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Histone-lysine N-methyltransferase, H3 lysine-9 specific (EC 2.1.1.43) (Cryptic loci regulator 4) (Histone H3-K9 methyltransferase) (H3-K9-HMTase) (Lysine N-methyltransferase 1)

 CLR4_SCHPO              Reviewed;         490 AA.
O60016; O74565;
08-DEC-2000, integrated into UniProtKB/Swiss-Prot.
08-DEC-2000, sequence version 2.
22-NOV-2017, entry version 169.
RecName: Full=Histone-lysine N-methyltransferase, H3 lysine-9 specific;
EC=2.1.1.43;
AltName: Full=Cryptic loci regulator 4;
AltName: Full=Histone H3-K9 methyltransferase;
Short=H3-K9-HMTase;
AltName: Full=Lysine N-methyltransferase 1;
Name=clr4; Synonyms=kmt1; ORFNames=SPBC428.08c;
Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast).
Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina;
Schizosaccharomycetes; Schizosaccharomycetales;
Schizosaccharomycetaceae; Schizosaccharomyces.
NCBI_TaxID=284812;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
PubMed=9620780; DOI=10.1038/566;
Ivanova A.V., Bonaduce M.J., Ivanov S.V., Klar A.J.S.;
"The chromo and SET domains of the Clr4 protein are essential for
silencing in fission yeast.";
Nat. Genet. 19:192-195(1998).
[2]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=SP813;
Lord P.;
Thesis (1998), University of Edinburgh, United Kingdom.
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=972 / ATCC 24843;
PubMed=11859360; DOI=10.1038/nature724;
Wood V., Gwilliam R., Rajandream M.A., Lyne M.H., Lyne R., Stewart A.,
Sgouros J.G., Peat N., Hayles J., Baker S.G., Basham D., Bowman S.,
Brooks K., Brown D., Brown S., Chillingworth T., Churcher C.M.,
Collins M., Connor R., Cronin A., Davis P., Feltwell T., Fraser A.,
Gentles S., Goble A., Hamlin N., Harris D.E., Hidalgo J., Hodgson G.,
Holroyd S., Hornsby T., Howarth S., Huckle E.J., Hunt S., Jagels K.,
James K.D., Jones L., Jones M., Leather S., McDonald S., McLean J.,
Mooney P., Moule S., Mungall K.L., Murphy L.D., Niblett D., Odell C.,
Oliver K., O'Neil S., Pearson D., Quail M.A., Rabbinowitsch E.,
Rutherford K.M., Rutter S., Saunders D., Seeger K., Sharp S.,
Skelton J., Simmonds M.N., Squares R., Squares S., Stevens K.,
Taylor K., Taylor R.G., Tivey A., Walsh S.V., Warren T., Whitehead S.,
Woodward J.R., Volckaert G., Aert R., Robben J., Grymonprez B.,
Weltjens I., Vanstreels E., Rieger M., Schaefer M., Mueller-Auer S.,
Gabel C., Fuchs M., Duesterhoeft A., Fritzc C., Holzer E., Moestl D.,
Hilbert H., Borzym K., Langer I., Beck A., Lehrach H., Reinhardt R.,
Pohl T.M., Eger P., Zimmermann W., Wedler H., Wambutt R., Purnelle B.,
Goffeau A., Cadieu E., Dreano S., Gloux S., Lelaure V., Mottier S.,
Galibert F., Aves S.J., Xiang Z., Hunt C., Moore K., Hurst S.M.,
Lucas M., Rochet M., Gaillardin C., Tallada V.A., Garzon A., Thode G.,
Daga R.R., Cruzado L., Jimenez J., Sanchez M., del Rey F., Benito J.,
Dominguez A., Revuelta J.L., Moreno S., Armstrong J., Forsburg S.L.,
Cerutti L., Lowe T., McCombie W.R., Paulsen I., Potashkin J.,
Shpakovski G.V., Ussery D., Barrell B.G., Nurse P.;
"The genome sequence of Schizosaccharomyces pombe.";
Nature 415:871-880(2002).
[4]
PARTIAL PROTEIN SEQUENCE, IDENTIFICATION IN THE RIK1-ASSOCIATED E3
UBIQUITIN LIGASE COMPLEX, AND FUNCTION.
PubMed=16024659; DOI=10.1101/gad.1328005;
Horn P.J., Bastie J.-N., Peterson C.L.;
"A Rik1-associated, cullin-dependent E3 ubiquitin ligase is essential
for heterochromatin formation.";
Genes Dev. 19:1705-1714(2005).
[5]
PROTEIN SEQUENCE OF 64-85; 127-150; 190-205; 371-406; 429-455 AND
486-490, AND INTERACTION WITH CUL4.
PubMed=16127433; DOI=10.1038/ncb1300;
Jia S., Kobayashi R., Grewal S.I.S.;
"Ubiquitin ligase component Cul4 associates with Clr4 histone
methyltransferase to assemble heterochromatin.";
Nat. Cell Biol. 7:1007-1013(2005).
[6]
FUNCTION.
PubMed=8138176;
Ekwall K., Ruusala T.;
"Mutations in rik1, clr2, clr3 and clr4 genes asymmetrically derepress
the silent mating-type loci in fission yeast.";
Genetics 136:53-64(1994).
[7]
ENZYME ACTIVITY, AND MUTAGENESIS OF TRP-31; TRP-41; ARG-320; GLY-378
AND GLY-486.
PubMed=11283354; DOI=10.1126/science.1060118;
Nakayama J., Rice J.C., Strahl B.D., Allis C.D., Grewal S.I.S.;
"Role of histone H3 lysine 9 methylation in epigenetic control of
heterochromatin assembly.";
Science 292:110-113(2001).
[8]
SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
PubMed=16823372; DOI=10.1038/nbt1222;
Matsuyama A., Arai R., Yashiroda Y., Shirai A., Kamata A., Sekido S.,
Kobayashi Y., Hashimoto A., Hamamoto M., Hiraoka Y., Horinouchi S.,
Yoshida M.;
"ORFeome cloning and global analysis of protein localization in the
fission yeast Schizosaccharomyces pombe.";
Nat. Biotechnol. 24:841-847(2006).
[9]
STRUCTURE BY NMR OF 2-69.
PubMed=11273706; DOI=10.1006/jmbi.2001.4515;
Horita D.A., Ivanova A.V., Altieri A.S., Klar A.J., Byrd R.A.;
"Solution structure, domain features, and structural implications of
mutants of the chromo domain from the fission yeast histone
methyltransferase Clr4.";
J. Mol. Biol. 307:861-870(2001).
[10]
X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 192-490 IN COMPLEX WITH ZINC
IONS.
PubMed=12389037; DOI=10.1038/nsb860;
Min J., Zhang X., Cheng X., Grewal S.I.S., Xu R.M.;
"Structure of the SET domain histone lysine methyltransferase Clr4.";
Nat. Struct. Biol. 9:828-832(2002).
-!- FUNCTION: Histone methyltransferase. Catalytic component of the
rik1-associated E3 ubiquitin ligase complex that shows ubiquitin
ligase activity and is required for histone H3K9 methylation.
H3K9me represents a specific tag for epigenetic transcriptional
repression by recruiting swi6/HP1 to methylated histones which
leads to transcriptional silencing within centromeric
heterochromatin, telomeric regions and at the silent mating-type
loci. {ECO:0000269|PubMed:16024659, ECO:0000269|PubMed:8138176}.
-!- CATALYTIC ACTIVITY: S-adenosyl-L-methionine + L-lysine-[histone] =
S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone].
{ECO:0000269|PubMed:11283354}.
-!- SUBUNIT: Component of the rik1-associated E3 ubiquitin ligase
complex composed of at least clr4, cul4, pip1, raf1 and raf2.
Interacts directly with cul4. {ECO:0000269|PubMed:12389037,
ECO:0000269|PubMed:16024659, ECO:0000269|PubMed:16127433}.
-!- INTERACTION:
O14122:cul4; NbExp=3; IntAct=EBI-354657, EBI-904890;
Q10426:rik1; NbExp=3; IntAct=EBI-354657, EBI-1111936;
O94276:SPBP8B7.28c; NbExp=2; IntAct=EBI-354657, EBI-2651917;
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:16823372}.
Cytoplasm, cytoskeleton, microtubule organizing center, spindle
pole body {ECO:0000269|PubMed:16823372}. Chromosome
{ECO:0000305|PubMed:16823372}.
-!- DOMAIN: In the pre-SET domain, Cys residues bind 3 zinc ions that
are arranged in a triangular cluster; some of these Cys residues
contribute to the binding of two zinc ions within the cluster.
-!- SIMILARITY: Belongs to the class V-like SAM-binding
methyltransferase superfamily. Histone-lysine methyltransferase
family. Suvar3-9 subfamily. {ECO:0000255|PROSITE-
ProRule:PRU00190}.
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EMBL; AF061854; AAC18302.1; -; Genomic_DNA.
EMBL; AJ007840; CAA07709.1; -; Genomic_DNA.
EMBL; CU329671; CAA22283.1; -; Genomic_DNA.
PIR; T43700; T43700.
PIR; T43745; T43745.
RefSeq; NP_595186.1; NM_001021094.2.
PDB; 1G6Z; NMR; -; A=2-69.
PDB; 1MVH; X-ray; 2.30 A; A=192-490.
PDB; 1MVX; X-ray; 3.00 A; A=192-490.
PDBsum; 1G6Z; -.
PDBsum; 1MVH; -.
PDBsum; 1MVX; -.
ProteinModelPortal; O60016; -.
SMR; O60016; -.
BioGrid; 277343; 298.
DIP; DIP-32588N; -.
IntAct; O60016; 8.
MINT; MINT-195370; -.
STRING; 4896.SPBC428.08c.1; -.
iPTMnet; O60016; -.
MaxQB; O60016; -.
PRIDE; O60016; -.
EnsemblFungi; SPBC428.08c.1; SPBC428.08c.1:pep; SPBC428.08c.
GeneID; 2540825; -.
KEGG; spo:SPBC428.08c; -.
EuPathDB; FungiDB:SPBC428.08c; -.
PomBase; SPBC428.08c; clr4.
InParanoid; O60016; -.
KO; K11419; -.
OrthoDB; EOG092C2EWO; -.
PhylomeDB; O60016; -.
Reactome; R-SPO-427359; SIRT1 negatively regulates rRNA expression.
EvolutionaryTrace; O60016; -.
PRO; PR:O60016; -.
Proteomes; UP000002485; Chromosome II.
GO; GO:0034507; C:chromosome, centromeric outer repeat region; IEA:GOC.
GO; GO:0000781; C:chromosome, telomeric region; IEA:GOC.
GO; GO:0043494; C:CLRC ubiquitin ligase complex; IDA:PomBase.
GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-KW.
GO; GO:0031934; C:mating-type region heterochromatin; NAS:PomBase.
GO; GO:0031618; C:nuclear pericentric heterochromatin; TAS:PomBase.
GO; GO:1990707; C:nuclear subtelomeric heterochromatin; NAS:PomBase.
GO; GO:0005634; C:nucleus; IDA:PomBase.
GO; GO:0005816; C:spindle pole body; IEA:UniProtKB-SubCell.
GO; GO:0003690; F:double-stranded DNA binding; IDA:PomBase.
GO; GO:0046974; F:histone methyltransferase activity (H3-K9 specific); IDA:UniProtKB.
GO; GO:0035064; F:methylated histone binding; IDA:PomBase.
GO; GO:0008168; F:methyltransferase activity; IDA:UniProtKB.
GO; GO:0003697; F:single-stranded DNA binding; IDA:PomBase.
GO; GO:0003727; F:single-stranded RNA binding; IDA:PomBase.
GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
GO; GO:0034613; P:cellular protein localization; IMP:PomBase.
GO; GO:0006338; P:chromatin remodeling; NAS:PomBase.
GO; GO:0030702; P:chromatin silencing at centromere; IMP:PomBase.
GO; GO:1990141; P:chromatin silencing at centromere outer repeat region; IMP:PomBase.
GO; GO:0000183; P:chromatin silencing at rDNA; IMP:PomBase.
GO; GO:0030466; P:chromatin silencing at silent mating-type cassette; IMP:PomBase.
GO; GO:0006348; P:chromatin silencing at telomere; TAS:PomBase.
GO; GO:0031048; P:chromatin silencing by small RNA; IMP:PomBase.
GO; GO:0007535; P:donor selection; IMP:PomBase.
GO; GO:1902368; P:heterochromatin maintenance involved in chromatin silencing at centromere outer repeat region; IGI:PomBase.
GO; GO:0045141; P:meiotic telomere clustering; IMP:PomBase.
GO; GO:0000122; P:negative regulation of transcription from RNA polymerase II promoter; IMP:PomBase.
GO; GO:0090065; P:regulation of production of siRNA involved in RNA interference; IMP:PomBase.
CDD; cd00024; CHROMO; 1.
InterPro; IPR016197; Chromo-like_dom_sf.
InterPro; IPR000953; Chromo/chromo_shadow_dom.
InterPro; IPR023780; Chromo_domain.
InterPro; IPR023779; Chromodomain_CS.
InterPro; IPR011381; Histone_H3-K9_MeTrfase.
InterPro; IPR003616; Post-SET_dom.
InterPro; IPR007728; Pre-SET_dom.
InterPro; IPR001214; SET_dom.
Pfam; PF00385; Chromo; 1.
Pfam; PF05033; Pre-SET; 1.
Pfam; PF00856; SET; 1.
PIRSF; PIRSF009343; SUV39_SET; 1.
SMART; SM00298; CHROMO; 1.
SMART; SM00508; PostSET; 1.
SMART; SM00468; PreSET; 1.
SMART; SM00317; SET; 1.
SUPFAM; SSF54160; SSF54160; 1.
PROSITE; PS00598; CHROMO_1; 1.
PROSITE; PS50013; CHROMO_2; 1.
PROSITE; PS50868; POST_SET; 1.
PROSITE; PS50867; PRE_SET; 1.
PROSITE; PS50280; SET; 1.
1: Evidence at protein level;
3D-structure; Chromatin regulator; Chromosome; Complete proteome;
Cytoplasm; Cytoskeleton; Direct protein sequencing; Metal-binding;
Methyltransferase; Nucleus; Reference proteome;
S-adenosyl-L-methionine; Transferase; Zinc.
CHAIN 1 490 Histone-lysine N-methyltransferase, H3
lysine-9 specific.
/FTId=PRO_0000186063.
DOMAIN 8 69 Chromo. {ECO:0000255|PROSITE-
ProRule:PRU00053}.
DOMAIN 258 325 Pre-SET. {ECO:0000255|PROSITE-
ProRule:PRU00157}.
DOMAIN 328 452 SET. {ECO:0000255|PROSITE-
ProRule:PRU00190}.
DOMAIN 473 489 Post-SET. {ECO:0000255|PROSITE-
ProRule:PRU00155}.
REGION 338 340 S-adenosyl-L-methionine binding.
{ECO:0000250}.
REGION 409 410 S-adenosyl-L-methionine binding.
{ECO:0000250}.
METAL 260 260 Zinc 1.
METAL 260 260 Zinc 2.
METAL 262 262 Zinc 1.
METAL 268 268 Zinc 1.
METAL 268 268 Zinc 3.
METAL 276 276 Zinc 1.
METAL 278 278 Zinc 2.
METAL 307 307 Zinc 2.
METAL 307 307 Zinc 3.
METAL 311 311 Zinc 2.
METAL 313 313 Zinc 3.
METAL 317 317 Zinc 3.
METAL 412 412 Zinc 4. {ECO:0000250}.
METAL 477 477 Zinc 4. {ECO:0000250}.
METAL 479 479 Zinc 4. {ECO:0000250}.
METAL 484 484 Zinc 4. {ECO:0000250}.
BINDING 381 381 S-adenosyl-L-methionine.
{ECO:0000255|PROSITE-ProRule:PRU00190}.
BINDING 406 406 S-adenosyl-L-methionine.
{ECO:0000255|PROSITE-ProRule:PRU00190}.
MUTAGEN 31 31 W->G: Weak effect on methyltransferase
activity. {ECO:0000269|PubMed:11283354}.
MUTAGEN 41 41 W->G: Weak effect on methyltransferase
activity. {ECO:0000269|PubMed:11283354}.
MUTAGEN 320 320 R->H: Abolishes methyltransferase
activity. {ECO:0000269|PubMed:11283354}.
MUTAGEN 378 378 G->S: Abolishes methyltransferase
activity. {ECO:0000269|PubMed:11283354}.
MUTAGEN 486 486 G->D: Abolishes methyltransferase
activity. {ECO:0000269|PubMed:11283354}.
CONFLICT 19 19 D -> G (in Ref. 1; AAC18302).
{ECO:0000305}.
CONFLICT 142 142 Missing (in Ref. 4; AA sequence).
{ECO:0000305}.
CONFLICT 437 437 A -> G (in Ref. 1; AAC18302).
{ECO:0000305}.
STRAND 14 17 {ECO:0000244|PDB:1G6Z}.
STRAND 26 29 {ECO:0000244|PDB:1G6Z}.
TURN 32 35 {ECO:0000244|PDB:1G6Z}.
STRAND 40 42 {ECO:0000244|PDB:1G6Z}.
HELIX 44 47 {ECO:0000244|PDB:1G6Z}.
HELIX 51 61 {ECO:0000244|PDB:1G6Z}.
TURN 62 65 {ECO:0000244|PDB:1G6Z}.
HELIX 196 214 {ECO:0000244|PDB:1MVH}.
STRAND 216 219 {ECO:0000244|PDB:1MVH}.
STRAND 221 224 {ECO:0000244|PDB:1MVH}.
STRAND 226 228 {ECO:0000244|PDB:1MVX}.
STRAND 237 239 {ECO:0000244|PDB:1MVH}.
HELIX 254 256 {ECO:0000244|PDB:1MVH}.
STRAND 265 268 {ECO:0000244|PDB:1MVH}.
TURN 273 275 {ECO:0000244|PDB:1MVH}.
STRAND 277 279 {ECO:0000244|PDB:1MVH}.
STRAND 294 296 {ECO:0000244|PDB:1MVH}.
STRAND 302 305 {ECO:0000244|PDB:1MVH}.
STRAND 311 313 {ECO:0000244|PDB:1MVX}.
HELIX 322 324 {ECO:0000244|PDB:1MVH}.
STRAND 330 334 {ECO:0000244|PDB:1MVH}.
STRAND 336 346 {ECO:0000244|PDB:1MVH}.
STRAND 353 356 {ECO:0000244|PDB:1MVH}.
STRAND 360 363 {ECO:0000244|PDB:1MVH}.
HELIX 364 371 {ECO:0000244|PDB:1MVH}.
STRAND 382 385 {ECO:0000244|PDB:1MVH}.
STRAND 390 392 {ECO:0000244|PDB:1MVH}.
STRAND 394 397 {ECO:0000244|PDB:1MVH}.
STRAND 399 402 {ECO:0000244|PDB:1MVH}.
HELIX 404 407 {ECO:0000244|PDB:1MVH}.
STRAND 415 423 {ECO:0000244|PDB:1MVH}.
STRAND 432 439 {ECO:0000244|PDB:1MVH}.
STRAND 455 458 {ECO:0000244|PDB:1MVH}.
SEQUENCE 490 AA; 55918 MW; 53C3EC87BCBA51FF CRC64;
MSPKQEEYEV ERIVDEKLDR NGAVKLYRIR WLNYSSRSDT WEPPENLSGC SAVLAEWKRR
KRRLKGSNSD SDSPHHASNP HPNSRQKHQH QTSKSVPRSQ RFSRELNVKK ENKKVFSSQT
TKRQSRKQST ALTTNDTSII LDDSLHTNSK KLGKTRNEVK EESQKRELVS NSIKEATSPK
TSSILTKPRN PSKLDSYTHL SFYEKRELFR KKLREIEGPE VTLVNEVDDE PCPSLDFQFI
SQYRLTQGVI PPDPNFQSGC NCSSLGGCDL NNPSRCECLD DLDEPTHFAY DAQGRVRADT
GAVIYECNSF CSCSMECPNR VVQRGRTLPL EIFKTKEKGW GVRSLRFAPA GTFITCYLGE
VITSAEAAKR DKNYDDDGIT YLFDLDMFDD ASEYTVDAQN YGDVSRFFNH SCSPNIAIYS
AVRNHGFRTI YDLAFFAIKD IQPLEELTFD YAGAKDFSPV QSQKSQQNRI SKLRRQCKCG
SANCRGWLFG


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GENTAUR France SARL
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Tel 01 43 25 01 50

Fax 01 43 25 01 60
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BNP PARIBAS PARIS PL MAUBERT BIC BNPAFRPPPRG

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GENTAUR GmbH
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Support Karolina Elandt
Tel: 0035929830070
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San Jose, CA 95123
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Tel (408) 780-0908,
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Genprice Inc, Invoices and accounting
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GENTAUR Poland Sp. z o.o.


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