DNMT3_ARATH
ID DNMT3_ARATH Reviewed; 1404 AA.
AC Q9T0I1;
DT 03-SEP-2014, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 140.
DE RecName: Full=DNA (cytosine-5)-methyltransferase 3;
DE EC=2.1.1.37;
DE AltName: Full=DNA methyltransferase 3;
DE AltName: Full=DNA methyltransferase III;
DE AltName: Full=Protein MATERNAL EFFECT EMBRYO ARREST 57;
GN Name=MET3; Synonyms=MEE57, METIII; OrderedLocusNames=At4g13610;
GN ORFNames=T6G15.160;
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=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(1999).
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 GENE FAMILY.
RC STRAIN=cv. Columbia;
RX PubMed=10579493; DOI=10.1023/a:1006347010369;
RA Genger R.K., Kovac K.A., Dennis E.S., Peacock W.J., Finnegan E.J.;
RT "Multiple DNA methyltransferase genes in Arabidopsis thaliana.";
RL Plant Mol. Biol. 41:269-278(1999).
RN [4]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=15634699; DOI=10.1242/dev.01595;
RA Pagnussat G.C., Yu H.-J., Ngo Q.A., Rajani S., Mayalagu S., Johnson C.S.,
RA Capron A., Xie L.-F., Ye D., Sundaresan V.;
RT "Genetic and molecular identification of genes required for female
RT gametophyte development and function in Arabidopsis.";
RL Development 132:603-614(2005).
RN [5]
RP GENE FAMILY, AND NOMENCLATURE.
RX PubMed=21257907; DOI=10.1073/pnas.1019273108;
RA Hsieh T.-F., Shin J., Uzawa R., Silva P., Cohen S., Bauer M.J.,
RA Hashimoto M., Kirkbride R.C., Harada J.J., Zilberman D., Fischer R.L.;
RT "Regulation of imprinted gene expression in Arabidopsis endosperm.";
RL Proc. Natl. Acad. Sci. U.S.A. 108:1755-1762(2011).
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 (By similarity). Required during the endosperm development in seeds.
CC {ECO:0000250, ECO:0000269|PubMed:15634699}.
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 -!- DISRUPTION PHENOTYPE: Endosperm development arrested.
CC {ECO:0000269|PubMed:15634699}.
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; AL049656; CAB41119.1; -; Genomic_DNA.
DR EMBL; AL161537; CAB78403.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE83302.1; -; Genomic_DNA.
DR PIR; T06663; T06663.
DR RefSeq; NP_193097.1; NM_117435.1.
DR AlphaFoldDB; Q9T0I1; -.
DR SMR; Q9T0I1; -.
DR STRING; 3702.AT4G13610.1; -.
DR REBASE; 2839; M.AthMET2.
DR PaxDb; Q9T0I1; -.
DR PRIDE; Q9T0I1; -.
DR EnsemblPlants; AT4G13610.1; AT4G13610.1; AT4G13610.
DR GeneID; 826994; -.
DR Gramene; AT4G13610.1; AT4G13610.1; AT4G13610.
DR KEGG; ath:AT4G13610; -.
DR Araport; AT4G13610; -.
DR TAIR; locus:2140892; AT4G13610.
DR eggNOG; ENOG502QPKK; Eukaryota.
DR HOGENOM; CLU_002247_0_0_1; -.
DR InParanoid; Q9T0I1; -.
DR OMA; KGKCEVM; -.
DR OrthoDB; 898916at2759; -.
DR PhylomeDB; Q9T0I1; -.
DR PRO; PR:Q9T0I1; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q9T0I1; baseline and differential.
DR Genevisible; Q9T0I1; 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:0006325; P:chromatin organization; IEA:UniProtKB-KW.
DR GO; GO:0009793; P:embryo development ending in seed dormancy; 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 3: Inferred from homology;
KW Chromatin regulator; DNA-binding; Isopeptide bond; Methyltransferase;
KW Nucleus; Reference proteome; Repeat; S-adenosyl-L-methionine; Transferase;
KW Ubl conjugation.
FT CHAIN 1..1404
FT /note="DNA (cytosine-5)-methyltransferase 3"
FT /id="PRO_0000430012"
FT DOMAIN 614..748
FT /note="BAH 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00370"
FT DOMAIN 788..929
FT /note="BAH 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00370"
FT DOMAIN 969..1402
FT /note="SAM-dependent MTase C5-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01016"
FT REGION 1..35
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 8..35
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 1085
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01016,
FT ECO:0000255|PROSITE-ProRule:PRU10018"
FT CROSSLNK 486
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in ubiquitin)"
FT /evidence="ECO:0000250|UniProtKB:O23273"
SQ SEQUENCE 1404 AA; 160212 MW; 2FC7B7AA8E5DCAA8 CRC64;
MKTKAGKQKK RSVDSDDDVS RERRPKRATS GTNFKEKSLR FSEKYETVEA KKEQIVGDDE
KEEKGVRFQS FGRVENWTIS GYEDGSPVIW ISTVIADYDC RKPSKKYKKL YDYFFEKACA
CVEVCKNLST NPDTSLKELL AAVVRSMNGR KIFSSGGVIQ EFVISQGEFI YNQLAGLDET
SKNHETKFVD NRVLVSLRDE SRKIHKAFSN VALRIDESKV LTSDQLMDGG EDEDLKYAKL
LQEEEHMKSM DRSRNKRSST TSAPNKFYIK INEDEIAHDY PLPSYYKNTK DETDELVLFN
AGYAVDARNL PCRTLHNWAL YNSDLMLISL EFLPMKPCAD IDVTYLGQIK EWKIDFGEDM
IFVLLRTDMA WYRLGKPSEQ YAPWFEPILK TVRIGTSILA LLKNETRMAK LSYTDVIKRL
CGLEENDQAY ISSTFFDVER YVIVHGQIIL QFLTECPDEY IKRCPFVTGL ASKMQDRHHT
KWIIKKKRKM LQKGENLNLR RGKAPKVSKM KAMQATTTRL INRIWGEFYS IYSPEDPLEE
IGAEEEFEEV EDVEEEDENE EEDTIQKAIE VQKADTLKKI RGSCKEMEIR WEGEILGETC
AGEPLYGQAL VGGRKMDVGG AVILEVDDQG ETPLIYFVEY MFESSDNSKK LHGKLLQRGS
ETVLGTAANE RELFLTNECL TVQLKDIKGT VSFEIRSRPW GHQYKKEHMA ADKLDRARAE
ERKAKDLPIE YYCKSLYSPE KGGFFSLPRS DMGLGSGFCS SCKIRENEEE RSKTKLNDSK
TRFLSNGIKY SVGDFVYQIP NYLSKDRGKR RPVFKYGRNV GLRAFVVCQI LDIVDLKEPK
KGNTTSFEVK VRRFYRPDDV SAEEAYASDI QEVYYSEDTY ILPPEAIKGK CEVMKKTDMP
LCREYPILDH VYFCDRFYDS SNGCLKKLPY NMMLKFSTIK DDTLLREKKT ETGSAMLLKP
DEVPKGKRLA TLDIFAGCGG LSYGLEKAGV SDTKWAIEYE EPAAQAFKQN HPKTTVFVDN
CNVILRISWL RLLINDRAIM EKCGDVDDCI STTEAAELAT KLDENQKSTL PLPGQVDFIS
GGPPCQGFSR LNRFSDGSWS KNQCQMILAF LSFADYFRPK YFLLENVKTF VSFNEGHTFH
LTVASLLEMG YQVRFGLLEA GAYGISQPRK RAFIWAAAPN EVLPEWPEPM HVFNNPGFKI
PLSQGLHYAA VQSTKFGAPF RSITVRDAIG DLPPIESGES KINKEEMRGS MTVLTDHICK
KMNELNLIRC KKIPKTPGAD WRDLPDEHVN LSNGIVKNIV PNLLNKAKDH NGYKGLYGRL
DWHGNLPTCI TNLQPMGLVG MCFHPDQDRI ISVRECARSQ GFPDSYKFSG NIKDKHRQVG
NAVPPPLAFA LGRKLKEALH LRNI
