ID CMT1_ORYSJ Reviewed; 1059 AA.
AC A0A0P0VUY4; C0SQ90; Q0DTT2; Q8H854;
DT 02-NOV-2016, integrated into UniProtKB/Swiss-Prot.
DT 20-JAN-2016, sequence version 1.
DT 27-MAR-2024, entry version 52.
DE RecName: Full=DNA (cytosine-5)-methyltransferase CMT1 {ECO:0000305};
DE EC=2.1.1.37 {ECO:0000305};
DE AltName: Full=Chromomethylase 1 {ECO:0000305};
DE AltName: Full=OsMET3b {ECO:0000303|PubMed:26243209};
GN Name=CMT1 {ECO:0000305};
GN OrderedLocusNames=Os03g0226800 {ECO:0000312|EMBL:BAS83066.1},
GN LOC_Os03g12570 {ECO:0000312|EMBL:ABF94750.1};
GN ORFNames=OJ1626B05.3 {ECO:0000312|EMBL:AAN60988.1};
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=16109971; DOI=10.1101/gr.3869505;
RG The rice chromosome 3 sequencing consortium;
RA Buell C.R., Yuan Q., Ouyang S., Liu J., Zhu W., Wang A., Maiti R., Haas B.,
RA Wortman J., Pertea M., Jones K.M., Kim M., Overton L., Tsitrin T.,
RA Fadrosh D., Bera J., Weaver B., Jin S., Johri S., Reardon M., Webb K.,
RA Hill J., Moffat K., Tallon L., Van Aken S., Lewis M., Utterback T.,
RA Feldblyum T., Zismann V., Iobst S., Hsiao J., de Vazeille A.R.,
RA Salzberg S.L., White O., Fraser C.M., Yu Y., Kim H., Rambo T., Currie J.,
RA Collura K., Kernodle-Thompson S., Wei F., Kudrna K., Ammiraju J.S.S.,
RA Luo M., Goicoechea J.L., Wing R.A., Henry D., Oates R., Palmer M.,
RA Pries G., Saski C., Simmons J., Soderlund C., Nelson W., de la Bastide M.,
RA Spiegel L., Nascimento L., Huang E., Preston R., Zutavern T., Palmer L.,
RA O'Shaughnessy A., Dike S., McCombie W.R., Minx P., Cordum H., Wilson R.,
RA Jin W., Lee H.R., Jiang J., Jackson S.;
RT "Sequence, annotation, and analysis of synteny between rice chromosome 3
RT and diverged grass species.";
RL Genome Res. 15:1284-1291(2005).
RN [2]
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 [3]
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 [4]
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 [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 309-998, FUNCTION, AND DISRUPTION
RP PHENOTYPE.
RC STRAIN=cv. Nipponbare;
RX PubMed=26243209; DOI=10.1111/tpj.12952;
RA Cheng C., Tarutani Y., Miyao A., Ito T., Yamazaki M., Sakai H., Fukai E.,
RA Hirochika H.;
RT "Loss of function mutations in the rice chromomethylase OsCMT3a cause a
RT burst of transposition.";
RL Plant J. 83:1069-1081(2015).
CC -!- FUNCTION: Involved in CpXpG DNA methylation (By similarity). May not
CC play a major role in maintaining CpXpG methylation (Probable).
CC {ECO:0000250|UniProtKB:C0SQ89, ECO:0000305|PubMed:26243209}.
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:0000305};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype under normal growth
CC conditions. {ECO:0000269|PubMed:26243209}.
CC -!- SIMILARITY: Belongs to the class I-like SAM-binding methyltransferase
CC superfamily. C5-methyltransferase family. {ECO:0000255|PROSITE-
CC ProRule:PRU01016}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAF11356.2; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=BAS83066.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AC104473; AAN60988.1; -; Genomic_DNA.
DR EMBL; DP000009; ABF94750.1; -; Genomic_DNA.
DR EMBL; AP008209; BAF11356.2; ALT_SEQ; Genomic_DNA.
DR EMBL; AP014959; BAS83066.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AB360584; BAH37020.1; -; Genomic_DNA.
DR RefSeq; XP_015630016.1; XM_015774530.1.
DR AlphaFoldDB; A0A0P0VUY4; -.
DR SMR; A0A0P0VUY4; -.
DR STRING; 39947.A0A0P0VUY4; -.
DR REBASE; 11925; M.OsaCMT3P.
DR PaxDb; 39947-A0A0P0VUY4; -.
DR EnsemblPlants; Os03t0226800-01; Os03t0226800-01; Os03g0226800.
DR GeneID; 4332128; -.
DR Gramene; Os03t0226800-01; Os03t0226800-01; Os03g0226800.
DR KEGG; osa:4332128; -.
DR eggNOG; ENOG502QW29; Eukaryota.
DR InParanoid; A0A0P0VUY4; -.
DR OMA; ISARCHY; -.
DR OrthoDB; 1215065at2759; -.
DR BRENDA; 2.1.1.37; 4460.
DR Proteomes; UP000000763; Chromosome 3.
DR Proteomes; UP000059680; Chromosome 3.
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; IBA:GO_Central.
DR GO; GO:0003677; F:DNA binding; IBA:GO_Central.
DR GO; GO:0010424; P:DNA methylation on cytosine within a CG sequence; IBA:GO_Central.
DR CDD; cd18635; CD_CMT3_like; 1.
DR Gene3D; 2.30.30.490; -; 1.
DR Gene3D; 3.90.120.10; DNA Methylase, subunit A, domain 2; 1.
DR Gene3D; 3.40.50.150; Vaccinia Virus protein VP39; 1.
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; IPR017198; DNMT1-like.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR PANTHER; PTHR10629; CYTOSINE-SPECIFIC METHYLTRANSFERASE; 1.
DR PANTHER; PTHR10629:SF60; DNA (CYTOSINE-5)-METHYLTRANSFERASE CMT1; 1.
DR Pfam; PF01426; BAH; 1.
DR Pfam; PF00385; Chromo; 1.
DR Pfam; PF00145; DNA_methylase; 1.
DR PIRSF; PIRSF037404; DNMT1; 1.
DR PRINTS; PR00105; C5METTRFRASE.
DR SMART; SM00439; BAH; 1.
DR SMART; SM00298; CHROMO; 1.
DR SUPFAM; SSF54160; Chromo domain-like; 1.
DR SUPFAM; SSF53335; S-adenosyl-L-methionine-dependent methyltransferases; 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 3: Inferred from homology;
KW DNA-binding; Methyltransferase; Nucleus; Reference proteome;
KW S-adenosyl-L-methionine; Transferase.
FT CHAIN 1..1059
FT /note="DNA (cytosine-5)-methyltransferase CMT1"
FT /id="PRO_0000438156"
FT DOMAIN 312..436
FT /note="BAH"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00370"
FT DOMAIN 479..1017
FT /note="SAM-dependent MTase C5-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01016"
FT DOMAIN 584..649
FT /note="Chromo"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00053"
FT REGION 1..196
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 230..272
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 38..133
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 662
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01016"
SQ SEQUENCE 1059 AA; 118880 MW; 7D30E862B60BDE48 CRC64;
MVPEPAPAAA TEPRRSTRRR LMTAAAMEAE AEAVADLDEI DREMSRAESR KRQRRTAKEK
PGARKGATEW KPEDVEKAAA AEGVAELDEI DREMPRPELR KRQRRTAKEK PSAHEGATEW
KPEDVEKAAA QEPEGTELDS GLSPAESRGK RQRGVEKVKR RTRKKTAKEK TKETTEKSAA
QAPEKMKVND AGGALAEDVC ADEPDAEQMA MEEEEEAADV LEAEERMGKC VGEGSAEKAA
TRKRVARPST ARRVEDSDDH FVGDPVPDDE ARQRWPVRYS RKGSDSLLKQ EPDEDEEMKA
RCHYLAANVD DEIYHLDDDV YVKAGPDEEN YIGRITEFFE GVDRGSYFSC QWFFRTADTV
ISSKLLKVHD HRHNHKRVFL SKEKNDNLIE CIVSKVKIAH VDPNMTPQAR AHAISDCDLY
YDMSYSVAYS TFANLPADND GALGSEATSN ISCDDADNSS KGKLSADIVA PYSEQTETAS
LLDLYSGCGA MSTGLCLGFA FSGINLETRW AVDINKYACA CLKHNHPYSQ VRNEKTEDFL
ALIQQWDALC RKYVVHKNDT LEPSIDMPLN DADDVNEPLP EDIFDVEELL EICYGDPSNT
GKNGLWFKVR WKGYDPSYDT WEPIDGLSDC PERIKEFVEK GHKENILPLP GAVDVICGGP
PCQGISGFNR FRKHNDPLED EKNKQLVVFM DIVKYLRPKY VLMENVVDIL KFADGFLGRY
AMSCLVAMNY QARLGMMAAG YYGLPQFRMR AFLWGALPSM VLPKFPLPTH DAVVRGIVPT
TFSQSVVAYN EVDTRCLRKA LLLADAISDL PKVGNDQPKD VIEYSVAPKT EFQRYIRNNR
KDIQDYSFRG DDPSEEGKLF DHQPLKLNKD DYERVQRIPV KKGANFRDLK GVIVGPDNTV
RLDPNISRER LSSGKPLVPD YAISFVKGKS TKPFGRLWWD ETVPTVVTRA EPHNQIILHP
SQDRVLTIRE NARLQGFPDY YRLIGPLKEK YIQVGNAVAI PVARALGYAL GLAYRGESDG
DRAVLKLPES FIYADQETVV KSSAGTPGSE IADSEQLFE
//
