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Histone-lysine N-methyltransferase, H3 lysine-4 specific (EC 2.1.1.43) (COMPASS component SET1) (Lysine N-methyltransferase 2) (SET domain-containing protein 1)

 SET1_YEAST              Reviewed;        1080 AA.
P38827; D3DL69;
01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
01-FEB-1995, sequence version 1.
12-SEP-2018, entry version 171.
RecName: Full=Histone-lysine N-methyltransferase, H3 lysine-4 specific;
EC=2.1.1.43;
AltName: Full=COMPASS component SET1;
AltName: Full=Lysine N-methyltransferase 2;
AltName: Full=SET domain-containing protein 1;
Name=SET1; Synonyms=KMT2, YTX1; OrderedLocusNames=YHR119W;
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=8091229; DOI=10.1126/science.8091229;
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., Louis E.J., Macri C., Mardis E., Menezes S., Mouser L.,
Nhan M., Rifkin L., Riles L., St Peter H., Trevaskis E., Vaughan K.,
Vignati D., Wilcox L., Wohldman P., Waterston R., Wilson R.,
Vaudin M.;
"Complete nucleotide sequence of Saccharomyces cerevisiae chromosome
VIII.";
Science 265:2077-2082(1994).
[2]
GENOME REANNOTATION.
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]
FUNCTION.
PubMed=9398665; DOI=10.1091/mbc.8.12.2421;
Nislow C., Ray E., Pillus L.;
"SET1, a yeast member of the Trithorax family, functions in
transcriptional silencing and diverse cellular processes.";
Mol. Biol. Cell 8:2421-2436(1997).
[4]
FUNCTION, AND INTERACTION WITH MEC3.
PubMed=9988274; DOI=10.1038/5991;
Corda Y., Schramke V., Longhese M.P., Smokvina T., Paciotti V.,
Brevet V., Gilson E., Geli V.;
"Interaction between Set1p and checkpoint protein Mec3p in DNA repair
and telomere functions.";
Nat. Genet. 21:204-208(1999).
[5]
IDENTIFICATION IN THE SET1 COMPLEX, AND FUNCTION OF THE SET1 COMPLEX.
PubMed=11742990; DOI=10.1093/emboj/20.24.7137;
Roguev A., Schaft D., Shevchenko A., Pijnappel W.W.M.P., Wilm M.,
Aasland R., Stewart A.F.;
"The Saccharomyces cerevisiae Set1 complex includes an Ash2 homologue
and methylates histone 3 lysine 4.";
EMBO J. 20:7137-7148(2001).
[6]
FUNCTION.
PubMed=11751634; DOI=10.1101/gad.940201;
Briggs S.D., Bryk M., Strahl B.D., Cheung W.L., Davie J.K.,
Dent S.Y.R., Winston F., Allis C.D.;
"Histone H3 lysine 4 methylation is mediated by Set1 and required for
cell growth and rDNA silencing in Saccharomyces cerevisiae.";
Genes Dev. 15:3286-3295(2001).
[7]
SUBUNIT.
PubMed=11687631; DOI=10.1073/pnas.231473398;
Miller T., Krogan N.J., Dover J., Erdjument-Bromage H., Tempst P.,
Johnston M., Greenblatt J.F., Shilatifard A.;
"COMPASS: a complex of proteins associated with a trithorax-related
SET domain protein.";
Proc. Natl. Acad. Sci. U.S.A. 98:12902-12907(2001).
[8]
FUNCTION.
PubMed=11818070; DOI=10.1016/S0960-9822(01)00652-2;
Bryk M., Briggs S.D., Strahl B.D., Curcio M.J., Allis C.D.,
Winston F.;
"Evidence that Set1, a factor required for methylation of histone H3,
regulates rDNA silencing in S. cerevisiae by a Sir2-independent
mechanism.";
Curr. Biol. 12:165-170(2002).
[9]
ENZYME ACTIVITY, AND FUNCTION.
PubMed=11805083; DOI=10.1074/jbc.C200023200;
Krogan N.J., Dover J., Khorrami S., Greenblatt J.F., Schneider J.,
Johnston M., Shilatifard A.;
"COMPASS, a histone H3 (Lysine 4) methyltransferase required for
telomeric silencing of gene expression.";
J. Biol. Chem. 277:10753-10755(2002).
[10]
FUNCTION.
PubMed=12353038; DOI=10.1038/nature01080;
Santos-Rosa H., Schneider R., Bannister A.J., Sherriff J.,
Bernstein B.E., Emre N.C.T., Schreiber S.L., Mellor J., Kouzarides T.;
"Active genes are tri-methylated at K4 of histone H3.";
Nature 419:407-411(2002).
[11]
IDENTIFICATION IN THE SET1 COMPLEX, AND FUNCTION OF THE SET1 COMPLEX.
PubMed=11752412; DOI=10.1073/pnas.221596698;
Nagy P.L., Griesenbeck J., Kornberg R.D., Cleary M.L.;
"A trithorax-group complex purified from Saccharomyces cerevisiae is
required for methylation of histone H3.";
Proc. Natl. Acad. Sci. U.S.A. 99:90-94(2002).
[12]
FUNCTION.
PubMed=12060701; DOI=10.1073/pnas.082249499;
Bernstein B.E., Humphrey E.L., Erlich R.L., Schneider R., Bouman P.,
Liu J.S., Kouzarides T., Schreiber S.L.;
"Methylation of histone H3 Lys 4 in coding regions of active genes.";
Proc. Natl. Acad. Sci. U.S.A. 99:8695-8700(2002).
[13]
FUNCTION.
PubMed=14636589; DOI=10.1016/S1097-2765(03)00438-6;
Santos-Rosa H., Schneider R., Bernstein B.E., Karabetsou N.,
Morillon A., Weise C., Schreiber S.L., Mellor J., Kouzarides T.;
"Methylation of histone H3 K4 mediates association of the Isw1p ATPase
with chromatin.";
Mol. Cell 12:1325-1332(2003).
[14]
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).
[15]
FUNCTION.
PubMed=12845608; DOI=10.1002/yea.995;
Boa S., Coert C., Patterton H.-G.;
"Saccharomyces cerevisiae Set1p is a methyltransferase specific for
lysine 4 of histone H3 and is required for efficient gene
expression.";
Yeast 20:827-835(2003).
[16]
FUNCTION OF THE COMPASS COMPLEX.
PubMed=15949446; DOI=10.1016/j.molcel.2005.05.009;
Morillon A., Karabetsou N., Nair A., Mellor J.;
"Dynamic lysine methylation on histone H3 defines the regulatory phase
of gene transcription.";
Mol. Cell 18:723-734(2005).
[17]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-625, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
STRAIN=ADR376;
PubMed=17330950; DOI=10.1021/pr060559j;
Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
Elias J.E., Gygi S.P.;
"Large-scale phosphorylation analysis of alpha-factor-arrested
Saccharomyces cerevisiae.";
J. Proteome Res. 6:1190-1197(2007).
[18]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-625 AND THR-875, 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).
-!- 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.
{ECO:0000269|PubMed:11742990, ECO:0000269|PubMed:11751634,
ECO:0000269|PubMed:11752412, ECO:0000269|PubMed:11805083,
ECO:0000269|PubMed:11818070, ECO:0000269|PubMed:12060701,
ECO:0000269|PubMed:12353038, ECO:0000269|PubMed:12845608,
ECO:0000269|PubMed:14636589, ECO:0000269|PubMed:15949446,
ECO:0000269|PubMed:9398665, ECO:0000269|PubMed:9988274}.
-!- CATALYTIC ACTIVITY: S-adenosyl-L-methionine + L-lysine-[histone] =
S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone].
{ECO:0000269|PubMed:11805083}.
-!- SUBUNIT: Component of the COMPASS (Set1C) complex which consists
of SET1(2), BRE2(2), SPP1(2), SDC1(1), SHG1(1), SWD1(1), SWD2(1),
and SWD3(1). Interacts with MEC3. {ECO:0000269|PubMed:11687631,
ECO:0000269|PubMed:11742990, ECO:0000269|PubMed:11752412,
ECO:0000269|PubMed:9988274}.
-!- INTERACTION:
P43132:BRE2; NbExp=7; IntAct=EBI-16977, EBI-27115;
Q02574:MEC3; NbExp=3; IntAct=EBI-16977, EBI-10658;
P38337:SHG1; NbExp=5; IntAct=EBI-16977, EBI-21106;
P0CS90:SSC1; NbExp=2; IntAct=EBI-16977, EBI-8637;
P36104:SWD2; NbExp=6; IntAct=EBI-16977, EBI-26608;
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305}. Chromosome
{ECO:0000305}.
-!- MISCELLANEOUS: Present with 172 molecules/cell in log phase SD
medium. {ECO:0000269|PubMed:14562106}.
-!- SIMILARITY: Belongs to the class V-like SAM-binding
methyltransferase superfamily. {ECO:0000255|PROSITE-
ProRule:PRU00190}.
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EMBL; U00059; AAB68867.1; -; Genomic_DNA.
EMBL; BK006934; DAA06813.1; -; Genomic_DNA.
PIR; S48961; S48961.
RefSeq; NP_011987.1; NM_001179249.1.
PDB; 2J8A; X-ray; 3.00 A; A=247-375.
PDBsum; 2J8A; -.
ProteinModelPortal; P38827; -.
SMR; P38827; -.
BioGrid; 36552; 450.
ComplexPortal; CPX-1039; COMPASS complex.
DIP; DIP-4616N; -.
ELM; P38827; -.
IntAct; P38827; 36.
MINT; P38827; -.
STRING; 4932.YHR119W; -.
iPTMnet; P38827; -.
MaxQB; P38827; -.
PaxDb; P38827; -.
PRIDE; P38827; -.
EnsemblFungi; YHR119W; YHR119W; YHR119W.
GeneID; 856519; -.
KEGG; sce:YHR119W; -.
EuPathDB; FungiDB:YHR119W; -.
SGD; S000001161; SET1.
GeneTree; ENSGT00760000119228; -.
HOGENOM; HOG000066111; -.
InParanoid; P38827; -.
KO; K11422; -.
OMA; PSCTAKI; -.
OrthoDB; EOG092C3T9B; -.
BioCyc; YEAST:G3O-31161-MONOMER; -.
Reactome; R-SCE-3214841; PKMTs methylate histone lysines.
EvolutionaryTrace; P38827; -.
PRO; PR:P38827; -.
Proteomes; UP000002311; Chromosome VIII.
GO; GO:0000781; C:chromosome, telomeric region; IEA:GOC.
GO; GO:0048188; C:Set1C/COMPASS complex; IPI:SGD.
GO; GO:0042054; F:histone methyltransferase activity; ISS:SGD.
GO; GO:0018024; F:histone-lysine N-methyltransferase activity; IEA:UniProtKB-EC.
GO; GO:0016279; F:protein-lysine N-methyltransferase activity; IMP:SGD.
GO; GO:0003723; F:RNA binding; IDA:SGD.
GO; GO:0030437; P:ascospore formation; IMP:SGD.
GO; GO:0030466; P:chromatin silencing at silent mating-type cassette; IMP:SGD.
GO; GO:0006348; P:chromatin silencing at telomere; IMP:SGD.
GO; GO:0044648; P:histone H3-K4 dimethylation; IMP:CACAO.
GO; GO:0051568; P:histone H3-K4 methylation; IDA:SGD.
GO; GO:0080182; P:histone H3-K4 trimethylation; IMP:CACAO.
GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; IMP:SGD.
GO; GO:0018027; P:peptidyl-lysine dimethylation; IMP:SGD.
GO; GO:0035066; P:positive regulation of histone acetylation; IGI:SGD.
GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; IMP:SGD.
GO; GO:1902275; P:regulation of chromatin organization; IMP:SGD.
GO; GO:1903341; P:regulation of meiotic DNA double-strand break formation; IMP:SGD.
GO; GO:0043618; P:regulation of transcription from RNA polymerase II promoter in response to stress; IMP:SGD.
GO; GO:0000723; P:telomere maintenance; IMP:SGD.
Gene3D; 3.30.70.330; -; 1.
InterPro; IPR024657; COMPASS_Set1_N-SET.
InterPro; IPR012677; Nucleotide-bd_a/b_plait_sf.
InterPro; IPR003616; Post-SET_dom.
InterPro; IPR017111; Set1.
InterPro; IPR024636; SET_assoc.
InterPro; IPR001214; SET_dom.
PANTHER; PTHR22884:SF462; PTHR22884:SF462; 1.
Pfam; PF11764; N-SET; 1.
Pfam; PF00856; SET; 1.
Pfam; PF11767; SET_assoc; 1.
PIRSF; PIRSF037104; Histone_H3-K4_mtfrase_Set1_fun; 1.
SMART; SM01291; N-SET; 1.
SMART; SM00508; PostSET; 1.
SMART; SM00317; SET; 1.
PROSITE; PS50868; POST_SET; 1.
PROSITE; PS51572; SAM_MT43_1; 1.
PROSITE; PS50280; SET; 1.
1: Evidence at protein level;
3D-structure; Chromatin regulator; Chromosome; Complete proteome;
Methyltransferase; Nucleus; Phosphoprotein; Reference proteome;
S-adenosyl-L-methionine; Transferase.
CHAIN 1 1080 Histone-lysine N-methyltransferase, H3
lysine-4 specific.
/FTId=PRO_0000186086.
DOMAIN 938 1055 SET. {ECO:0000255|PROSITE-
ProRule:PRU00190}.
DOMAIN 1064 1080 Post-SET. {ECO:0000255|PROSITE-
ProRule:PRU00155}.
MOD_RES 625 625 Phosphoserine.
{ECO:0000244|PubMed:17330950,
ECO:0000244|PubMed:19779198}.
MOD_RES 875 875 Phosphothreonine.
{ECO:0000244|PubMed:19779198}.
STRAND 249 258 {ECO:0000244|PDB:2J8A}.
HELIX 265 273 {ECO:0000244|PDB:2J8A}.
STRAND 279 285 {ECO:0000244|PDB:2J8A}.
TURN 287 289 {ECO:0000244|PDB:2J8A}.
STRAND 292 299 {ECO:0000244|PDB:2J8A}.
HELIX 310 320 {ECO:0000244|PDB:2J8A}.
TURN 321 324 {ECO:0000244|PDB:2J8A}.
STRAND 326 328 {ECO:0000244|PDB:2J8A}.
STRAND 331 337 {ECO:0000244|PDB:2J8A}.
HELIX 342 364 {ECO:0000244|PDB:2J8A}.
SEQUENCE 1080 AA; 123912 MW; B7FA5D60F71063FD CRC64;
MSNYYRRAHA SSGSYRQPQE QPQYSRSGHY QYSNGHSHQQ YSSQYNQRRR YNHNDGTRRR
YNDDRPHSSN NASTRQYYAT NNSQSGPYVN KKSDISSRRG MSQSRYSNSN VHNTLASSSG
SLPTESALLL QQRPPSVLRY NTDNLKSKFH YFDPIKGEFF NKDKMLSWKA TDKEFSETGY
YVVKELQDGQ FKFKIKHRHP EIKASDPRNE NGIMTSGKVA THRKCRNSLI LLPRISYDRY
SLGPPPSCEI VVYPAQDSTT TNIQDISIKN YFKKYGEISH FEAFNDPNSA LPLHVYLIKY
ASSDGKINDA AKAAFSAVRK HESSGCFIMG FKFEVILNKH SILNNIISKF VEINVKKLQK
LQENLKKAKE KEAENEKAKE LQGKDITLPK EPKVDTLSHS SGSEKRIPYD LLGVVNNRPV
LHVSKIFVAK HRFCVEDFKY KLRGYRCAKF IDHPTGIYII FNDIAHAQTC SNAESGNLTI
MSRSRRIPIL IKFHLILPRF QNRTRFNKSS SSSNSTNVPI KYESKEEFIE ATAKQILKDL
EKTLHVDIKK RLIGPTVFDA LDHANFPELL AKRELKEKEK RQQIASKIAE DELKRKEEAK
RDFDLFGLYG GYAKSNKRNL KRHNSLALDH TSLKRKKLSN GIKPMAHLLN EETDSKETTP
LNDEGITRVS KEHDEEDENM TSSSSEEEEE EAPDKKFKSE SEPTTPESDH LHGIKPLVPD
QNGSSDVLDA SSMYKPTATE IPEPVYPPEE YDLKYSQTLS SMDLQNAIKD EEDMLILKQL
LSTYTPTVTP ETSAALEYKI WQSRRKVLEE EKASDWQIEL NGTLFDSELQ PGSSFKAEGF
RKIADKLKIN YLPHRRRVHQ PLNTVNIHNE RNEYTPELCQ REESSNKEPS DSVPQEVSSS
RDNRASNRRF QQDIEAQKAA IGTESELLSL NQLNKRKKPV MFARSAIHNW GLYALDSIAA
KEMIIEYVGE RIRQPVAEMR EKRYLKNGIG SSYLFRVDEN TVIDATKKGG IARFINHCCD
PNCTAKIIKV GGRRRIVIYA LRDIAASEEL TYDYKFEREK DDEERLPCLC GAPNCKGFLN


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