:0030437; P:ascospore formation; IMP:SGD.
GO; GO:0006354; P:DNA-templated transcription, elongation; IDA:SGD.
GO; GO:0006353; P:DNA-templated transcription, termination; IMP:SGD.
GO; GO:0016575; P:histone deacetylation; IMP:SGD.
GO; GO:0016571; P:histone methylation; IDA:SGD.
GO; GO:0060195; P:negative regulation of antisense RNA transcription; IMP:SGD.
GO; GO:0071441; P:negative regulation of histone H3-K14 acetylation; IMP:SGD.
GO; GO:2000616; P:negative regulation of histone H3-K9 acetylation; IMP:SGD.
GO; GO:0045128; P:negative regulation of reciprocal meiotic recombination; IMP:SGD.
GO; GO:0035066; P:positive regulation of histone acetylation; IGI:SGD.
GO; GO:0030174; P:regulation of DNA-dependent DNA replication initiation; IMP:SGD.
GO; GO:1900049; P:regulation of histone exchange; IMP:SGD.
GO; GO:0006355; P:regulation of transcription, DNA-templated; IDA:SGD.
InterPro; IPR006560; AWS_dom.
InterPro; IPR025788; Hist-Lys_N-MeTrfase_SET2_fun.
InterPro; IPR003616; Post-SET_dom.
InterPro; IPR001214; SET_dom.
InterPro; IPR013257; SRI.
InterPro; IPR001202; WW_dom.
InterPro; IPR036020; WW_dom_sf.
Pfam; PF00856; SET; 1.
Pfam; PF08236; SRI; 1.
SMART; SM00570; AWS; 1.
SMART; SM00508; PostSET; 1.
SMART; SM00317; SET; 1.
SMART; SM00456; WW; 1.
SUPFAM; SSF51045; SSF51045; 1.
PROSITE; PS51215; AWS; 1.
PROSITE; PS50868; POST_SET; 1.
PROSITE; PS51568; SAM_MT43_SET2_1; 1.
PROSITE; PS50280; SET; 1.
1: Evidence at protein level;
3D-structure; Chromosome; Coiled coil; Complete proteome;
Methyltransferase; Nucleus; Phosphoprotein; Reference proteome;
Repressor; S-adenosyl-L-methionine; Transcription;
Transcription regulation; Transferase.
CHAIN 1 733 Histone-lysine N-methyltransferase, H3
lysine-36 specific.
/FTId=PRO_0000186087.
DOMAIN 63 118 AWS. {ECO:0000255|PROSITE-
ProRule:PRU00562}.
DOMAIN 120 237 SET. {ECO:0000255|PROSITE-
ProRule:PRU00190}.
DOMAIN 244 260 Post-SET. {ECO:0000255|PROSITE-
ProRule:PRU00155}.
DOMAIN 475 507 WW.
REGION 619 718 Binding to RNA polymerase II CTD.
COILED 548 630 {ECO:0000255}.
MOD_RES 10 10 Phosphoserine.
{ECO:0000244|PubMed:19779198}.
MOD_RES 522 522 Phosphoserine.
{ECO:0000244|PubMed:19779198}.
MUTAGEN 195 195 R->G: Reduces dramatically histone
methyltransferase activity toward
nucleosomes.
{ECO:0000269|PubMed:11839797}.
MUTAGEN 201 201 C->A: Reduces dramatically histone
methyltransferase activity toward
nucleosomes.
{ECO:0000269|PubMed:11839797}.
CONFLICT 594 594 A -> F (in Ref. 1; CAA89464).
{ECO:0000305}.
CONFLICT 605 605 A -> S (in Ref. 1; CAA89464).
{ECO:0000305}.
CONFLICT 716 716 A -> G (in Ref. 1; CAA89464).
{ECO:0000305}.
STRAND 481 494 {ECO:0000244|PDB:1E0N}.
TURN 495 498 {ECO:0000244|PDB:1E0N}.
STRAND 499 503 {ECO:0000244|PDB:1E0N}.
HELIX 624 645 {ECO:0000244|PDB:2C5Z}.
TURN 648 652 {ECO:0000244|PDB:2C5Z}.
HELIX 655 676 {ECO:0000244|PDB:2C5Z}.
HELIX 688 712 {ECO:0000244|PDB:2C5Z}.
SEQUENCE 733 AA; 84461 MW; 05436B181E88EFF5 CRC64;
MSKNQSVSAS EDEKEILNNN AEGHKPQRLF DQEPDLTEEA LTKFENLDDC IYANKRIGTF
KNNDFMECDC YEEFSDGVNH ACDEDSDCIN RLTLIECVND LCSSCGNDCQ NQRFQKKQYA
PIAIFKTKHK GYGVRAEQDI EANQFIYEYK GEVIEEMEFR DRLIDYDQRH FKHFYFMMLQ
NGEFIDATIK GSLARFCNHS CSPNAYVNKW VVKDKLRMGI FAQRKILKGE EITFDYNVDR
YGAQAQKCYC EEPNCIGFLG GKTQTDAASL LPQNIADALG VTVSMEKKWL KLKKLSGEPI
IKNENENINI EFLQSLEVQP IDSPVDVTKI MSVLLQQDNK IIASKLLKRL FTIDDDSLRH
QAIKLHGYTC FSKMLKLFIT EQPQVDGKGN ETEEDDIKFI KGILDFLLEL PKTTRNGIES
SQIDNVVKTL PAKFPFLKPN CDELLEKWSK FETYKRITKK DINVAASKMI DLRRVRLPPG
WEIIHENGRP LYYNAEQKTK LHYPPSGSSK VFSSRSNTQV NSPSSSGIPK TPGALDSKKH
KLSDEEYERK KQKRLEYERI ALERAKQEEL ESLKQKLKLE NERKSVLEDI IAEANKQKEL
QKEEAKKLVE AKEAKRLKRK TVSQSQRLEH NWNKFFASFV PNLIKKNPQS KQFDHENIKQ
CAKDIVKILT TKELKKDSSR APPDDLTKGK RHKVKEFINS YMDKIILKKK QKKALALSSA
STRMSSPPPS TSS


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