DNMT4_ARATH
ID DNMT4_ARATH Reviewed; 1519 AA.
AC O23273; F4JUL5; Q9SEG3;
DT 03-SEP-2014, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 03-AUG-2022, entry version 157.
DE RecName: Full=DNA (cytosine-5)-methyltransferase 4;
DE EC=2.1.1.37;
DE AltName: Full=DNA methyltransferase 4;
DE AltName: Full=DNA methyltransferase IIa;
DE Short=DMT02;
DE Short=MET02;
GN Name=MET4; Synonyms=DMT2, MET2, METIIa; OrderedLocusNames=At4g14140;
GN ORFNames=dl3110w;
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 [GENOMIC DNA], TISSUE SPECIFICITY, AND 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 [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=9461215; DOI=10.1038/35140;
RA Bevan M., Bancroft I., Bent E., Love K., Goodman H.M., Dean C.,
RA Bergkamp R., Dirkse W., van Staveren M., Stiekema W., Drost L., Ridley P.,
RA Hudson S.-A., Patel K., Murphy G., Piffanelli P., Wedler H., Wedler E.,
RA Wambutt R., Weitzenegger T., Pohl T., Terryn N., Gielen J., Villarroel R.,
RA De Clercq R., van Montagu M., Lecharny A., Aubourg S., Gy I., Kreis M.,
RA Lao N., Kavanagh T., Hempel S., Kotter P., Entian K.-D., Rieger M.,
RA Schaefer M., Funk B., Mueller-Auer S., Silvey M., James R., Monfort A.,
RA Pons A., Puigdomenech P., Douka A., Voukelatou E., Milioni D.,
RA Hatzopoulos P., Piravandi E., Obermaier B., Hilbert H., Duesterhoeft A.,
RA Moores T., Jones J.D.G., Eneva T., Palme K., Benes V., Rechmann S.,
RA Ansorge W., Cooke R., Berger C., Delseny M., Voet M., Volckaert G.,
RA Mewes H.-W., Klosterman S., Schueller C., Chalwatzis N.;
RT "Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis
RT thaliana.";
RL Nature 391:485-488(1998).
RN [3]
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 [4]
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 [5]
RP UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-583, AND IDENTIFICATION BY
RP MASS SPECTROMETRY.
RX PubMed=19292762; DOI=10.1111/j.1365-313x.2009.03862.x;
RA Saracco S.A., Hansson M., Scalf M., Walker J.M., Smith L.M., Vierstra R.D.;
RT "Tandem affinity purification and mass spectrometric analysis of
RT ubiquitylated proteins in Arabidopsis.";
RL Plant J. 59:344-358(2009).
RN [6]
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). {ECO:0000250}.
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 -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=O23273-1; Sequence=Displayed;
CC Name=2;
CC IsoId=O23273-2; Sequence=VSP_055401;
CC -!- TISSUE SPECIFICITY: Expressed at low levels in vegetative and floral
CC organs. {ECO:0000269|PubMed:10579493}.
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=AAF14882.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AF138283; AAF14882.1; ALT_INIT; Genomic_DNA.
DR EMBL; Z97335; CAB10193.1; -; Genomic_DNA.
DR EMBL; AL161538; CAB78456.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE83379.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE83380.1; -; Genomic_DNA.
DR EMBL; CP002687; ANM66066.1; -; Genomic_DNA.
DR PIR; G71402; G71402.
DR RefSeq; NP_001190725.1; NM_001203796.1. [O23273-2]
DR RefSeq; NP_001319931.1; NM_001340902.1. [O23273-1]
DR RefSeq; NP_193150.1; NM_117491.1. [O23273-1]
DR AlphaFoldDB; O23273; -.
DR SMR; O23273; -.
DR BioGRID; 12349; 1.
DR STRING; 3702.AT4G14140.2; -.
DR iPTMnet; O23273; -.
DR PaxDb; O23273; -.
DR PRIDE; O23273; -.
DR ProteomicsDB; 220528; -. [O23273-1]
DR EnsemblPlants; AT4G14140.1; AT4G14140.1; AT4G14140. [O23273-1]
DR EnsemblPlants; AT4G14140.2; AT4G14140.2; AT4G14140. [O23273-2]
DR EnsemblPlants; AT4G14140.3; AT4G14140.3; AT4G14140. [O23273-1]
DR GeneID; 827052; -.
DR Gramene; AT4G14140.1; AT4G14140.1; AT4G14140. [O23273-1]
DR Gramene; AT4G14140.2; AT4G14140.2; AT4G14140. [O23273-2]
DR Gramene; AT4G14140.3; AT4G14140.3; AT4G14140. [O23273-1]
DR KEGG; ath:AT4G14140; -.
DR Araport; AT4G14140; -.
DR TAIR; locus:2129450; AT4G14140.
DR eggNOG; ENOG502QPKK; Eukaryota.
DR HOGENOM; CLU_002247_0_0_1; -.
DR OMA; RIENWAL; -.
DR OrthoDB; 898916at2759; -.
DR PhylomeDB; O23273; -.
DR PRO; PR:O23273; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; O23273; baseline and differential.
DR Genevisible; O23273; 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:0009294; P:DNA-mediated transformation; 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 Alternative splicing; Chromatin regulator; DNA-binding; Isopeptide bond;
KW Methyltransferase; Nucleus; Reference proteome; Repeat;
KW S-adenosyl-L-methionine; Transferase; Ubl conjugation.
FT CHAIN 1..1519
FT /note="DNA (cytosine-5)-methyltransferase 4"
FT /id="PRO_0000430013"
FT DOMAIN 715..849
FT /note="BAH 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00370"
FT DOMAIN 916..1033
FT /note="BAH 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00370"
FT DOMAIN 1078..1512
FT /note="SAM-dependent MTase C5-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01016"
FT REGION 1..31
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 641..668
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 1183
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01016,
FT ECO:0000255|PROSITE-ProRule:PRU10018"
FT CROSSLNK 583
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in ubiquitin)"
FT /evidence="ECO:0000269|PubMed:19292762"
FT VAR_SEQ 1099..1135
FT /note="VSTTKWAIEYEEPAGHAFKQNHPEATVFVDNCNVILR -> MYLYSHVMHIL
FT LSSKHLKTFIKMHVLCNKVYLLQSGRSSMKSQLVMRLNKTILKQRFLLTTAM (in
FT isoform 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_055401"
SQ SEQUENCE 1519 AA; 171586 MW; 8BD760A15FA90DA4 CRC64;
MEMETKAGKQ KKRSVDSDDD VSKERRPKRA AACTNFKEKS LRISDKSETV EAKKEQILAE
EIVAIQLTSS LESNDDPRPN RRLTDFVLHD SEGVPQPVEM LELGDIFIEG VVLPLGDEKK
EEKGVRFQSF GRVENWNISG YEDGSPVIWI STALADYDCR KPSKKYKKLY DYFFEKACAC
VEVFKSLSKN PDTSLDELLA AVSRSMSGSK IFSSGGAIQE FVISQGEFIY NQLAGLDETA
KNHETCFVEN RVLVSLRDHE SNKIHKALSN VALRIDESKV VTSDHLVDGA EDEDVKYAKL
IQEEEYRKSM ERSRNKRSST TSGGSSRFYI KISEDEIADD YPLPSYYKNT KEETDELVLF
EAGYEVDTRD LPCRTLHNWT LYNSDSRMIS LEVLPMRPCA EIDVTVFGSG VVAEDDGSGF
CLDDSESSTS TQSNDHDGMN IFLSQIKEWM IEFGAEMIFV TLRTDMAWYR LGKPSKQYAP
WFGTVMKTVR VGISIFNMLM RESRVAKLSY ANVIKRLCGL EENDKAYISS KLLDVERYVV
VHGQIILQLF EEYPDKDIKR CPFVTSLASK MQDIHHTKWI IKKKKKILQK GKNLNPRAGI
APVVSRMKAM QATTTRLVNR IWGEFYSIYS PEVPSEAINA ENVEEEELEE VEEEDENEED
DPEENELEAV EIQNSPTPKK IKGISEDMEI KWDGEILGKT SAGEPLYGRA FVGGDVVVVG
SAVILEVDDQ DDTQLICFVE FMFESSNHSK MLHGKLLQRG SETVLGMAAN ERELFLTNEC
LTVQLKDIKG TVSLEIRSRL WGHQYRKENI DVDKLDRARA EERKTNGLPT DYYCKSLYSP
ERGGFFSLPR NDMGLGSGFC SSCKIRENEE ERSKTKLNDS KTGFLSNGIE YHNGDFVYVL
PNYITKDGLK KGSRRTTLKC GRNVGLKAFV VCQLLDVIVL EESRKASKAS FQVKLTRFYR
PEDISEEKAY ASDIQELYYS QDTYILPPEA IQGKCEVRKK SDMPLCREYP ILDHIFFCEV
FYDSSTGYLK QFPANMKLKF STIKDETLLR EKKGKGVETG TSSGMLMKPD EVPKEKPLAT
LDIFAGCGGL SHGLENAGVS TTKWAIEYEE PAGHAFKQNH PEATVFVDNC NVILRAIMEK
CGDVDDCVST VEAAELAAKL DENQKSTLPL PGQVDFINGG PPCQGFSGMN RFSHGSWSKV
QCEMILAFLS FADYFRPKYF LLENVKKFVT YNKGRTFQLT MASLLEMGYQ VRFGILEAGT
YGVSQPRKRV IIWAASPEEV LPEWPEPMHV FDNPGSKISL PRGLRYDAGC NTKFGAPFRS
ITVRDTIGDL PPVENGESKI NKEYGTTPAS WFQKKIRGNM SVLTDHICKG LNELNLIRCK
KIPKRPGADW RDLPDENVTL SNGLVEKLRP LALSKTAKNH NEWKGLYGRL DWQGNLPISI
TDPQPMGKVG MCFHPEQDRI ITVRECARSQ GFPDSYEFSG TTKHKHRQIG NAVPPPLAFA
LGRKLKEALY LKSSLQHQS
