DNM1B_ORYSJ
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 03-AUG-2022, entry version 75.
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. [B1Q3J6-1]
DR RefSeq; XP_015645009.1; XM_015789523.1. [B1Q3J6-1]
DR AlphaFoldDB; B1Q3J6; -.
DR SMR; B1Q3J6; -.
DR STRING; 4530.OS07T0182900-01; -.
DR REBASE; 7659; M.OsaDnmt1B.
DR PaxDb; B1Q3J6; -.
DR PRIDE; 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; 898916at2759; -.
DR BRENDA; 2.1.1.37; 4460.
DR Proteomes; UP000000763; Chromosome 7.
DR Proteomes; UP000059680; Chromosome 7.
DR Genevisible; B1Q3J6; 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; IMP:UniProtKB.
DR GO; GO:0009793; P:embryo development ending in seed dormancy; IMP:UniProtKB.
DR GO; GO:0010216; P:maintenance of DNA methylation; IMP:UniProtKB.
DR GO; GO:0006349; P:regulation of gene expression by genomic imprinting; IMP: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..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
