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