ID   DNM1B_ORYSJ             Reviewed;        1529 AA.
AC   B1Q3J6; A0A0P0X2V1; B1Q3J7; Q0D857; Q69W70; Q7PC77;
DT   01-SEP-2009, integrated into UniProtKB/Swiss-Prot.
DT   20-MAY-2008, sequence version 1.
DT   27-MAR-2024, entry version 83.
DE   RecName: Full=DNA (cytosine-5)-methyltransferase 1B {ECO:0000303|PubMed:18281124};
DE            Short=OsMET1b {ECO:0000303|PubMed:18281124};
DE            EC=2.1.1.37 {ECO:0000255|PROSITE-ProRule:PRU01016};
DE   AltName: Full=DNA methyltransferase 1-2 {ECO:0000303|PubMed:14513380};
DE            Short=OsMET1-2 {ECO:0000303|PubMed:14513380};
GN   Name=MET1B; Synonyms=MET1-2 {ECO:0000303|PubMed:14513380};
GN   OrderedLocusNames=Os07g0182900 {ECO:0000312|EMBL:BAT00335.1},
GN   LOC_Os07g08500 {ECO:0000305};
GN   ORFNames=OJ1506_G02.17 {ECO:0000312|EMBL:BAD30340.1};
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], TISSUE SPECIFICITY, AND ALTERNATIVE
RP   SPLICING.
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   [2]
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   [3]
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   [4]
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   [5]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1085-1529.
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   [6]
RP   IDENTIFICATION, AND TISSUE SPECIFICITY.
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   [7]
RP   INDUCTION.
RX   PubMed=19788421; DOI=10.1111/j.1742-4658.2009.07338.x;
RA   Sharma R., Mohan Singh R.K., Malik G., Deveshwar P., Tyagi A.K., Kapoor S.,
RA   Kapoor M.;
RT   "Rice cytosine DNA methyltransferases - gene expression profiling during
RT   reproductive development and abiotic stress.";
RL   FEBS J. 276:6301-6311(2009).
RN   [8]
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).
RN   [9]
RP   FUNCTION, AND DISRUPTION PHENOTYPE.
RX   PubMed=25002488; DOI=10.1073/pnas.1410761111;
RA   Hu L., Li N., Xu C., Zhong S., Lin X., Yang J., Zhou T., Yuliang A., Wu Y.,
RA   Chen Y.R., Cao X., Zemach A., Rustgi S., von Wettstein D., Liu B.;
RT   "Mutation of a major CG methylase in rice causes genome-wide
RT   hypomethylation, dysregulated genome expression, and seedling lethality.";
RL   Proc. Natl. Acad. Sci. U.S.A. 111:10642-10647(2014).
CC   -!- FUNCTION: Major CG methylase that methylates chromatin CpG residues and
CC       maintains DNA methylation (PubMed:24535433, PubMed:25002488). Plays a
CC       major role in genomic imprinting, regulation of embryogenesis and seed
CC       viability (PubMed:24535433, PubMed:25002488). Maintains DNA methylation
CC       at the FIE1 gene locus in the embryo (PubMed:24535433).
CC       {ECO:0000269|PubMed:24535433, ECO:0000269|PubMed:25002488}.
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:0000250}.
CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative splicing; Named isoforms=3;
CC       Name=1;
CC         IsoId=B1Q3J6-1; Sequence=Displayed;
CC       Name=2;
CC         IsoId=B1Q3J6-2; Sequence=VSP_037852, VSP_037853;
CC       Name=3;
CC         IsoId=B1Q3J6-3; Sequence=VSP_037851;
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   -!- INDUCTION: Induced by salt stress, cold stress and drought stress.
CC       {ECO:0000269|PubMed:19788421}.
CC   -!- DISRUPTION PHENOTYPE: Non-viable and shrunk seeds, and embryonic
CC       lethality when homozygous. {ECO:0000269|PubMed:24535433,
CC       ECO:0000269|PubMed:25002488}.
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=AK111461; Type=Frameshift; Evidence={ECO:0000305};
CC       Sequence=BAD30340.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC       Sequence=BAF20966.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR   EMBL; AB362511; BAG15929.1; -; Genomic_DNA.
DR   EMBL; AB362511; BAG15930.1; -; Genomic_DNA.
DR   EMBL; AP003835; BAD30340.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; AP008213; BAF20966.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; AP014963; BAT00335.1; -; Genomic_DNA.
DR   EMBL; AP014963; BAT00336.1; -; Genomic_DNA.
DR   EMBL; AP014963; BAT00337.1; -; Genomic_DNA.
DR   EMBL; AK111461; -; NOT_ANNOTATED_CDS; mRNA.
DR   EMBL; BK001405; DAA01513.1; -; Genomic_DNA.
DR   RefSeq; XP_015645008.1; XM_015789522.1.
DR   RefSeq; XP_015645009.1; XM_015789523.1. [B1Q3J6-1]
DR   AlphaFoldDB; B1Q3J6; -.
DR   SMR; B1Q3J6; -.
DR   STRING; 39947.B1Q3J6; -.
DR   REBASE; 7659; M.OsaDnmt1B.
DR   PaxDb; 39947-B1Q3J6; -.
DR   EnsemblPlants; Os07t0182900-01; Os07t0182900-01; Os07g0182900. [B1Q3J6-2]
DR   EnsemblPlants; Os07t0182900-02; Os07t0182900-02; Os07g0182900. [B1Q3J6-1]
DR   EnsemblPlants; Os07t0182900-03; Os07t0182900-03; Os07g0182900. [B1Q3J6-1]
DR   EnsemblPlants; Os07t0182900-04; Os07t0182900-04; Os07g0182900. [B1Q3J6-1]
DR   EnsemblPlants; Os07t0182900-05; Os07t0182900-05; Os07g0182900. [B1Q3J6-3]
DR   EnsemblPlants; Os07t0182900-06; Os07t0182900-06; Os07g0182900. [B1Q3J6-3]
DR   GeneID; 4342575; -.
DR   Gramene; Os07t0182900-01; Os07t0182900-01; Os07g0182900. [B1Q3J6-2]
DR   Gramene; Os07t0182900-02; Os07t0182900-02; Os07g0182900. [B1Q3J6-1]
DR   Gramene; Os07t0182900-03; Os07t0182900-03; Os07g0182900. [B1Q3J6-1]
DR   Gramene; Os07t0182900-04; Os07t0182900-04; Os07g0182900. [B1Q3J6-1]
DR   Gramene; Os07t0182900-05; Os07t0182900-05; Os07g0182900. [B1Q3J6-3]
DR   Gramene; Os07t0182900-06; Os07t0182900-06; Os07g0182900. [B1Q3J6-3]
DR   KEGG; osa:4342575; -.
DR   eggNOG; ENOG502QPKK; Eukaryota.
DR   HOGENOM; CLU_006958_2_3_1; -.
DR   InParanoid; B1Q3J6; -.
DR   OrthoDB; 317994at2759; -.
DR   BRENDA; 2.1.1.37; 4460.
DR   Proteomes; UP000000763; Chromosome 7.
DR   Proteomes; UP000059680; Chromosome 7.
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:0009793; P:embryo development ending in seed dormancy; IMP:UniProtKB.
DR   GO; GO:0071514; P:genomic imprinting; IMP:UniProtKB.
DR   GO; GO:0044027; P:negative regulation of gene expression via CpG island methylation; IMP: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:SF58; DNA (CYTOSINE-5)-METHYLTRANSFERASE 1B; 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; B1Q3J6; 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..1529
FT                   /note="DNA (cytosine-5)-methyltransferase 1B"
FT                   /id="PRO_0000381940"
FT   DOMAIN          741..873
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          1093..1527
FT                   /note="SAM-dependent MTase C5-type"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01016"
FT   REGION          1..56
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          674..706
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        18..39
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        674..691
FT                   /note="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   VAR_SEQ         1..43
FT                   /note="Missing (in isoform 3)"
FT                   /evidence="ECO:0000305"
FT                   /id="VSP_037851"
FT   VAR_SEQ         1..32
FT                   /note="Missing (in isoform 2)"
FT                   /evidence="ECO:0000305"
FT                   /id="VSP_037852"
FT   VAR_SEQ         33..43
FT                   /note="LDEGPLDATKE -> MLSCGVFRKEK (in isoform 2)"
FT                   /evidence="ECO:0000305"
FT                   /id="VSP_037853"
FT   CONFLICT        923
FT                   /note="D -> E (in Ref. 1; DAA01513)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   1529 AA;  171908 MW;  F7471690926042C6 CRC64;
     MVKSPCSPVT TGKKRCRAKP QKKDEDTTDK GKLDEGPLDA TKEMNGVGKG DSRAACKRPR
     RAAACSDFKE KSVRLSDKSS VVATNGNKME EEEMDAVKLT KLGPEVQRPC RKLIDFILHD
     ADGKLQPFEM SEIDDFFITA LIMPMDDDLE KDRQKGVRCE GFGRIEDWAI SGYDEGTAVV
     WVSTEVADYE CVKPAGNYKS YYDHFYEKAQ VCVEVYRKLA RSVGGNPNLG LEELLASVVR
     SINAIKGYSG TLSKDFVISN GEFVYNQLIG LDETANTDDE KFATLPVLLA LRDGCKSRVE
     VSKLQPNISN GSLKINDAEC KEVSEDDDEK LARLLQQEEE WKMMKQRGKR GTTSQKNVYI
     KISEAEIAND YPLPAYYKPS SQEMDEYIFD SEDSFYSDVP VRILNNWALY NADSRLIPLE
     LIPMKAGAEN DIVVFGSGFM REDDGSCCST AESAKLSSSS SSNHQDAGVS IYLSPIKEWV
     IEFGGSMICI TIRTDVAWYK LRQPTKQYAP WCEPVLKTAR LSVSIITLLK EQSRASKLSF
     ADVIKKVAEF DKGSPAFVSS NVALVERYIV VHGQIILQQF SDFPDETIRR SAFATGLLMK
     MEQRRHTKLV MKKKVQVMRG ENLNPSATMG PASRRKVMRA TTTRLINRIW SDYYTHHFPE
     DSKDADVNEA KEIDDELEEN EDEDAEEEAQ IEEENVSKTP PSTRSRKLVS QTCKEIRWEG
     EAIGKTPSGE ALYKCAYVRE LRINLGRTVA LEDDSGELVM CFVEYMFQKL NGAKMVHGRL
     LQKGSETVLG NAANERDLFL TNECLEFELE DIKELMSVNL QSLPWGHKYR KENAEADRIE
     RAKAEDRKKK GLPMEYLCKS LYWPEKGAFF SLPHDKLGLG NGFCSSCQQK EPDCDELQIL
     SKNSFIYRNI TYNVNDYLYI RPDFFSQEED RATFKGGRNV GLKPYVVCHL LDVHEPAGSR
     KIHPASTKIS VRRFYRPDDI SSAKAYVSDI REVYYSENIV KVPVDMIEGK CEVKKKIDIS
     NSDVPVMVEH EFFCEHFYDP ATGALKQLPP NVKLMSVQQK ATGALKKNKG KQICESDQVD
     SDKCTKVSKE NRLATLDIFA GCGGLSEGLQ QAGVSFTKWA IEYEEPAGEA FTKNHPEAAV
     FVDNCNVILK AIMDKCGDAD DCISTSEAAE QAAKFSQDNI MNLPVPGEVE FINGGPPCQG
     FSGMNRFNQS PWSKVQCEMI LAFLSFAEYF RPRFFLLENV RNFVSFNKGQ TFRLTVASLL
     EMGYQVRFGI LEAGTFGVAQ SRKRAFIWAA APGETLPDWP EPMHVFASPE LKINLPDGKY
     YAAAKSTAGG APFRAITVRD TIGDLPKVEN GASKLLLEYG GEPISWFQKK IRGNTIALND
     HISKEMNELN LIRCQRIPKR PGCDWHDLPD EKVKLSSGQL VDLIPWCLPN TAKRHNQWKG
     LYGRLDWEGN FPTSVTDPQP MGKVGMCFHP DQDRIITVRE CARSQGFPDN YQFAGNIQSK
     HRQIGNAVPP PLAFALGRKL KEAVDAKRQ
//