DNMT1_ARATH
ID DNMT1_ARATH Reviewed; 1534 AA.
AC P34881; Q0WLP5; Q0WPP9; Q5C994;
DT 01-FEB-1994, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1994, sequence version 1.
DT 03-AUG-2022, entry version 160.
DE RecName: Full=DNA (cytosine-5)-methyltransferase 1;
DE EC=2.1.1.37;
DE AltName: Full=DNA methyltransferase 01;
DE AltName: Full=DNA methyltransferase 2;
DE AltName: Full=DNA methyltransferase AthI;
DE Short=DNA Metase AthI;
DE Short=M.AthI;
DE AltName: Full=DNA methyltransferase DDM2;
DE AltName: Full=Protein DECREASED DNA METHYLATION 2;
GN Name=DMT1; Synonyms=ATHIM, DDM2, DMT01, MET1, MET2;
GN OrderedLocusNames=At5g49160; ORFNames=K21P3.3;
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 [MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=8389441; DOI=10.1093/nar/21.10.2383;
RA Finnegan E.J., Dennis E.S.;
RT "Isolation and identification by sequence homology of a putative cytosine
RT methyltransferase from Arabidopsis thaliana.";
RL Nucleic Acids Res. 21:2383-2388(1993).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10048488; DOI=10.1093/dnares/5.6.379;
RA Asamizu E., Sato S., Kaneko T., Nakamura Y., Kotani H., Miyajima N.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. VIII. Sequence
RT features of the regions of 1,081,958 bp covered by seventeen physically
RT assigned P1 and TAC clones.";
RL DNA Res. 5:379-391(1998).
RN [3]
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 [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-1517.
RC STRAIN=cv. C24;
RA Chang S., Pikaard C.S.;
RT "Identification of suppressors of transgene silencing in Arabidopsis.";
RL Submitted (JUL-2004) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 932-1534 AND 1371-1534.
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP FUNCTION.
RX PubMed=12456661; DOI=10.1093/emboj/cdf657;
RA Soppe W.J.J., Jasencakova Z., Houben A., Kakutani T., Meister A.,
RA Huang M.S., Jacobsen S.E., Schubert I., Fransz P.F.;
RT "DNA methylation controls histone H3 lysine 9 methylation and
RT heterochromatin assembly in Arabidopsis.";
RL EMBO J. 21:6549-6559(2002).
RN [7]
RP FUNCTION, AND MUTAGENESIS OF GLU-1272 AND GLY-1465.
RX PubMed=14667411; DOI=10.1016/s1534-5807(03)00361-7;
RA Xiao W., Gehring M., Choi Y., Margossian L., Pu H., Harada J.J.,
RA Goldberg R.B., Pennell R.I., Fischer R.L.;
RT "Imprinting of the MEA Polycomb gene is controlled by antagonism between
RT MET1 methyltransferase and DME glycosylase.";
RL Dev. Cell 5:891-901(2003).
RN [8]
RP FUNCTION, AND MUTAGENESIS OF GLY-1101 AND PRO-1300.
RX PubMed=12663548; DOI=10.1093/genetics/163.3.1109;
RA Kankel M.W., Ramsey D.E., Stokes T.L., Flowers S.K., Haag J.R.,
RA Jeddeloh J.A., Riddle N.C., Verbsky M.L., Richards E.J.;
RT "Arabidopsis MET1 cytosine methyltransferase mutants.";
RL Genetics 163:1109-1122(2003).
RN [9]
RP FUNCTION.
RX PubMed=12669067; DOI=10.1038/ng1138;
RA Saze H., Mittelsten Scheid O., Paszkowski J.;
RT "Maintenance of CpG methylation is essential for epigenetic inheritance
RT during plant gametogenesis.";
RL Nat. Genet. 34:65-69(2003).
RN [10]
RP FUNCTION, AND TISSUE SPECIFICITY.
RX PubMed=17012404; DOI=10.1104/pp.106.088849;
RA Xiao W., Brown R.C., Lemmon B.E., Harada J.J., Goldberg R.B., Fischer R.L.;
RT "Regulation of seed size by hypomethylation of maternal and paternal
RT genomes.";
RL Plant Physiol. 142:1160-1168(2006).
RN [11]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=16531498; DOI=10.1105/tpc.105.038836;
RA Xiao W., Custard K.D., Brown R.C., Lemmon B.E., Harada J.J., Goldberg R.B.,
RA Fischer R.L.;
RT "DNA methylation is critical for Arabidopsis embryogenesis and seed
RT viability.";
RL Plant Cell 18:805-814(2006).
RN [12]
RP FUNCTION.
RX PubMed=18820427;
RA Kim M., Ohr H., Lee J.W., Hyun Y., Fischer R.L., Choi Y.;
RT "Temporal and spatial downregulation of Arabidopsis MET1 activity results
RT in global DNA hypomethylation and developmental defects.";
RL Mol. Cells 26:611-615(2008).
CC -!- FUNCTION: Maintains chromatin CpG methylation that plays a role in
CC genomic imprinting, regulation of embryogenesis and seed viability.
CC Required for proper patterns of CG DNA methylation in dividing cells.
CC Required for MEA promoter methylation in seeds.
CC {ECO:0000269|PubMed:12456661, ECO:0000269|PubMed:12663548,
CC ECO:0000269|PubMed:12669067, ECO:0000269|PubMed:14667411,
CC ECO:0000269|PubMed:16531498, ECO:0000269|PubMed:17012404,
CC ECO:0000269|PubMed:18820427}.
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 -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305}.
CC -!- TISSUE SPECIFICITY: Expressed in flowers, embryos and endosperm.
CC {ECO:0000269|PubMed:17012404}.
CC -!- DISRUPTION PHENOTYPE: Late-flowering phenotype caused by ectopic
CC expression of FWA gene. Asymmetric zygote division and abnormal
CC embryos. Displays genome hypomethylation, strong reduction of CpG
CC methylation in centromeric repeats, reduction of heterochromatin and
CC chromocenter size and gametes with fully demethylated and
CC hemidemethylated DNA. {ECO:0000269|PubMed:16531498}.
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=AAX22756.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; L10692; AAA32829.1; -; mRNA.
DR EMBL; AB016872; BAB10334.1; -; Genomic_DNA.
DR EMBL; CP002688; AED95777.1; -; Genomic_DNA.
DR EMBL; AY699012; AAX22756.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AK229013; BAF00900.1; -; mRNA.
DR EMBL; AK230148; BAF01962.1; -; mRNA.
DR PIR; S59604; S59604.
DR RefSeq; NP_199727.1; NM_124293.4.
DR AlphaFoldDB; P34881; -.
DR SMR; P34881; -.
DR BioGRID; 20221; 5.
DR STRING; 3702.AT5G49160.1; -.
DR REBASE; 11752; M.AthMET1.
DR PaxDb; P34881; -.
DR PRIDE; P34881; -.
DR ProteomicsDB; 220525; -.
DR EnsemblPlants; AT5G49160.1; AT5G49160.1; AT5G49160.
DR GeneID; 834975; -.
DR Gramene; AT5G49160.1; AT5G49160.1; AT5G49160.
DR KEGG; ath:AT5G49160; -.
DR Araport; AT5G49160; -.
DR TAIR; locus:2155959; AT5G49160.
DR eggNOG; ENOG502QPKK; Eukaryota.
DR HOGENOM; CLU_002247_0_0_1; -.
DR InParanoid; P34881; -.
DR OMA; KINDAEC; -.
DR OrthoDB; 898916at2759; -.
DR PhylomeDB; P34881; -.
DR PRO; PR:P34881; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; P34881; baseline and differential.
DR Genevisible; P34881; 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; IEA:UniProtKB-EC.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0008168; F:methyltransferase activity; TAS:TAIR.
DR GO; GO:0010424; P:DNA methylation on cytosine within a CG sequence; IMP:TAIR.
DR GO; GO:0009294; P:DNA-mediated transformation; IMP:TAIR.
DR GO; GO:0010216; P:maintenance of DNA methylation; IMP:TAIR.
DR GO; GO:0009910; P:negative regulation of flower development; IMP:TAIR.
DR GO; GO:0006349; P:regulation of gene expression by genomic imprinting; IMP:TAIR.
DR GO; GO:0010069; P:zygote asymmetric cytokinesis in embryo sac; IMP:TAIR.
DR Gene3D; 2.30.30.490; -; 2.
DR Gene3D; 3.40.50.150; -; 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; IPR031303; C5_meth_CS.
DR InterPro; IPR022702; Cytosine_MeTrfase1_RFD.
DR InterPro; IPR017198; DNMT1-like.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR Pfam; PF01426; BAH; 2.
DR Pfam; PF00145; DNA_methylase; 2.
DR Pfam; PF12047; DNMT1-RFD; 2.
DR PIRSF; PIRSF037404; DNMT1; 1.
DR PRINTS; PR00105; C5METTRFRASE.
DR SMART; SM00439; BAH; 2.
DR SUPFAM; SSF53335; SSF53335; 1.
DR TIGRFAMs; TIGR00675; dcm; 1.
DR PROSITE; PS51038; BAH; 2.
DR PROSITE; PS00094; C5_MTASE_1; 1.
DR PROSITE; PS00095; C5_MTASE_2; 1.
DR PROSITE; PS51679; SAM_MT_C5; 1.
PE 1: Evidence at protein level;
KW Chromatin regulator; DNA-binding; Isopeptide bond; Methyltransferase;
KW Nucleus; Reference proteome; Repeat; S-adenosyl-L-methionine; Transferase;
KW Ubl conjugation.
FT CHAIN 1..1534
FT /note="DNA (cytosine-5)-methyltransferase 1"
FT /id="PRO_0000088039"
FT DOMAIN 735..869
FT /note="BAH 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00370"
FT DOMAIN 909..1049
FT /note="BAH 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00370"
FT DOMAIN 1093..1527
FT /note="SAM-dependent MTase C5-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01016"
FT REGION 1..33
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 321..341
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 647..717
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 657..682
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 689..715
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 1198
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01016,
FT ECO:0000255|PROSITE-ProRule:PRU10018"
FT CROSSLNK 599
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in ubiquitin)"
FT /evidence="ECO:0000250|UniProtKB:O23273"
FT MUTAGEN 1101
FT /note="G->S: In met1-2/ddm2-2; reduced activity."
FT /evidence="ECO:0000269|PubMed:12663548"
FT MUTAGEN 1272
FT /note="E->K: In met1-5; reduced activity."
FT /evidence="ECO:0000269|PubMed:14667411"
FT MUTAGEN 1300
FT /note="P->S: In met1-1/ddm2-1; reduced activity."
FT /evidence="ECO:0000269|PubMed:12663548"
FT MUTAGEN 1465
FT /note="G->E: In met1-7; reduced activity."
FT /evidence="ECO:0000269|PubMed:14667411"
FT CONFLICT 306
FT /note="L -> M (in Ref. 4; AAX22756)"
FT /evidence="ECO:0000305"
FT CONFLICT 837
FT /note="W -> R (in Ref. 4; AAX22756)"
FT /evidence="ECO:0000305"
FT CONFLICT 901
FT /note="K -> R (in Ref. 4; AAX22756)"
FT /evidence="ECO:0000305"
FT CONFLICT 932
FT /note="K -> N (in Ref. 5; BAF01962)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1534 AA; 172431 MW; 23FC944AA7074C5A CRC64;
MVENGAKAAK RKKRPLPEIQ EVEDVPRTRR PRRAAACTSF KEKSIRVCEK SATIEVKKQQ
IVEEEFLALR LTALETDVED RPTRRLNDFV LFDSDGVPQP LEMLEIHDIF VSGAILPSDV
CTDKEKEKGV RCTSFGRVEH WSISGYEDGS PVIWISTELA DYDCRKPAAS YRKVYDYFYE
KARASVAVYK KLSKSSGGDP DIGLEELLAA VVRSMSSGSK YFSSGAAIID FVISQGDFIY
NQLAGLDETA KKHESSYVEI PVLVALREKS SKIDKPLQRE RNPSNGVRIK EVSQVAESEA
LTSDQLVDGT DDDRRYAILL QDEENRKSMQ QPRKNSSSGS ASNMFYIKIN EDEIANDYPL
PSYYKTSEEE TDELILYDAS YEVQSEHLPH RMLHNWALYN SDLRFISLEL LPMKQCDDID
VNIFGSGVVT DDNGSWISLN DPDSGSQSHD PDGMCIFLSQ IKEWMIEFGS DDIISISIRT
DVAWYRLGKP SKLYAPWWKP VLKTARVGIS ILTFLRVESR VARLSFADVT KRLSGLQAND
KAYISSDPLA VERYLVVHGQ IILQLFAVYP DDNVKRCPFV VGLASKLEDR HHTKWIIKKK
KISLKELNLN PRAGMAPVAS KRKAMQATTT RLVNRIWGEF YSNYSPEDPL QATAAENGED
EVEEEGGNGE EEVEEEGENG LTEDTVPEPV EVQKPHTPKK IRGSSGKREI KWDGESLGKT
SAGEPLYQQA LVGGEMVAVG GAVTLEVDDP DEMPAIYFVE YMFESTDHCK MLHGRFLQRG
SMTVLGNAAN ERELFLTNEC MTTQLKDIKG VASFEIRSRP WGHQYRKKNI TADKLDWARA
LERKVKDLPT EYYCKSLYSP ERGGFFSLPL SDIGRSSGFC TSCKIREDEE KRSTIKLNVS
KTGFFINGIE YSVEDFVYVN PDSIGGLKEG SKTSFKSGRN IGLRAYVVCQ LLEIVPKESR
KADLGSFDVK VRRFYRPEDV SAEKAYASDI QELYFSQDTV VLPPGALEGK CEVRKKSDMP
LSREYPISDH IFFCDLFFDT SKGSLKQLPA NMKPKFSTIK DDTLLRKKKG KGVESEIESE
IVKPVEPPKE IRLATLDIFA GCGGLSHGLK KAGVSDAKWA IEYEEPAGQA FKQNHPESTV
FVDNCNVILR AIMEKGGDQD DCVSTTEANE LAAKLTEEQK STLPLPGQVD FINGGPPCQG
FSGMNRFNQS SWSKVQCEMI LAFLSFADYF RPRYFLLENV RTFVSFNKGQ TFQLTLASLL
EMGYQVRFGI LEAGAYGVSQ SRKRAFIWAA APEEVLPEWP EPMHVFGVPK LKISLSQGLH
YAAVRSTALG APFRPITVRD TIGDLPSVEN GDSRTNKEYK EVAVSWFQKE IRGNTIALTD
HICKAMNELN LIRCKLIPTR PGADWHDLPK RKVTLSDGRV EEMIPFCLPN TAERHNGWKG
LYGRLDWQGN FPTSVTDPQP MGKVGMCFHP EQHRILTVRE CARSQGFPDS YEFAGNINHK
HRQIGNAVPP PLAFALGRKL KEALHLKKSP QHQP
