CMT3_ARATH
ID CMT3_ARATH Reviewed; 839 AA.
AC Q94F88; Q94FN4; Q9C9L8;
DT 25-JUL-2006, integrated into UniProtKB/Swiss-Prot.
DT 25-JUL-2006, sequence version 2.
DT 03-AUG-2022, entry version 140.
DE RecName: Full=DNA (cytosine-5)-methyltransferase CMT3 {ECO:0000305};
DE EC=2.1.1.37 {ECO:0000255|PROSITE-ProRule:PRU10018};
DE AltName: Full=Protein CHROMOMETHYLASE 3 {ECO:0000303|PubMed:11349138, ECO:0000303|PubMed:11459824, ECO:0000303|PubMed:15457214};
GN Name=CMT3 {ECO:0000303|PubMed:11349138, ECO:0000303|PubMed:11459824,
GN ECO:0000303|PubMed:15457214};
GN OrderedLocusNames=At1g69770 {ECO:0000312|Araport:AT1G69770};
GN ORFNames=T6C23.3 {ECO:0000312|EMBL:AAG52543.1};
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(2000).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], MUTAGENESIS OF GLY-279; GLY-456;
RP GLY-465; LEU-542; ARG-683; LEU-733; PRO-748 AND GLY-807, AND FUNCTION.
RC STRAIN=cv. Wassilewskija;
RX PubMed=11459824; DOI=10.1101/gad.905701;
RA Bartee L., Malagnac F., Bender J.;
RT "Arabidopsis cmt3 chromomethylase mutations block non-CG methylation and
RT silencing of an endogenous gene.";
RL Genes Dev. 15:1753-1758(2001).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], MUTAGENESIS OF ARG-470; GLY-541;
RP GLY-724; SER-763 AND ARG-769, AND FUNCTION.
RC STRAIN=cv. Landsberg erecta;
RX PubMed=11349138; DOI=10.1126/science.1059745;
RA Lindroth A.M., Cao X., Jackson J.P., Zilberman D., McCallum C.M.,
RA Henikoff S., Jacobsen S.E.;
RT "Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation.";
RL Science 292:2077-2080(2001).
RN [5]
RP INTERACTION WITH H3, AND MUTAGENESIS OF PHE-382.
RX PubMed=15457214; DOI=10.1038/sj.emboj.7600430;
RA Lindroth A.M., Shultis D., Jasencakova Z., Fuchs J., Johnson L.,
RA Schubert D., Patnaik D., Pradhan S., Goodrich J., Schubert I., Jenuwein T.,
RA Khorasanizadeh S., Jacobsen S.E.;
RT "Dual histone H3 methylation marks at lysines 9 and 27 required for
RT interaction with CHROMOMETHYLASE3.";
RL EMBO J. 23:4286-4296(2004).
RN [6]
RP INTERACTION WITH HP1.
RX PubMed=11898023; DOI=10.1038/nature731;
RA Jackson J.P., Lindroth A.M., Cao X., Jacobsen S.E.;
RT "Control of CpNpG DNA methylation by the KRYPTONITE histone H3
RT methyltransferase.";
RL Nature 416:556-560(2002).
RN [7]
RP FUNCTION.
RX PubMed=11790305; DOI=10.1016/s0960-9822(01)00622-4;
RA Tompa R., McCallum C.M., Delrow J., Henikoff J.G., van Steensel B.,
RA Henikoff S.;
RT "Genome-wide profiling of DNA methylation reveals transposon targets of
RT CHROMOMETHYLASE3.";
RL Curr. Biol. 12:65-68(2002).
RN [8]
RP FUNCTION.
RX PubMed=14680640; DOI=10.1016/j.cub.2003.11.052;
RA Cao X., Aufsatz W., Zilberman D., Mette M.F., Huang M.S., Matzke M.,
RA Jacobsen S.E.;
RT "Role of the DRM and CMT3 methyltransferases in RNA-directed DNA
RT methylation.";
RL Curr. Biol. 13:2212-2217(2003).
RN [9]
RP FUNCTION, DISRUPTION PHENOTYPE, PTM, AND INTERACTION WITH JMJ24.
RC STRAIN=cv. Columbia;
RX PubMed=26798133; DOI=10.1101/gad.274647.115;
RA Deng S., Jang I.-C., Su L., Xu J., Chua N.-H.;
RT "JMJ24 targets CHROMOMETHYLASE3 for proteasomal degradation in
RT Arabidopsis.";
RL Genes Dev. 30:251-256(2016).
CC -!- FUNCTION: Involved in the CpXpG methylation (e.g. CHG cytosine) and in
CC gene silencing (PubMed:26798133). Methylates preferentially transposon-
CC related sequences. Functionally redundant to DRM1/DRM2 to maintain non-
CC CpG methylation. Involved in RNA-directed DNA methylation.
CC {ECO:0000269|PubMed:11349138, ECO:0000269|PubMed:11459824,
CC ECO:0000269|PubMed:11790305, ECO:0000269|PubMed:14680640,
CC ECO:0000269|PubMed:26798133}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 2'-deoxycytidine in DNA + S-adenosyl-L-methionine = a 5-
CC methyl-2'-deoxycytidine in DNA + H(+) + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:13681, Rhea:RHEA-COMP:11369, Rhea:RHEA-COMP:11370,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:85452, ChEBI:CHEBI:85454; EC=2.1.1.37;
CC Evidence={ECO:0000255|PROSITE-ProRule:PRU10018};
CC -!- SUBUNIT: Homodimer. Interacts with HP1 and, through its chromodomain,
CC with the N-terminal tail of histone H3 doubly methylated at 'Lys-9' and
CC 'Lys-27'. Binds to JMJ24 (PubMed:26798133).
CC {ECO:0000269|PubMed:11898023, ECO:0000269|PubMed:15457214,
CC ECO:0000269|PubMed:26798133}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}.
CC -!- PTM: Ubiquitinated by JMJ24, subsequently beingargeted to proteasomal
CC degradation thus initiating the destabilization of the heterochromatic
CC state of endogenous silenced loci. {ECO:0000269|PubMed:26798133}.
CC -!- DISRUPTION PHENOTYPE: Reduced DNA methylation (e.g. CHG cytosine) at
CC least on FWA, QQS and SDC loci. {ECO:0000269|PubMed:26798133}.
CC -!- SIMILARITY: Belongs to the class I-like SAM-binding methyltransferase
CC superfamily. C5-methyltransferase family. {ECO:0000255|PROSITE-
CC ProRule:PRU01016}.
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DR EMBL; AC013289; AAG52543.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE34973.1; -; Genomic_DNA.
DR EMBL; AF383170; AAK69756.1; -; Genomic_DNA.
DR EMBL; AF364174; AAK71870.1; -; Genomic_DNA.
DR PIR; G96719; G96719.
DR RefSeq; NP_177135.1; NM_105645.4.
DR AlphaFoldDB; Q94F88; -.
DR SMR; Q94F88; -.
DR BioGRID; 28534; 3.
DR DIP; DIP-60719N; -.
DR STRING; 3702.AT1G69770.1; -.
DR REBASE; 4853; M.AthCMT3.
DR PaxDb; Q94F88; -.
DR PRIDE; Q94F88; -.
DR ProteomicsDB; 241236; -.
DR EnsemblPlants; AT1G69770.1; AT1G69770.1; AT1G69770.
DR GeneID; 843313; -.
DR Gramene; AT1G69770.1; AT1G69770.1; AT1G69770.
DR KEGG; ath:AT1G69770; -.
DR Araport; AT1G69770; -.
DR TAIR; locus:2205015; AT1G69770.
DR eggNOG; ENOG502QW29; Eukaryota.
DR HOGENOM; CLU_004921_0_0_1; -.
DR InParanoid; Q94F88; -.
DR OMA; SNCDFYY; -.
DR OrthoDB; 898916at2759; -.
DR PhylomeDB; Q94F88; -.
DR BRENDA; 2.1.1.37; 399.
DR PRO; PR:Q94F88; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q94F88; baseline and differential.
DR Genevisible; Q94F88; AT.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0003682; F:chromatin binding; IEA:InterPro.
DR GO; GO:0003886; F:DNA (cytosine-5-)-methyltransferase activity; IMP:TAIR.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0031625; F:ubiquitin protein ligase binding; IPI:UniProtKB.
DR GO; GO:0006306; P:DNA methylation; IMP:TAIR.
DR GO; GO:0010425; P:DNA methylation on cytosine within a CNG sequence; IMP:UniProtKB.
DR GO; GO:0051567; P:histone H3-K9 methylation; IGI:TAIR.
DR GO; GO:0045814; P:negative regulation of gene expression, epigenetic; IGI:TAIR.
DR GO; GO:0010069; P:zygote asymmetric cytokinesis in embryo sac; IMP:TAIR.
DR Gene3D; 2.30.30.490; -; 1.
DR Gene3D; 3.40.50.150; -; 2.
DR InterPro; IPR001025; BAH_dom.
DR InterPro; IPR043151; BAH_sf.
DR InterPro; IPR018117; C5_DNA_meth_AS.
DR InterPro; IPR001525; C5_MeTfrase.
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; IPR029063; SAM-dependent_MTases_sf.
DR Pfam; PF01426; BAH; 1.
DR Pfam; PF00385; Chromo; 1.
DR Pfam; PF00145; DNA_methylase; 1.
DR PRINTS; PR00105; C5METTRFRASE.
DR SMART; SM00439; BAH; 1.
DR SMART; SM00298; CHROMO; 1.
DR SUPFAM; SSF53335; SSF53335; 1.
DR SUPFAM; SSF54160; SSF54160; 1.
DR TIGRFAMs; TIGR00675; dcm; 1.
DR PROSITE; PS51038; BAH; 1.
DR PROSITE; PS00094; C5_MTASE_1; 1.
DR PROSITE; PS00598; CHROMO_1; 1.
DR PROSITE; PS50013; CHROMO_2; 1.
DR PROSITE; PS51679; SAM_MT_C5; 1.
PE 1: Evidence at protein level;
KW Chromatin regulator; DNA-binding; Methyltransferase; Nucleus;
KW Reference proteome; S-adenosyl-L-methionine; Transcription;
KW Transcription regulation; Transferase; Ubl conjugation.
FT CHAIN 1..839
FT /note="DNA (cytosine-5)-methyltransferase CMT3"
FT /id="PRO_0000246693"
FT DOMAIN 108..227
FT /note="BAH"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00370"
FT DOMAIN 269..813
FT /note="SAM-dependent MTase C5-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01016"
FT DOMAIN 382..447
FT /note="Chromo"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00053"
FT REGION 1..38
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 51..86
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..20
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 51..66
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 460
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01016,
FT ECO:0000255|PROSITE-ProRule:PRU10018"
FT MUTAGEN 279
FT /note="G->E: Loss of activity."
FT /evidence="ECO:0000269|PubMed:11459824"
FT MUTAGEN 382
FT /note="F->A: Loss of binding to H3."
FT /evidence="ECO:0000269|PubMed:15457214"
FT MUTAGEN 456
FT /note="G->D: Loss of activity."
FT /evidence="ECO:0000269|PubMed:11459824"
FT MUTAGEN 465
FT /note="G->D: Loss of activity."
FT /evidence="ECO:0000269|PubMed:11459824"
FT MUTAGEN 470
FT /note="R->K: In cmt3-10; partial loss of activity."
FT /evidence="ECO:0000269|PubMed:11349138"
FT MUTAGEN 541
FT /note="G->E: In cmt3-6; loss of activity."
FT /evidence="ECO:0000269|PubMed:11349138"
FT MUTAGEN 542
FT /note="L->F: Loss of activity."
FT /evidence="ECO:0000269|PubMed:11459824"
FT MUTAGEN 683
FT /note="R->K: Loss of activity."
FT /evidence="ECO:0000269|PubMed:11459824"
FT MUTAGEN 724
FT /note="G->E: In cmt3-4; loss of activity."
FT /evidence="ECO:0000269|PubMed:11349138"
FT MUTAGEN 733
FT /note="L->F: Loss of activity."
FT /evidence="ECO:0000269|PubMed:11459824"
FT MUTAGEN 748
FT /note="P->L: Loss of activity."
FT /evidence="ECO:0000269|PubMed:11459824"
FT MUTAGEN 763
FT /note="S->F: In cmt3-8; partial loss of activity."
FT /evidence="ECO:0000269|PubMed:11349138"
FT MUTAGEN 769
FT /note="R->K: In cmt3-3; loss of activity."
FT /evidence="ECO:0000269|PubMed:11349138"
FT MUTAGEN 807
FT /note="G->R: Loss of activity."
FT /evidence="ECO:0000269|PubMed:11459824"
FT CONFLICT 138
FT /note="A -> V (in Ref. 4; AAK71870)"
FT /evidence="ECO:0000305"
FT CONFLICT 165
FT /note="K -> N (in Ref. 4; AAK71870)"
FT /evidence="ECO:0000305"
FT CONFLICT 166
FT /note="K -> E (in Ref. 3; AAK69756)"
FT /evidence="ECO:0000305"
FT CONFLICT 266..268
FT /note="HKK -> QKE (in Ref. 4; AAK71870)"
FT /evidence="ECO:0000305"
FT CONFLICT 433
FT /note="E -> G (in Ref. 4; AAK71870)"
FT /evidence="ECO:0000305"
FT CONFLICT 821..822
FT /note="LT -> II (in Ref. 4; AAK71870)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 839 AA; 94905 MW; B1B4D5F7AE0A3AAC CRC64;
MAPKRKRPAT KDDTTKSIPK PKKRAPKRAK TVKEEPVTVV EEGEKHVARF LDEPIPESEA
KSTWPDRYKP IEVQPPKASS RKKTKDDEKV EIIRARCHYR RAIVDERQIY ELNDDAYVQS
GEGKDPFICK IIEMFEGANG KLYFTARWFY RPSDTVMKEF EILIKKKRVF FSEIQDTNEL
GLLEKKLNIL MIPLNENTKE TIPATENCDF FCDMNYFLPY DTFEAIQQET MMAISESSTI
SSDTDIREGA AAISEIGECS QETEGHKKAT LLDLYSGCGA MSTGLCMGAQ LSGLNLVTKW
AVDMNAHACK SLQHNHPETN VRNMTAEDFL FLLKEWEKLC IHFSLRNSPN SEEYANLHGL
NNVEDNEDVS EESENEDDGE VFTVDKIVGI SFGVPKKLLK RGLYLKVRWL NYDDSHDTWE
PIEGLSNCRG KIEEFVKLGY KSGILPLPGG VDVVCGGPPC QGISGHNRFR NLLDPLEDQK
NKQLLVYMNI VEYLKPKFVL MENVVDMLKM AKGYLARFAV GRLLQMNYQV RNGMMAAGAY
GLAQFRLRFF LWGALPSEII PQFPLPTHDL VHRGNIVKEF QGNIVAYDEG HTVKLADKLL
LKDVISDLPA VANSEKRDEI TYDKDPTTPF QKFIRLRKDE ASGSQSKSKS KKHVLYDHHP
LNLNINDYER VCQVPKRKGA NFRDFPGVIV GPGNVVKLEE GKERVKLESG KTLVPDYALT
YVDGKSCKPF GRLWWDEIVP TVVTRAEPHN QVIIHPEQNR VLSIRENARL QGFPDDYKLF
GPPKQKYIQV GNAVAVPVAK ALGYALGTAF QGLAVGKDPL LTLPEGFAFM KPTLPSELA
