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 03-AUG-2022, entry version 127.
DE RecName: Full=Histone-lysine N-methyltransferase CLF {ECO:0000305};
DE Short=OsCLF {ECO:0000303|PubMed:19825651};
DE EC=2.1.1.356 {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; Magnoliopsida; 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., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT 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 polycomb
RT 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., Zhang X.,
RA 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 a
RT 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., Peng Z.;
RT "Polycomb group gene OsFIE2 regulates rice (Oryza sativa) seed development
RT and grain filling via a mechanism distinct from 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 of
RT 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 respectively
RT involved in long day and short day signaling to mediate the accurate
RT photoperiod control of flowering time.";
RL Front. Plant Sci. 5:591-591(2014).
CC -!- FUNCTION: Polycomb group (PcG) protein. Catalytic subunit of some PcG
CC multiprotein complex, which methylates 'Lys-27' of histone H3, leading
CC to transcriptional repression of the affected target genes. PcG
CC proteins act by forming multiprotein complexes, which are required to
CC maintain the transcriptionally repressive state of homeotic genes
CC throughout development. PcG proteins are not required to initiate
CC repression, but to maintain it during later stages of development
CC (Probable). Involved in the regulation of flowering. Represses
CC flowering under long day (LD) conditions. Regulates the trimethylation
CC on histone H3 'Lys-27' (H3K27me3) of the flowering regulators MADS14,
CC MADS15, RFT1, EHD1, HD3A and LF (PubMed:25400654).
CC {ECO:0000269|PubMed:25400654, ECO:0000305|PubMed:25400654}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-lysyl(27)-[histone H3] + 3 S-adenosyl-L-methionine = 3 H(+)
CC + N(6),N(6),N(6)-trimethyl-L-lysyl(27)-[histone H3] + 3 S-adenosyl-L-
CC homocysteine; Xref=Rhea:RHEA:60292, Rhea:RHEA-COMP:15535, Rhea:RHEA-
CC COMP:15548, ChEBI:CHEBI:15378, ChEBI:CHEBI:29969, ChEBI:CHEBI:57856,
CC ChEBI:CHEBI:59789, ChEBI:CHEBI:61961; EC=2.1.1.356;
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 of
CC histone H3 (H3K27me3), leading to transcriptional repression of the
CC affected target gene (PubMed:23505380). {ECO:0000269|PubMed:23150632,
CC 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 respectively,
CC represses and promotes flowering in long day (LD), but has no effect in
CC short day (SD). {ECO:0000269|PubMed:25400654}.
CC -!- SIMILARITY: Belongs to the class V-like SAM-binding methyltransferase
CC superfamily. Histone-lysine methyltransferase family. EZ subfamily.
CC {ECO:0000255|PROSITE-ProRule:PRU00909}.
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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 AlphaFoldDB; Q5VN06; -.
DR SMR; Q5VN06; -.
DR STRING; 4530.OS06T0275500-01; -.
DR PaxDb; Q5VN06; -.
DR PRIDE; 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 HOGENOM; CLU_011060_0_0_1; -.
DR InParanoid; Q5VN06; -.
DR OMA; DESICRQ; -.
DR OrthoDB; 875190at2759; -.
DR Proteomes; UP000000763; Chromosome 6.
DR Proteomes; UP000059680; Chromosome 6.
DR GO; GO:0005677; C:chromatin silencing complex; IDA:UniProtKB.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0031519; C:PcG protein complex; IDA:UniProtKB.
DR GO; GO:0003682; F:chromatin binding; IBA:GO_Central.
DR GO; GO:0046976; F:histone methyltransferase activity (H3-K27 specific); IBA:GO_Central.
DR GO; GO:0003727; F:single-stranded RNA binding; IEA:EnsemblPlants.
DR GO; GO:1990110; P:callus formation; IEA:EnsemblPlants.
DR GO; GO:0030154; P:cell differentiation; IEA:UniProtKB-KW.
DR GO; GO:0006338; P:chromatin remodeling; IEA:InterPro.
DR GO; GO:0009294; P:DNA-mediated transformation; IEA:EnsemblPlants.
DR GO; GO:0009908; P:flower development; IEA:UniProtKB-KW.
DR GO; GO:0031507; P:heterochromatin assembly; IMP:UniProtKB.
DR GO; GO:0070734; P:histone H3-K27 methylation; IMP:UniProtKB.
DR GO; GO:0098532; P:histone H3-K27 trimethylation; IBA:GO_Central.
DR GO; GO:0009965; P:leaf morphogenesis; IEA:EnsemblPlants.
DR GO; GO:0009909; P:regulation of flower development; IEA:EnsemblPlants.
DR GO; GO:0006349; P:regulation of gene expression by genomic imprinting; IEA:EnsemblPlants.
DR GO; GO:1900055; P:regulation of leaf senescence; IEA:EnsemblPlants.
DR GO; GO:0048586; P:regulation of long-day photoperiodism, flowering; IMP:UniProtKB.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; IEA:EnsemblPlants.
DR GO; GO:0009737; P:response to abscisic acid; IEA:EnsemblPlants.
DR GO; GO:0010228; P:vegetative to reproductive phase transition of meristem; IEA:EnsemblPlants.
DR GO; GO:0010048; P:vernalization response; IEA:EnsemblPlants.
DR Gene3D; 2.170.270.10; -; 1.
DR InterPro; IPR026489; CXC_dom.
DR InterPro; IPR045318; EZH1/2-like.
DR InterPro; IPR025778; Hist-Lys_N-MeTrfase_plant.
DR InterPro; IPR041355; Pre-SET_CXC.
DR InterPro; IPR001214; SET_dom.
DR InterPro; IPR046341; SET_dom_sf.
DR InterPro; IPR033467; Tesmin/TSO1-like_CXC.
DR PANTHER; PTHR45747; PTHR45747; 1.
DR Pfam; PF18264; preSET_CXC; 1.
DR Pfam; PF00856; SET; 1.
DR SMART; SM01114; CXC; 1.
DR SMART; SM00317; SET; 1.
DR SUPFAM; SSF82199; SSF82199; 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; Developmental protein; Differentiation; Flowering;
KW Methyltransferase; Reference proteome; S-adenosyl-L-methionine;
KW Transcription; Transcription regulation; Transferase.
FT CHAIN 1..896
FT /note="Histone-lysine N-methyltransferase CLF"
FT /id="PRO_0000444465"
FT DOMAIN 633..732
FT /note="CXC"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00970"
FT DOMAIN 747..862
FT /note="SET"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT REGION 344..419
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 459..514
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 869..896
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 345..400
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 460..499
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 500..514
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 861
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="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
