ID   CMT1_ARATH              Reviewed;         791 AA.
AC   O49139; O49137; O49138; O49141; O50057; O50073; Q38940; Q7G196;
DT   25-JUL-2006, integrated into UniProtKB/Swiss-Prot.
DT   25-JUL-2006, sequence version 2.
DT   27-MAR-2024, entry version 164.
DE   RecName: Full=Putative DNA (cytosine-5)-methyltransferase CMT1;
DE            EC=2.1.1.37;
DE   AltName: Full=Chromomethylase 1;
DE   AltName: Full=Protein CHROMOMETHYLASE 1;
GN   Name=CMT1; OrderedLocusNames=At1g80740; ORFNames=F23A5.9;
OS   Arabidopsis thaliana (Mouse-ear cress).
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC   rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX   NCBI_TaxID=3702;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA] (ISOFORMS 1 AND 2), AND TISSUE
RP   SPECIFICITY.
RC   STRAIN=cv. Columbia, cv. Kl-0, cv. Landsberg erecta, cv. Metz-0, cv.
RC   Nd-0, cv. Nd-1, and cv. RLD;
RX   PubMed=9584105; DOI=10.1093/genetics/149.1.307;
RA   Henikoff S., Comai L.;
RT   "A DNA methyltransferase homolog with a chromodomain exists in multiple
RT   polymorphic forms in Arabidopsis.";
RL   Genetics 149:307-318(1998).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=cv. Columbia;
RA   Goodman H.M., Gallant P., Keifer-Higgins S., Rubenfield M., Church G.M.;
RT   "A 37.5 Kb sequence from Arabidopsis thaliana chromosome I.";
RL   Submitted (APR-1996) to the EMBL/GenBank/DDBJ databases.
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Columbia;
RX   PubMed=11130712; DOI=10.1038/35048500;
RA   Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA   Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA   Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA   Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA   Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA   Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA   Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA   Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA   Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA   Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA   Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA   Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA   Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA   Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA   Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT   "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL   Nature 408:816-820(2000).
RN   [4]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Columbia;
RX   PubMed=27862469; DOI=10.1111/tpj.13415;
RA   Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA   Town C.D.;
RT   "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT   genome.";
RL   Plant J. 89:789-804(2017).
CC   -!- FUNCTION: May be involved in the CpXpG methylation and in gene
CC       silencing. {ECO:0000250}.
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   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}.
CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative splicing; Named isoforms=2;
CC       Name=1;
CC         IsoId=O49139-1; Sequence=Displayed;
CC       Name=2;
CC         IsoId=O49139-2; Sequence=VSP_019857, VSP_019858;
CC   -!- TISSUE SPECIFICITY: Expressed in flowers. Not detected in leaves,
CC       roots, seedlings and plants prior formation of flower buds.
CC       {ECO:0000269|PubMed:9584105}.
CC   -!- MISCELLANEOUS: [Isoform 2]: Alternative splice site used 50% of the
CC       time in cv. Columbia. {ECO:0000305}.
CC   -!- SIMILARITY: Belongs to the class I-like SAM-binding methyltransferase
CC       superfamily. C5-methyltransferase family. {ECO:0000255|PROSITE-
CC       ProRule:PRU01016}.
CC   -!- CAUTION: Could be the product of a pseudogene. The protein is severely
CC       truncated in several ecotypes and the gene even harbors a complete
CC       retrotransposon in 3 ecotypes. {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=AAA98912.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR   EMBL; AF039364; AAB95485.1; -; mRNA.
DR   EMBL; AF039366; AAC02659.1; -; Genomic_DNA.
DR   EMBL; AF039367; AAC02660.1; -; Genomic_DNA.
DR   EMBL; AF039368; AAC02661.1; -; Genomic_DNA.
DR   EMBL; AF039369; AAC02662.1; -; Genomic_DNA.
DR   EMBL; AF039370; AAC02663.1; -; Genomic_DNA.
DR   EMBL; AF039371; AAC02665.1; -; Genomic_DNA.
DR   EMBL; AF039372; AAC02667.1; -; Genomic_DNA.
DR   EMBL; AF039373; AAC02668.1; -; Genomic_DNA.
DR   EMBL; U53501; AAA98912.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; AC011713; AAF14662.1; -; Genomic_DNA.
DR   EMBL; CP002684; AEE36442.1; -; Genomic_DNA.
DR   PIR; H96839; H96839.
DR   RefSeq; NP_565245.1; NM_106722.2. [O49139-1]
DR   AlphaFoldDB; O49139; -.
DR   SMR; O49139; -.
DR   STRING; 3702.O49139; -.
DR   REBASE; 3261; M.AthCMT1P.
DR   PaxDb; 3702-AT1G80740-1; -.
DR   EnsemblPlants; AT1G80740.1; AT1G80740.1; AT1G80740. [O49139-1]
DR   GeneID; 844413; -.
DR   Gramene; AT1G80740.1; AT1G80740.1; AT1G80740. [O49139-1]
DR   KEGG; ath:AT1G80740; -.
DR   Araport; AT1G80740; -.
DR   TAIR; AT1G80740; CMT1.
DR   eggNOG; ENOG502QW29; Eukaryota.
DR   HOGENOM; CLU_004921_0_0_1; -.
DR   InParanoid; O49139; -.
DR   OMA; PPCDLYY; -.
DR   OrthoDB; 1215065at2759; -.
DR   PhylomeDB; O49139; -.
DR   Proteomes; UP000006548; Chromosome 1.
DR   ExpressionAtlas; O49139; baseline and differential.
DR   GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
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:0006325; P:chromatin organization; IEA:UniProtKB-KW.
DR   GO; GO:0009294; P:DNA-mediated transformation; IMP:TAIR.
DR   CDD; cd04716; BAH_plantDCM_I; 1.
DR   CDD; cd18635; CD_CMT3_like; 1.
DR   Gene3D; 2.30.30.490; -; 1.
DR   Gene3D; 3.90.120.10; DNA Methylase, subunit A, domain 2; 1.
DR   Gene3D; 3.40.50.150; Vaccinia Virus protein VP39; 2.
DR   InterPro; IPR001025; BAH_dom.
DR   InterPro; IPR043151; BAH_sf.
DR   InterPro; IPR001525; C5_MeTfrase.
DR   InterPro; IPR016197; Chromo-like_dom_sf.
DR   InterPro; IPR000953; Chromo/chromo_shadow_dom.
DR   InterPro; IPR017984; Chromo_dom_subgr.
DR   InterPro; IPR023780; Chromo_domain.
DR   InterPro; IPR023779; Chromodomain_CS.
DR   InterPro; IPR029063; SAM-dependent_MTases_sf.
DR   PANTHER; PTHR10629; CYTOSINE-SPECIFIC METHYLTRANSFERASE; 1.
DR   PANTHER; PTHR10629:SF59; DNA (CYTOSINE-5)-METHYLTRANSFERASE CMT1-RELATED; 1.
DR   Pfam; PF01426; BAH; 1.
DR   Pfam; PF00385; Chromo; 1.
DR   Pfam; PF00145; DNA_methylase; 1.
DR   PRINTS; PR00105; C5METTRFRASE.
DR   PRINTS; PR00504; CHROMODOMAIN.
DR   SMART; SM00439; BAH; 1.
DR   SMART; SM00298; CHROMO; 1.
DR   SUPFAM; SSF54160; Chromo domain-like; 1.
DR   SUPFAM; SSF53335; S-adenosyl-L-methionine-dependent methyltransferases; 1.
DR   PROSITE; PS51038; BAH; 1.
DR   PROSITE; PS00598; CHROMO_1; 1.
DR   PROSITE; PS50013; CHROMO_2; 1.
DR   PROSITE; PS51679; SAM_MT_C5; 1.
DR   Genevisible; O49139; AT.
PE   5: Uncertain;
KW   Alternative splicing; Chromatin regulator; Coiled coil; DNA-binding;
KW   Methyltransferase; Nucleus; Reference proteome; S-adenosyl-L-methionine;
KW   Transcription; Transcription regulation; Transferase.
FT   CHAIN           1..791
FT                   /note="Putative DNA (cytosine-5)-methyltransferase CMT1"
FT                   /id="PRO_0000246691"
FT   DOMAIN          79..199
FT                   /note="BAH"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00370"
FT   DOMAIN          225..768
FT                   /note="SAM-dependent MTase C5-type"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01016"
FT   DOMAIN          339..404
FT                   /note="Chromo"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00053"
FT   REGION          37..59
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COILED          308..333
FT                   /evidence="ECO:0000255"
FT   ACT_SITE        417
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01016"
FT   VAR_SEQ         568..570
FT                   /note="VTN -> CCR (in isoform 2)"
FT                   /evidence="ECO:0000303|PubMed:9584105"
FT                   /id="VSP_019857"
FT   VAR_SEQ         571..791
FT                   /note="Missing (in isoform 2)"
FT                   /evidence="ECO:0000303|PubMed:9584105"
FT                   /id="VSP_019858"
FT   VARIANT         148
FT                   /note="D -> G (in strain: cv. Metz-0)"
FT   VARIANT         196
FT                   /note="T -> I (in strain: cv. Kl-0)"
FT   VARIANT         198
FT                   /note="A -> T (in strain: cv. No-0)"
FT   VARIANT         249..791
FT                   /note="Missing (in strain: cv. Metz-0)"
FT   VARIANT         560
FT                   /note="D -> V (in strain: cv. Landsberg erecta, cv. No-0
FT                   and cv. RLD)"
FT   VARIANT         561..791
FT                   /note="Missing (in strain: cv. Landsberg erecta, cv. No-0
FT                   and cv. RLD)"
FT   VARIANT         604
FT                   /note="F -> C (in strain: cv. Nd-1, Nd-0 and cv. Kl-0)"
SQ   SEQUENCE   791 AA;  89219 MW;  A5ECFDBC274B215C CRC64;
     MAARNKQKKR AEPESDLCFA GKPMSVVEST IRWPHRYQSK KTKLQAPTKK PANKGGKKED
     EEIIKQAKCH FDKALVDGVL INLNDDVYVT GLPGKLKFIA KVIELFEADD GVPYCRFRWY
     YRPEDTLIER FSHLVQPKRV FLSNDENDNP LTCIWSKVNI AKVPLPKITS RIEQRVIPPC
     DYYYDMKYEV PYLNFTSADD GSDASSSLSS DSALNCFENL HKDEKFLLDL YSGCGAMSTG
     FCMGASISGV KLITKWSVDI NKFACDSLKL NHPETEVRNE AAEDFLALLK EWKRLCEKFS
     LVSSTEPVES ISELEDEEVE ENDDIDEAST GAELEPGEFE VEKFLGIMFG DPQGTGEKTL
     QLMVRWKGYN SSYDTWEPYS GLGNCKEKLK EYVIDGFKSH LLPLPGTVYT VCGGPPCQGI
     SGYNRYRNNE APLEDQKNQQ LLVFLDIIDF LKPNYVLMEN VVDLLRFSKG FLARHAVASF
     VAMNYQTRLG MMAAGSYGLP QLRNRVFLWA AQPSEKLPPY PLPTHEVAKK FNTPKEFKDL
     QVGRIQMEFL KLDNALTLAD AISDLPPVTN YVANDVMDYN DAAPKTEFEN FISLKRSETL
     LPAFGGDPTR RLFDHQPLVL GDDDLERVSY IPKQKGANYR DMPGVLVHNN KAEINPRFRA
     KLKSGKNVVP AYAISFIKGK SKKPFGRLWG DEIVNTVVTR AEPHNQCVIH PMQNRVLSVR
     ENARLQGFPD CYKLCGTIKE KYIQVGNAVA VPVGVALGYA FGMASQGLTD DEPVIKLPFK
     YPECMQAKDQ I
//