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Database: UniProt/SWISS-PROT
Entry: CLF_ORYSJ
LinkDB: CLF_ORYSJ
Original site: CLF_ORYSJ 
ID   CLF_ORYSJ               Reviewed;         896 AA.
AC   Q5VN06;
DT   20-JUN-2018, integrated into UniProtKB/Swiss-Prot.
DT   07-DEC-2004, sequence version 1.
DT   05-DEC-2018, entry version 112.
DE   RecName: Full=Histone-lysine N-methyltransferase CLF {ECO:0000305};
DE            Short=OsCLF {ECO:0000303|PubMed:19825651};
DE            EC=2.1.1.43 {ECO:0000255|PROSITE-ProRule:PRU00909};
DE   AltName: Full=Protein SET DOMAIN GROUP 711 {ECO:0000305};
DE   AltName: Full=SET family protein 24 {ECO:0000305};
DE            Short=OsSET24 {ECO:0000303|PubMed:23762371};
GN   Name=CLF {ECO:0000303|PubMed:19825651};
GN   Synonyms=SDG711 {ECO:0000303|PubMed:25400654};
GN   OrderedLocusNames=Os06g0275500 {ECO:0000312|EMBL:BAF19293.1},
GN   LOC_Os06g16390 {ECO:0000305};
GN   ORFNames=P0038C05.29 {ECO:0000312|EMBL:BAD68028.1},
GN   P0676F10.40 {ECO:0000312|EMBL:BAD69169.1};
OS   Oryza sativa subsp. japonica (Rice).
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BOP clade;
OC   Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX   NCBI_TaxID=39947;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=16100779; DOI=10.1038/nature03895;
RG   International rice genome sequencing project (IRGSP);
RT   "The map-based sequence of the rice genome.";
RL   Nature 436:793-800(2005).
RN   [2]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Nipponbare;
RX   PubMed=18089549; DOI=10.1093/nar/gkm978;
RG   The rice annotation project (RAP);
RT   "The rice annotation project database (RAP-DB): 2008 update.";
RL   Nucleic Acids Res. 36:D1028-D1033(2008).
RN   [3]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Nipponbare;
RX   PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA   Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H.,
RA   McCombie W.R., Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S.,
RA   Childs K.L., Davidson R.M., Lin H., Quesada-Ocampo L.,
RA   Vaillancourt B., Sakai H., Lee S.S., Kim J., Numa H., Itoh T.,
RA   Buell C.R., Matsumoto T.;
RT   "Improvement of the Oryza sativa Nipponbare reference genome using
RT   next generation sequence and optical map data.";
RL   Rice 6:4-4(2013).
RN   [4]
RP   TISSUE SPECIFICITY.
RX   PubMed=19825651; DOI=10.1093/mp/ssp036;
RA   Luo M., Platten D., Chaudhury A., Peacock W.J., Dennis E.S.;
RT   "Expression, imprinting, and evolution of rice homologs of the
RT   polycomb group genes.";
RL   Mol. Plant 2:711-723(2009).
RN   [5]
RP   INTERACTION WITH FIE1.
RX   PubMed=23150632; DOI=10.1105/tpc.112.102269;
RA   Zhang L., Cheng Z., Qin R., Qiu Y., Wang J.L., Cui X., Gu L.,
RA   Zhang X., Guo X., Wang D., Jiang L., Wu C.Y., Wang H., Cao X., Wan J.;
RT   "Identification and characterization of an epi-allele of FIE1 reveals
RT   a regulatory linkage between two epigenetic marks in rice.";
RL   Plant Cell 24:4407-4421(2012).
RN   [6]
RP   IDENTIFICATION BY MASS SPECTROMETRY, AND SUBUNIT.
RX   PubMed=23505380; DOI=10.1371/journal.pgen.1003322;
RA   Nallamilli B.R., Zhang J., Mujahid H., Malone B.M., Bridges S.M.,
RA   Peng Z.;
RT   "Polycomb group gene OsFIE2 regulates rice (Oryza sativa) seed
RT   development and grain filling via a mechanism distinct from
RT   Arabidopsis.";
RL   PLoS Genet. 9:E1003322-E1003322(2013).
RN   [7]
RP   TISSUE SPECIFICITY, GENE FAMILY, AND NOMENCLATURE.
RX   PubMed=23762371; DOI=10.1371/journal.pone.0065426;
RA   Lu Z., Huang X., Ouyang Y., Yao J.;
RT   "Genome-wide identification, phylogenetic and co-expression analysis
RT   of OsSET gene family in rice.";
RL   PLoS ONE 8:E65426-E65426(2013).
RN   [8]
RP   FUNCTION.
RX   PubMed=25400654; DOI=10.3389/fpls.2014.00591;
RA   Liu X., Zhou C., Zhao Y., Zhou S., Wang W., Zhou D.X.;
RT   "The rice enhancer of zeste [E(z)] genes SDG711 and SDG718 are
RT   respectively involved in long day and short day signaling to mediate
RT   the accurate photoperiod control of flowering time.";
RL   Front. Plant Sci. 5:591-591(2014).
CC   -!- FUNCTION: Polycomb group (PcG) protein. Catalytic subunit of some
CC       PcG multiprotein complex, which methylates 'Lys-27' of histone H3,
CC       leading to transcriptional repression of the affected target
CC       genes. PcG proteins act by forming multiprotein complexes, which
CC       are required to maintain the transcriptionally repressive state of
CC       homeotic genes throughout development. PcG proteins are not
CC       required to initiate repression, but to maintain it during later
CC       stages of development (Probable). Involved in the regulation of
CC       flowering. Represses flowering under long day (LD) conditions.
CC       Regulates the trimethylation on histone H3 'Lys-27' (H3K27me3) of
CC       the flowering regulators MADS14, MADS15, RFT1, EHD1, HD3A and LF
CC       (PubMed:25400654). {ECO:0000269|PubMed:25400654,
CC       ECO:0000305|PubMed:25400654}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=L-lysyl-[histone] + S-adenosyl-L-methionine = H(+) +
CC         N(6)-methyl-L-lysyl-[histone] + S-adenosyl-L-homocysteine;
CC         Xref=Rhea:RHEA:10024, Rhea:RHEA-COMP:9845, Rhea:RHEA-COMP:9846,
CC         ChEBI:CHEBI:15378, ChEBI:CHEBI:29969, ChEBI:CHEBI:57856,
CC         ChEBI:CHEBI:59789, ChEBI:CHEBI:61929; EC=2.1.1.43;
CC         Evidence={ECO:0000255|PROSITE-ProRule:PRU00909};
CC   -!- SUBUNIT: Interacts with FIE1 (PubMed:23150632). Component of the
CC       polycomb repressive complex 2 (PRC2), composed of the core PRC2
CC       components FIE2, EMF2B and EZ1. PRC2 methylates 'Lys-27' residues
CC       of histone H3 (H3K27me3), leading to transcriptional repression of
CC       the affected target gene (PubMed:23505380).
CC       {ECO:0000269|PubMed:23150632, ECO:0000269|PubMed:23505380}.
CC   -!- TISSUE SPECIFICITY: Widely expressed (PubMed:19825651). Highly
CC       expressed in young panicle (PubMed:23762371).
CC       {ECO:0000269|PubMed:19825651, ECO:0000269|PubMed:23762371}.
CC   -!- MISCELLANEOUS: Over-expression and down-regulation of CLF
CC       respectively, represses and promotes flowering in long day (LD),
CC       but has no effect in short day (SD).
CC       {ECO:0000269|PubMed:25400654}.
CC   -!- SIMILARITY: Belongs to the class V-like SAM-binding
CC       methyltransferase superfamily. Histone-lysine methyltransferase
CC       family. EZ subfamily. {ECO:0000255|PROSITE-ProRule:PRU00909}.
DR   EMBL; AP003044; BAD68028.1; -; Genomic_DNA.
DR   EMBL; AP005813; BAD69169.1; -; Genomic_DNA.
DR   EMBL; AP008212; BAF19293.1; -; Genomic_DNA.
DR   EMBL; AP014962; BAS97226.1; -; Genomic_DNA.
DR   RefSeq; XP_015644234.1; XM_015788748.1.
DR   UniGene; Os.44686; -.
DR   ProteinModelPortal; Q5VN06; -.
DR   STRING; 39947.LOC_Os06g16390.1; -.
DR   PaxDb; Q5VN06; -.
DR   EnsemblPlants; Os06t0275500-01; Os06t0275500-01; Os06g0275500.
DR   GeneID; 4340748; -.
DR   Gramene; Os06t0275500-01; Os06t0275500-01; Os06g0275500.
DR   KEGG; osa:4340748; -.
DR   eggNOG; KOG1079; Eukaryota.
DR   eggNOG; COG2940; LUCA.
DR   InParanoid; Q5VN06; -.
DR   KO; K11430; -.
DR   OMA; CAVNSRE; -.
DR   OrthoDB; EOG09360260; -.
DR   Reactome; R-OSA-212300; PRC2 methylates histones and DNA.
DR   Reactome; R-OSA-2559580; Oxidative Stress Induced Senescence.
DR   Reactome; R-OSA-8953750; Transcriptional Regulation by E2F6.
DR   Proteomes; UP000059680; Chromosome 6.
DR   ExpressionAtlas; Q5VN06; differential.
DR   GO; GO:0005677; C:chromatin silencing complex; IDA:UniProtKB.
DR   GO; GO:0031519; C:PcG protein complex; IDA:UniProtKB.
DR   GO; GO:0018024; F:histone-lysine N-methyltransferase activity; IEA:UniProtKB-EC.
DR   GO; GO:0003727; F:single-stranded RNA binding; IEA:EnsemblPlants.
DR   GO; GO:0030154; P:cell differentiation; IEA:UniProtKB-KW.
DR   GO; GO:0006342; P:chromatin silencing; IMP:UniProtKB.
DR   GO; GO:0009294; P:DNA mediated transformation; IEA:EnsemblPlants.
DR   GO; GO:0009908; P:flower development; IEA:UniProtKB-KW.
DR   GO; GO:0070734; P:histone H3-K27 methylation; IMP:UniProtKB.
DR   GO; GO:0009965; P:leaf morphogenesis; IEA:EnsemblPlants.
DR   GO; GO:0045857; P:negative regulation of molecular function, epigenetic; IEA:EnsemblPlants.
DR   GO; GO:0006349; P:regulation of gene expression by genetic imprinting; IEA:EnsemblPlants.
DR   GO; GO:0048586; P:regulation of long-day photoperiodism, flowering; IMP:UniProtKB.
DR   GO; GO:0010228; P:vegetative to reproductive phase transition of meristem; IEA:EnsemblPlants.
DR   InterPro; IPR026489; CXC_dom.
DR   InterPro; IPR025778; Hist-Lys_N-MeTrfase_EZ.
DR   InterPro; IPR001214; SET_dom.
DR   InterPro; IPR033467; Tesmin/TSO1-like_CXC.
DR   PANTHER; PTHR22884:SF237; PTHR22884:SF237; 1.
DR   Pfam; PF00856; SET; 1.
DR   SMART; SM01114; CXC; 1.
DR   SMART; SM00317; SET; 1.
DR   PROSITE; PS51633; CXC; 1.
DR   PROSITE; PS51576; SAM_MT43_EZ; 1.
DR   PROSITE; PS50280; SET; 1.
PE   1: Evidence at protein level;
KW   Chromatin regulator; Complete proteome; Developmental protein;
KW   Differentiation; Flowering; Methyltransferase; Reference proteome;
KW   S-adenosyl-L-methionine; Transcription; Transcription regulation;
KW   Transferase.
FT   CHAIN         1    896       Histone-lysine N-methyltransferase CLF.
FT                                /FTId=PRO_0000444465.
FT   DOMAIN      633    732       CXC. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00970}.
FT   DOMAIN      747    862       SET. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00190}.
FT   BINDING     861    861       S-adenosyl-L-methionine.
FT                                {ECO:0000255|PROSITE-ProRule:PRU00190}.
SQ   SEQUENCE   896 AA;  100296 MW;  7DCE38E04E7505DF CRC64;
     MAGDSRNEPM FCEEGSSESG YVLCVIDSLK KKITSDRFVY IQKRVEENSI KLSPITLHSH
     NLSKNRQTST SNSTDLVSNL LTKRKEDALC AVNSRESSPD ESEGANCQDE CSSTVIVGGN
     LSARNSVRPI RLPEVATLPP YTTWIFLDRN QRMQEDQSVL GRRRIYYDTN CGEALICSDS
     EDEAVEDEEE KKEFKDSEDC IIRMTIQECG MSDAVLETLA RDIERAPDDI KARYEILQGE
     KPEGSSKKVS ELNVKMEDVY GDKDLDAALD SFDNLFCRRC LVFDCKLHGC SQDLVFPTEK
     QAPLCSSDEG TPCGIHCYKL VSKPDAIMEI DSHLLVDVEE PTSDNLKDQI GSNKKKLGSS
     GQKTKSQQSE SSSTARVSSE SSESEVQLLS NKSPQHSPGL SKNKLGAKGG IKKSTNRRIA
     ERILMSVKKG QQEMSPDSNS IVNGCHWPRD MKLRSDTRSG IKDSVVSSQC NSPSTRSFRK
     KGTLQMENNS SFVDAQSDSM EDTNNEHSAT DGCDSSRKEE CVDESICRQE AHGRSWKVIE
     QGLLLKGLEI FGKNSCLIAR NLLGGMKTCT DVFQYMNYIE NSSASGALSG VDSLVKGYMK
     GNELRTRSRF VRRRGRVRRL KYTWKTAGYH FIRKRITERK DQPCRQYTPC GCQSACGKQC
     PCLTNGTCCE KYCGCPKMCK NRFRGCHCAK SQCRSRQCPC FAADRECDPD VCRNCWVGCG
     DGTLGVPNQR GDNYECRNMK LLLKQQQRVL LGRSDVSGWG AFLKNSVGKH EYLGEYTGEL
     ISHKEADKRG KIYDRENSSF LFNLNNEYVL DAYRMGDKLK FANHSPDPNC YAKVIMVAGD
     HRVGIFAKER ISAGEELFYD YRYEPDRAPA WARKPEGPGA KDDAQPSTGR AKKLAH
//
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