ID DNM1A_ORYSJ Reviewed; 1527 AA. AC Q7Y1I7; A0A0P0W479; Q0DMQ5; Q10C15; Q8S4C3; DT 01-SEP-2009, integrated into UniProtKB/Swiss-Prot. DT 01-OCT-2003, sequence version 1. DT 24-JAN-2024, entry version 108. DE RecName: Full=DNA (cytosine-5)-methyltransferase 1A {ECO:0000303|PubMed:18281124}; DE Short=OsMET1a {ECO:0000303|PubMed:18281124}; DE EC=2.1.1.37 {ECO:0000255|PROSITE-ProRule:PRU01016}; DE AltName: Full=DNA methyltransferase 1-1 {ECO:0000303|PubMed:14513380}; DE Short=OsMET1-1 {ECO:0000303|PubMed:14513380}; GN Name=MET1A {ECO:0000303|PubMed:18281124}; GN Synonyms=MET1-1 {ECO:0000303|PubMed:14513380}; GN OrderedLocusNames=Os03g0798300 {ECO:0000312|EMBL:BAS86863.1}, GN LOC_Os03g58400 {ECO:0000312|EMBL:ABF99362.1}; GN ORFNames=OsJ_12965 {ECO:0000312|EMBL:EEE60102.1}, OSJNBa0094F01.4 GN {ECO:0000312|EMBL:AAP44671.1}; 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 [GENOMIC DNA], FUNCTION, AND TISSUE SPECIFICITY. RC STRAIN=cv. Nipponbare; RX PubMed=14513380; DOI=10.1007/s00425-003-1112-6; RA Teerawanichpan P., Chandrasekharan M.B., Jiang Y., Narangajavana J., RA Hall T.C.; RT "Characterization of two rice DNA methyltransferase genes and RNAi-mediated RT reactivation of a silenced transgene in rice callus."; RL Planta 218:337-349(2004). RN [2] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND TISSUE SPECIFICITY. RC STRAIN=cv. Nipponbare; RX PubMed=18281124; DOI=10.1016/j.jplph.2007.12.003; RA Yamauchi T., Moritoh S., Johzuka-Hisatomi Y., Ono A., Terada R., RA Nakamura I., Iida S.; RT "Alternative splicing of the rice OsMET1 genes encoding maintenance DNA RT methyltransferase."; RL J. Plant Physiol. 165:1774-1782(2008). RN [3] 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 [4] 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 [5] 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 [6] 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 [7] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=cv. Nipponbare; RX PubMed=15685292; DOI=10.1371/journal.pbio.0030038; RA Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S., RA Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L., RA Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J., RA Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X., RA Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y., RA Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L., RA Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H., RA Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z., RA Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L., RA Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F., RA Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q., RA Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J., RA Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M., RA McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.; RT "The genomes of Oryza sativa: a history of duplications."; RL PLoS Biol. 3:266-281(2005). RN [8] RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1115-1527. RC STRAIN=cv. Nipponbare; RX PubMed=12869764; DOI=10.1126/science.1081288; RG The rice full-length cDNA consortium; RT "Collection, mapping, and annotation of over 28,000 cDNA clones from RT japonica rice."; RL Science 301:376-379(2003). RN [9] RP FUNCTION, TISSUE SPECIFICITY, AND DISRUPTION PHENOTYPE. RX PubMed=24535433; DOI=10.1007/s11103-014-0178-9; RA Yamauchi T., Johzuka-Hisatomi Y., Terada R., Nakamura I., Iida S.; RT "The MET1b gene encoding a maintenance DNA methyltransferase is RT indispensable for normal development in rice."; RL Plant Mol. Biol. 85:219-232(2014). CC -!- FUNCTION: Probably methylates CpG residues and maintains DNA CC methylation (PubMed:14513380, PubMed:24535433). May be involved in CC methylation-dependent gene silencing (PubMed:14513380). May play a CC minor role in the maintenance of DNA methylation (PubMed:24535433). CC {ECO:0000269|PubMed:14513380, ECO:0000269|PubMed:24535433}. 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=Q7Y1I7-1; Sequence=Displayed; CC Name=2; CC IsoId=Q7Y1I7-2; Sequence=VSP_037849, VSP_037850; CC -!- TISSUE SPECIFICITY: Expressed in roots and inflorescences CC (PubMed:14513380). Expressed in roots, panicles, anthers, pistils, CC endosperm and imbibed embryos (PubMed:18281124). Expressed in tissues CC containing actively replicating and dividing cells, such as shoot and CC root meristems (PubMed:24535433). {ECO:0000269|PubMed:14513380, CC ECO:0000269|PubMed:18281124, ECO:0000269|PubMed:24535433}. CC -!- DISRUPTION PHENOTYPE: No visible phenotype under normal growth CC conditions. {ECO:0000269|PubMed:24535433}. 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=ABF99362.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; CC Sequence=BAF13483.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; CC Sequence=BAG98259.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR EMBL; AF462029; AAL77415.1; -; Genomic_DNA. DR EMBL; AB362510; BAG15928.1; -; Genomic_DNA. DR EMBL; AC093713; AAP44671.1; -; Genomic_DNA. DR EMBL; DP000009; ABF99362.1; ALT_SEQ; Genomic_DNA. DR EMBL; AP008209; BAF13483.1; ALT_SEQ; Genomic_DNA. DR EMBL; AP014959; BAS86863.1; -; Genomic_DNA. DR EMBL; AP014959; BAS86864.1; -; Genomic_DNA. DR EMBL; CM000140; EEE60102.1; -; Genomic_DNA. DR EMBL; AK108034; BAG98259.1; ALT_INIT; mRNA. DR RefSeq; XP_015628331.1; XM_015772845.1. DR RefSeq; XP_015628332.1; XM_015772846.1. DR RefSeq; XP_015628333.1; XM_015772847.1. [Q7Y1I7-1] DR AlphaFoldDB; Q7Y1I7; -. DR SMR; Q7Y1I7; -. DR STRING; 39947.Q7Y1I7; -. DR REBASE; 7658; M.OsaDnmt1A. DR PaxDb; 39947-Q7Y1I7; -. DR EnsemblPlants; Os03t0798300-01; Os03t0798300-01; Os03g0798300. [Q7Y1I7-2] DR EnsemblPlants; Os03t0798300-02; Os03t0798300-02; Os03g0798300. [Q7Y1I7-1] DR EnsemblPlants; Os03t0798300-03; Os03t0798300-03; Os03g0798300. [Q7Y1I7-1] DR EnsemblPlants; Os03t0798300-04; Os03t0798300-04; Os03g0798300. [Q7Y1I7-1] DR GeneID; 4334435; -. DR Gramene; Os03t0798300-01; Os03t0798300-01; Os03g0798300. [Q7Y1I7-2] DR Gramene; Os03t0798300-02; Os03t0798300-02; Os03g0798300. [Q7Y1I7-1] DR Gramene; Os03t0798300-03; Os03t0798300-03; Os03g0798300. [Q7Y1I7-1] DR Gramene; Os03t0798300-04; Os03t0798300-04; Os03g0798300. [Q7Y1I7-1] DR KEGG; osa:4334435; -. DR eggNOG; ENOG502QPKK; Eukaryota. DR HOGENOM; CLU_006958_2_3_1; -. DR InParanoid; Q7Y1I7; -. DR OrthoDB; 317994at2759; -. DR BRENDA; 2.1.1.37; 4460. DR Proteomes; UP000000763; Chromosome 3. DR Proteomes; UP000007752; 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; ISS:UniProtKB. DR GO; GO:0006346; P:DNA methylation-dependent heterochromatin formation; IMP:GO_Central. DR GO; GO:0044027; P:negative regulation of gene expression via CpG island methylation; ISS:UniProtKB. DR CDD; cd04708; BAH_plantDCM_II; 1. DR Gene3D; 2.30.30.490; -; 2. DR Gene3D; 3.90.120.10; DNA Methylase, subunit A, domain 2; 2. 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; IPR031303; C5_meth_CS. DR InterPro; IPR022702; Cytosine_MeTrfase1_RFD. DR InterPro; IPR017198; DNMT1-like. DR InterPro; IPR029063; SAM-dependent_MTases_sf. DR NCBIfam; TIGR00675; dcm; 1. DR PANTHER; PTHR10629; CYTOSINE-SPECIFIC METHYLTRANSFERASE; 1. DR PANTHER; PTHR10629:SF52; DNA (CYTOSINE-5)-METHYLTRANSFERASE 1; 1. DR Pfam; PF01426; BAH; 2. DR Pfam; PF00145; DNA_methylase; 1. DR Pfam; PF12047; DNMT1-RFD; 2. DR PIRSF; PIRSF037404; DNMT1; 1. DR PRINTS; PR00105; C5METTRFRASE. DR SMART; SM00439; BAH; 2. DR SUPFAM; SSF53335; S-adenosyl-L-methionine-dependent methyltransferases; 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. DR Genevisible; Q7Y1I7; OS. PE 2: Evidence at transcript level; KW Alternative splicing; DNA-binding; Methyltransferase; Nucleus; KW Reference proteome; Repeat; S-adenosyl-L-methionine; Transferase. FT CHAIN 1..1527 FT /note="DNA (cytosine-5)-methyltransferase 1A" FT /id="PRO_0000381939" FT DOMAIN 742..874 FT /note="BAH 1" FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00370" FT DOMAIN 910..1049 FT /note="BAH 2" FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00370" FT DOMAIN 1092..1526 FT /note="SAM-dependent MTase C5-type" FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01016" FT REGION 1..62 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT REGION 661..718 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 17..42 FT /note="Basic and acidic residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 669..690 FT /note="Acidic residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT ACT_SITE 1197 FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01016" FT VAR_SEQ 1..5 FT /note="Missing (in isoform 2)" FT /evidence="ECO:0000305" FT /id="VSP_037849" FT VAR_SEQ 6..11 FT /note="RSVVTT -> MDTCLY (in isoform 2)" FT /evidence="ECO:0000305" FT /id="VSP_037850" SQ SEQUENCE 1527 AA; 170856 MW; 75159928CDDCF098 CRC64; MAKSPRSVVT TGTKRRRAKV HKEDEPVENE NLESEFDVSK KESNGATEPG NEPVASKRPK RAAACSNFKE KSLDLSEKDS IITIKESRVE EKEIEAVNLT RTGPEDGQPC RKIIDFILHD GDGNLQPFEM SEVDDIFITA LIMPLDDDLE KDRGKGICCS GFGRIENWAI SGYDEGAAVI WVSTETSDYK CVKPASSYRS YFEHFSEKAR VCVEVYKKLA RSVGGNPQVD LEELIAGVVR SINSNRSFNG TVTKDFVISS GEFIYKQLIG LDHTAGNDDE MLATLPVLVA LKDECKSRAG FTHLPAMPSN GTLRIKDGQD KGLTEDEDAK LARLLQEEEE WKMMKQRGKR GTSQKNIYIK ICETEIANDY PLPAYYKPYN QEMDEYIFDS DIGMYSDDVP VRILDNWALY NSDSRLISLE LIPMKAGAEN DIVVFGSGFM REDDGSCCST AELAQLHSSS SKSGREDPGV PIYLSPIKEW VVEFGGSMIC ITIRTDVAWY KLRQPTKQYA PWCEPVLKTA RLAVSIITLL KEQSRASKLS FAEVIKKVAE FDSRHPAFIS SKAPTVERYV VVHGQIILQQ FADFPDESVK RCAFITGLLA KMEESRHTKL AIKKKSQQMR GENLNPSAKM GPILRKKLMR ATTTMLISKI WGEYYATYFP GDTKEEDQNE PKEIDDDQEE NEDNDAEEEV NVQDEKATRT PPSTRSRKSS ADTRKEIKWE GQTAGKTVSG EVLYKCVIVQ DLSISVGATV TTEDDSGETI MCFVEYMYEK LDGKNMIHGI ILQEGSQTVL GNAANDREVF LTNDCLEFEA SDIKELVTVN IQSLPWGHKY RKENSEAKRI EKAKAEERKR KGLPVEYICK SLYWPEKGGF FSLPYDKIGN GTGICSSCER KPVGNEFKLL SESSFVFENI TYNIHDFLYI RPEFFSQGEG HETYKAGRNV GLKPYAVCHL LSVHGPAGSR KANPESTKVK VRRFYRPDDI SSTKAYSSDI REVYYSEDII SVPVVMIEGK CEVRLKDDLP NSDLPAVVEH VFCCEYLYDP ANGALKQLPP NVRLVTLTRK VPASKKNKGK QICDIELGGS DKPKDGQSEN CLATLDIFAG CGGLSEGLQR SGLSLTKWAI EYEEPAGDAF GENHPEAAVF VENCNVILKA IMDKCGDSDD CISTSEAAER AAKLSEDKIK NLPVPGEVEF INGGPPCQGF SGMNRFNQSP WSKVQCEMIL AFLSFAEYFR PRFFLLENVR NFVSFNKGQT FRLTLASLLE MGYQVRFGIL EAGAYGVAQS RKRAFIWAAA PGETLPEWPE PMHVFASPEL KITLPDGKFY AAVKSTAAGA PFRSITVRDT IGDLPAVENG AGKPTIQYGS GPVSWFQKKI RSDMASLNDH ISKEMNELNL IRCKHIPKRP GCDWHDLPDE KVKLSTGQMV DLIPWCLPNT AKRHNQWKGL YGRLDWEGNF PTSVTDPQPM GKVGMCFHPE QDRIITVREC ARSQGFPDSY RFAGNIQNKH RQIGNAVPPP LAYALGRKLK QAIDAKR //