DNM1A_ORYSJ
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 03-AUG-2022, entry version 101.
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},
GN OSJNBa0094F01.4 {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};
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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. [Q7Y1I7-1]
DR RefSeq; XP_015628333.1; XM_015772847.1. [Q7Y1I7-1]
DR AlphaFoldDB; Q7Y1I7; -.
DR SMR; Q7Y1I7; -.
DR STRING; 4530.OS03T0798300-01; -.
DR REBASE; 7658; M.OsaDnmt1A.
DR PaxDb; Q7Y1I7; -.
DR PRIDE; 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; 898916at2759; -.
DR BRENDA; 2.1.1.37; 4460.
DR Proteomes; UP000000763; Chromosome 3.
DR Proteomes; UP000007752; Chromosome 3.
DR Proteomes; UP000059680; Chromosome 3.
DR Genevisible; Q7Y1I7; OS.
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:0010424; P:DNA methylation on cytosine within a CG sequence; ISS:UniProtKB.
DR GO; GO:0006346; P:DNA methylation-dependent heterochromatin assembly; IMP:GO_Central.
DR GO; GO:0010216; P:maintenance of DNA methylation; ISS:UniProtKB.
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; 1.
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 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
