CMT3_ORYSJ
ID CMT3_ORYSJ Reviewed; 907 AA.
AC C0SQ89; B9G594; Q0IZC8; Q33BI4; Q9AYI4;
DT 02-NOV-2016, integrated into UniProtKB/Swiss-Prot.
DT 26-MAY-2009, sequence version 1.
DT 03-AUG-2022, entry version 75.
DE RecName: Full=DNA (cytosine-5)-methyltransferase CMT3 {ECO:0000305};
DE EC=2.1.1.37 {ECO:0000305};
DE AltName: Full=Chromomethylase 3 {ECO:0000305};
DE AltName: Full=OsCMT3a {ECO:0000303|PubMed:26243209};
GN Name=CMT3 {ECO:0000305};
GN OrderedLocusNames=Os10g0104900 {ECO:0000312|EMBL:BAT09590.1},
GN LOC_Os10g01570 {ECO:0000312|EMBL:ABB46585.2};
GN ORFNames=OsJ_30466 {ECO:0000312|EMBL:EEE50451.1},
GN OSJNBa0071K19.14 {ECO:0000312|EMBL:AAL75760.1};
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 DISRUPTION PHENOTYPE.
RC STRAIN=cv. Nipponbare;
RX PubMed=26243209; DOI=10.1111/tpj.12952;
RA Cheng C., Tarutani Y., Miyao A., Ito T., Yamazaki M., Sakai H., Fukai E.,
RA Hirochika H.;
RT "Loss of function mutations in the rice chromomethylase OsCMT3a cause a
RT burst of transposition.";
RL Plant J. 83:1069-1081(2015).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12791992; DOI=10.1126/science.1083523;
RA Yu Y., Rambo T., Currie J., Saski C., Kim H.-R., Collura K., Thompson S.,
RA Simmons J., Yang T.-J., Nah G., Patel A.J., Thurmond S., Henry D.,
RA Oates R., Palmer M., Pries G., Gibson J., Anderson H., Paradkar M.,
RA Crane L., Dale J., Carver M.B., Wood T., Frisch D., Engler F.,
RA Soderlund C., Palmer L.E., Teytelman L., Nascimento L., De la Bastide M.,
RA Spiegel L., Ware D., O'Shaughnessy A., Dike S., Dedhia N., Preston R.,
RA Huang E., Ferraro K., Kuit K., Miller B., Zutavern T., Katzenberger F.,
RA Muller S., Balija V., Martienssen R.A., Stein L., Minx P., Johnson D.,
RA Cordum H., Mardis E., Cheng Z., Jiang J., Wilson R., McCombie W.R.,
RA Wing R.A., Yuan Q., Ouyang S., Liu J., Jones K.M., Gansberger K.,
RA Moffat K., Hill J., Tsitrin T., Overton L., Bera J., Kim M., Jin S.,
RA Tallon L., Ciecko A., Pai G., Van Aken S., Utterback T., Reidmuller S.,
RA Bormann J., Feldblyum T., Hsiao J., Zismann V., Blunt S., de Vazeille A.R.,
RA Shaffer T., Koo H., Suh B., Yang Q., Haas B., Peterson J., Pertea M.,
RA Volfovsky N., Wortman J., White O., Salzberg S.L., Fraser C.M., Buell C.R.,
RA Messing J., Song R., Fuks G., Llaca V., Kovchak S., Young S., Bowers J.E.,
RA Paterson A.H., Johns M.A., Mao L., Pan H., Dean R.A.;
RT "In-depth view of structure, activity, and evolution of rice chromosome
RT 10.";
RL Science 300:1566-1569(2003).
RN [3]
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 [4]
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 [5]
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 [6]
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 [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).
CC -!- FUNCTION: Involved in CpXpG DNA methylation. Plays a critical role in
CC the maintenance of CpXpG DNA methylation and suppression of a wide
CC spectrum of transposable element (TE) activities. Required for proper
CC plant development in reproductive stage. {ECO:0000269|PubMed:26243209}.
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:0000305};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305}.
CC -!- INDUCTION: Down-regulated by salt and dehydration stresses.
CC {ECO:0000269|PubMed:19788421}.
CC -!- DISRUPTION PHENOTYPE: Reduced overall plant height, early flowering and
CC reduced fertility. {ECO:0000269|PubMed:26243209}.
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=AAL75760.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=ABB46585.2; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=BAF25937.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=BAT09590.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AB360583; BAH37019.1; -; Genomic_DNA.
DR EMBL; AC069324; AAL75760.1; ALT_SEQ; Genomic_DNA.
DR EMBL; DP000086; ABB46585.2; ALT_SEQ; Genomic_DNA.
DR EMBL; AP008216; BAF25937.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AP014966; BAT09590.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CM000147; EEE50451.1; -; Genomic_DNA.
DR RefSeq; XP_015613201.1; XM_015757715.1.
DR AlphaFoldDB; C0SQ89; -.
DR SMR; C0SQ89; -.
DR STRING; 4530.OS10T0104900-01; -.
DR PRIDE; C0SQ89; -.
DR EnsemblPlants; Os10t0104900-01; Os10t0104900-01; Os10g0104900.
DR GeneID; 4347954; -.
DR Gramene; Os10t0104900-01; Os10t0104900-01; Os10g0104900.
DR KEGG; osa:4347954; -.
DR eggNOG; ENOG502QW29; Eukaryota.
DR OrthoDB; 898916at2759; -.
DR Proteomes; UP000000763; Chromosome 10.
DR Proteomes; UP000007752; Chromosome 10.
DR Proteomes; UP000059680; Chromosome 10.
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:0032776; P:DNA methylation on cytosine; IMP:UniProtKB.
DR GO; GO:0010216; P:maintenance of DNA methylation; IMP:UniProtKB.
DR Gene3D; 2.30.30.490; -; 1.
DR Gene3D; 3.40.50.150; -; 2.
DR InterPro; IPR001025; BAH_dom.
DR InterPro; IPR043151; BAH_sf.
DR InterPro; IPR018117; C5_DNA_meth_AS.
DR InterPro; IPR001525; C5_MeTfrase.
DR InterPro; IPR016197; Chromo-like_dom_sf.
DR InterPro; IPR000953; Chromo/chromo_shadow_dom.
DR InterPro; IPR023780; Chromo_domain.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR Pfam; PF01426; BAH; 1.
DR Pfam; PF00385; Chromo; 1.
DR Pfam; PF00145; DNA_methylase; 1.
DR PRINTS; PR00105; C5METTRFRASE.
DR SMART; SM00439; BAH; 1.
DR SMART; SM00298; CHROMO; 1.
DR SUPFAM; SSF53335; SSF53335; 1.
DR SUPFAM; SSF54160; SSF54160; 1.
DR PROSITE; PS51038; BAH; 1.
DR PROSITE; PS00094; C5_MTASE_1; 1.
DR PROSITE; PS50013; CHROMO_2; 1.
DR PROSITE; PS51679; SAM_MT_C5; 1.
PE 2: Evidence at transcript level;
KW DNA-binding; Methyltransferase; Nucleus; Reference proteome;
KW S-adenosyl-L-methionine; Transferase.
FT CHAIN 1..907
FT /note="DNA (cytosine-5)-methyltransferase CMT3"
FT /id="PRO_0000438158"
FT DOMAIN 172..297
FT /note="BAH"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00370"
FT DOMAIN 335..868
FT /note="SAM-dependent MTase C5-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01016"
FT DOMAIN 437..500
FT /note="Chromo"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00053"
FT REGION 1..154
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 303..323
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..32
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 33..63
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 64..89
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 111..154
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 513
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01016"
FT CONFLICT 99
FT /note="A -> P (in Ref. 6; EEE50451)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 907 AA; 101415 MW; 90EF5B0E0DD151CF CRC64;
MAPSSPSSAA APTRTSTRKR AASASASAKA TDEPSTKRTR RPKAETKPRK KKDEVKEEEK
PPMEDDACGE EPDAEEMALG EEAEAEEAEA EQKQLDAPAP GVARKRVAQP SRVRHGSDGD
HDPEFVGDPF PAKEARDKWP QRYQRNAATR RPDEEEDIKA RCHYSSAKVD GTLYCLHDDV
YVKAEEDKAD YIGRITEFFE GTDHCHYFTC RWFFRAEDTV ISSIMMENAD DEKHDLKRVF
LSEEKNDNVL DCIISKVKIV YIDPNMESEA KARRLADCDL YYDMSYTVAY STFANIPLEN
GASGSDTASD ISSDDVDSSK GKVVSDSEAS SVGKATLLDL YSGCGGMSTG LCLGAALAGL
NLETRWAVDF NSFACESLKY NHPRTEVRNE KADEFLALLK GWHSLCDEYV KKDIDFSSAG
ASENEEDDDE PLEKDEFVVE KLAGICYGGS GREDGLYFKV QWKGYGREED TWEPIENLRD
CPLKIKEFVQ EGYRRKILPL PGDVDVICGG PPCQGISGFN RFRNRKEPLK DEKNKQMVTF
MDIVAYLKPK YVLMENVVDI LKFADGYLGR YALSRLVAMK YQARLGMMVA GCYGLPQFRM
RVFLWGALPT MVLPKYPLPT HNVVVRGGAP NAFSQSIVAY DETQKPTLKN ALLLGDAISD
LPEVNNHQPN EVMEYGSSPK TEFQRYIRLS RKEMLDSSFE GKDGPDLGKL LDHQPLKLNK
DDHERVQQIP VKKGANFRDL KGVRVGANNI VEWDPDVPRV YLSSGKPLVP DYAMSFIKGR
SLKPFGRLWW DETVPTVVTR AEPHNQIILH PNQARVLTVR ENARLQGFPD YYKMFGPIKE
KYIQVGNAVA VPVARALGYS LGLAYQRESE GSSPLFVLPD SFTEVGRQAA PARASSVGIP
VGEVVEQ
