DRM2_ARATH
ID DRM2_ARATH Reviewed; 626 AA.
AC Q9M548; Q9LYJ7; Q9LYJ8;
DT 01-SEP-2009, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 139.
DE RecName: Full=DNA (cytosine-5)-methyltransferase DRM2;
DE EC=2.1.1.37;
DE AltName: Full=Protein DOMAINS REARRANGED METHYLASE 2;
GN Name=DRM2; OrderedLocusNames=At5g14620/At5g14630;
GN ORFNames=T15N1.110/T15N1.120;
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 [MRNA], AND TISSUE SPECIFICITY.
RC STRAIN=cv. Columbia;
RX PubMed=10781108; DOI=10.1073/pnas.97.9.4979;
RA Cao X., Springer N.M., Muszynski M.G., Phillips R.L., Kaeppler S.,
RA Jacobsen S.E.;
RT "Conserved plant genes with similarity to mammalian de novo DNA
RT methyltransferases.";
RL Proc. Natl. Acad. Sci. U.S.A. 97:4979-4984(2000).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130714; DOI=10.1038/35048507;
RA Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E.,
RA Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M.,
RA Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.,
RA Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M.,
RA Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L.,
RA O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D.,
RA Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M.,
RA Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L.,
RA Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B.,
RA Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P.,
RA Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M.,
RA Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D.,
RA Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A.,
RA Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I.,
RA Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T.,
RA Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A.,
RA McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U.,
RA Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W.,
RA Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M.,
RA Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S.,
RA Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G.,
RA Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W.,
RA Bevan M., Fransz P.F.;
RT "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana.";
RL Nature 408:823-826(2000).
RN [3]
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).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP FUNCTION.
RX PubMed=12151602; DOI=10.1073/pnas.162371599;
RA Cao X., Jacobsen S.E.;
RT "Locus-specific control of asymmetric and CpNpG methylation by the DRM and
RT CMT3 methyltransferase genes.";
RL Proc. Natl. Acad. Sci. U.S.A. 99:16491-16498(2002).
RN [6]
RP FUNCTION.
RX PubMed=12121623; DOI=10.1016/s0960-9822(02)00925-9;
RA Cao X., Jacobsen S.E.;
RT "Role of the arabidopsis DRM methyltransferases in de novo DNA methylation
RT and gene silencing.";
RL Curr. Biol. 12:1138-1144(2002).
RN [7]
RP FUNCTION.
RX PubMed=14680640; DOI=10.1016/j.cub.2003.11.052;
RA Cao X., Aufsatz W., Zilberman D., Mette M.F., Huang M.S., Matzke M.,
RA Jacobsen S.E.;
RT "Role of the DRM and CMT3 methyltransferases in RNA-directed DNA
RT methylation.";
RL Curr. Biol. 13:2212-2217(2003).
RN [8]
RP INTERACTION WITH RDM1, AND SUBCELLULAR LOCATION.
RX PubMed=20410883; DOI=10.1038/nature09025;
RA Gao Z., Liu H.L., Daxinger L., Pontes O., He X., Qian W., Lin H., Xie M.,
RA Lorkovic Z.J., Zhang S., Miki D., Zhan X., Pontier D., Lagrange T., Jin H.,
RA Matzke A.J., Matzke M., Pikaard C.S., Zhu J.K.;
RT "An RNA polymerase II- and AGO4-associated protein acts in RNA-directed DNA
RT methylation.";
RL Nature 465:106-109(2010).
RN [9]
RP FUNCTION, AND MUTAGENESIS OF CYS-587.
RX PubMed=21060858; DOI=10.1371/journal.pgen.1001182;
RA Henderson I.R., Deleris A., Wong W., Zhong X., Chin H.G., Horwitz G.A.,
RA Kelly K.A., Pradhan S., Jacobsen S.E.;
RT "The de novo cytosine methyltransferase DRM2 requires intact UBA domains
RT and a catalytically mutated paralog DRM3 during RNA-directed DNA
RT methylation in Arabidopsis thaliana.";
RL PLoS Genet. 6:E1001182-E1001182(2010).
RN [10]
RP FUNCTION, AND MUTAGENESIS OF SER-585.
RX PubMed=21212233; DOI=10.1534/genetics.110.125401;
RA Naumann U., Daxinger L., Kanno T., Eun C., Long Q., Lorkovic Z.J.,
RA Matzke M., Matzke A.J.;
RT "Genetic evidence that DNA methyltransferase DRM2 has a direct catalytic
RT role in RNA-directed DNA methylation in Arabidopsis thaliana.";
RL Genetics 187:977-979(2011).
RN [11]
RP FUNCTION.
RX PubMed=24862207; DOI=10.1111/tpj.12563;
RA Boehmdorfer G., Rowley M.J., Kucinski J., Zhu Y., Amies I.,
RA Wierzbicki A.T.;
RT "RNA-directed DNA methylation requires stepwise binding of silencing
RT factors to long non-coding RNA.";
RL Plant J. 79:181-191(2014).
CC -!- FUNCTION: Involved in de novo DNA methylation. Controls asymmetric and
CC CpNpG methylation. Required for FWA gene silencing but not for the
CC maintenance of SUP gene silencing. Functionally redundant to CMT3 to
CC maintain non-CpG methylation. Involved in RNA-directed DNA methylation
CC (RdDM) (PubMed:12121623, PubMed:12151602, PubMed:14680640). Acts as
CC major DNA methyltransferase in the RdDM pathway, and is essential for
CC RNA-directed de novo DNA methylation of cytosines in all sequence
CC contexts (PubMed:21060858, PubMed:21212233). Associates with long non-
CC coding RNA (lncRNA) produced by RNA polymerase V (Pol V). This
CC association is dependent on AGO4 and IDN2, and results in DNA
CC methylation of RdDM target loci (PubMed:24862207).
CC {ECO:0000269|PubMed:12121623, ECO:0000269|PubMed:12151602,
CC ECO:0000269|PubMed:14680640, ECO:0000269|PubMed:21060858,
CC ECO:0000269|PubMed:21212233, ECO:0000269|PubMed:24862207}.
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:PRU01017};
CC -!- SUBUNIT: Interacts with RDM1. {ECO:0000269|PubMed:20410883}.
CC -!- INTERACTION:
CC Q9M548; Q9ZVD5: AGO4; NbExp=2; IntAct=EBI-6923904, EBI-2352199;
CC Q9M548; Q9LUJ3: RDM1; NbExp=2; IntAct=EBI-6923904, EBI-15850569;
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleoplasm
CC {ECO:0000269|PubMed:20410883}. Note=Peri-nucleolar.
CC -!- TISSUE SPECIFICITY: Expressed in roots, inflorescences and at lower
CC levels in leaves. {ECO:0000269|PubMed:10781108}.
CC -!- MISCELLANEOUS: DRM2 is expressed at much higher levels than DRM1, which
CC is scarcely detected, suggesting that DRM2 is the predominant de novo
CC methylase.
CC -!- SIMILARITY: Belongs to the class I-like SAM-binding methyltransferase
CC superfamily. DRM-methyltransferase family. {ECO:0000255|PROSITE-
CC ProRule:PRU01017}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAB87629.1; Type=Erroneous gene model prediction; Note=Was originally thought to correspond to two different genes At5g14620 and At5g14630.; Evidence={ECO:0000305};
CC Sequence=CAB87630.1; Type=Erroneous gene model prediction; Note=Was originally thought to correspond to two different genes At5g14620 and At5g14630.; Evidence={ECO:0000305};
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DR EMBL; AF240695; AAF66129.1; -; mRNA.
DR EMBL; AL163792; CAB87629.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL163792; CAB87630.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002688; AED92056.1; -; Genomic_DNA.
DR EMBL; AK176138; BAD43901.1; -; mRNA.
DR EMBL; AK220953; BAD94486.1; -; mRNA.
DR EMBL; AK229197; BAF01067.1; -; mRNA.
DR PIR; T48635; T48635.
DR PIR; T48636; T48636.
DR RefSeq; NP_196966.2; NM_121466.3.
DR PDB; 7L4C; X-ray; 2.11 A; A=274-626.
DR PDB; 7L4F; X-ray; 2.55 A; A/B=270-626.
DR PDB; 7L4H; X-ray; 2.56 A; A=275-626.
DR PDB; 7L4K; X-ray; 2.61 A; A=270-626.
DR PDB; 7L4M; X-ray; 2.81 A; A/B=270-626.
DR PDB; 7L4N; X-ray; 2.25 A; A=270-626.
DR PDBsum; 7L4C; -.
DR PDBsum; 7L4F; -.
DR PDBsum; 7L4H; -.
DR PDBsum; 7L4K; -.
DR PDBsum; 7L4M; -.
DR PDBsum; 7L4N; -.
DR AlphaFoldDB; Q9M548; -.
DR SMR; Q9M548; -.
DR BioGRID; 16592; 2.
DR DIP; DIP-59279N; -.
DR IntAct; Q9M548; 9.
DR MINT; Q9M548; -.
DR STRING; 3702.AT5G14620.1; -.
DR iPTMnet; Q9M548; -.
DR PaxDb; Q9M548; -.
DR PRIDE; Q9M548; -.
DR ProteomicsDB; 224353; -.
DR EnsemblPlants; AT5G14620.1; AT5G14620.1; AT5G14620.
DR GeneID; 831315; -.
DR Gramene; AT5G14620.1; AT5G14620.1; AT5G14620.
DR KEGG; ath:AT5G14620; -.
DR Araport; AT5G14620; -.
DR TAIR; locus:2222627; AT5G14620.
DR eggNOG; ENOG502QVZV; Eukaryota.
DR HOGENOM; CLU_006805_2_0_1; -.
DR InParanoid; Q9M548; -.
DR OMA; PPKYTIH; -.
DR OrthoDB; 412711at2759; -.
DR PhylomeDB; Q9M548; -.
DR PRO; PR:Q9M548; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q9M548; baseline and differential.
DR Genevisible; Q9M548; AT.
DR GO; GO:0005654; C:nucleoplasm; IDA:UniProtKB.
DR GO; GO:0005634; C:nucleus; ISS:TAIR.
DR GO; GO:0003886; F:DNA (cytosine-5-)-methyltransferase activity; IBA:GO_Central.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0009008; F:DNA-methyltransferase activity; IMP:CACAO.
DR GO; GO:0050832; P:defense response to fungus; IGI:TAIR.
DR GO; GO:0006306; P:DNA methylation; IMP:TAIR.
DR GO; GO:0006346; P:DNA methylation-dependent heterochromatin assembly; IMP:UniProtKB.
DR GO; GO:0051567; P:histone H3-K9 methylation; IGI:TAIR.
DR Gene3D; 3.40.50.150; -; 2.
DR InterPro; IPR001525; C5_MeTfrase.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR InterPro; IPR030380; SAM_MeTfrase_DRM.
DR InterPro; IPR015940; UBA.
DR InterPro; IPR009060; UBA-like_sf.
DR Pfam; PF00145; DNA_methylase; 1.
DR SMART; SM00165; UBA; 3.
DR SUPFAM; SSF46934; SSF46934; 3.
DR SUPFAM; SSF53335; SSF53335; 2.
DR PROSITE; PS51680; SAM_MT_DRM; 1.
DR PROSITE; PS50030; UBA; 2.
PE 1: Evidence at protein level;
KW 3D-structure; DNA-binding; Methyltransferase; Nucleus; Reference proteome;
KW Repeat; S-adenosyl-L-methionine; Transferase.
FT CHAIN 1..626
FT /note="DNA (cytosine-5)-methyltransferase DRM2"
FT /id="PRO_0000381942"
FT DOMAIN 59..101
FT /note="UBA 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00212"
FT DOMAIN 109..150
FT /note="UBA 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00212"
FT DOMAIN 190..232
FT /note="UBA 3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00212"
FT DOMAIN 295..626
FT /note="SAM-dependent MTase DRM-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01017"
FT REGION 160..196
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 245..282
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 245..273
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MUTAGEN 585
FT /note="S->A: Loss of function in maintaining non-CpG
FT methylation."
FT /evidence="ECO:0000269|PubMed:21060858"
FT MUTAGEN 587
FT /note="C->A: Loss of function in maintaining non-CpG
FT methylation."
FT /evidence="ECO:0000269|PubMed:21060858"
FT HELIX 301..303
FT /evidence="ECO:0007829|PDB:7L4C"
FT STRAND 306..315
FT /evidence="ECO:0007829|PDB:7L4C"
FT HELIX 321..328
FT /evidence="ECO:0007829|PDB:7L4C"
FT TURN 329..331
FT /evidence="ECO:0007829|PDB:7L4C"
FT STRAND 335..338
FT /evidence="ECO:0007829|PDB:7L4C"
FT HELIX 339..341
FT /evidence="ECO:0007829|PDB:7L4C"
FT STRAND 343..345
FT /evidence="ECO:0007829|PDB:7L4C"
FT STRAND 348..353
FT /evidence="ECO:0007829|PDB:7L4C"
FT HELIX 371..374
FT /evidence="ECO:0007829|PDB:7L4C"
FT HELIX 376..380
FT /evidence="ECO:0007829|PDB:7L4C"
FT STRAND 389..391
FT /evidence="ECO:0007829|PDB:7L4C"
FT HELIX 401..411
FT /evidence="ECO:0007829|PDB:7L4C"
FT HELIX 412..414
FT /evidence="ECO:0007829|PDB:7L4C"
FT STRAND 415..419
FT /evidence="ECO:0007829|PDB:7L4C"
FT HELIX 422..434
FT /evidence="ECO:0007829|PDB:7L4C"
FT STRAND 438..441
FT /evidence="ECO:0007829|PDB:7L4C"
FT STRAND 444..446
FT /evidence="ECO:0007829|PDB:7L4C"
FT HELIX 450..456
FT /evidence="ECO:0007829|PDB:7L4C"
FT TURN 461..464
FT /evidence="ECO:0007829|PDB:7L4C"
FT HELIX 471..480
FT /evidence="ECO:0007829|PDB:7L4C"
FT HELIX 484..491
FT /evidence="ECO:0007829|PDB:7L4C"
FT HELIX 494..497
FT /evidence="ECO:0007829|PDB:7L4C"
FT STRAND 502..508
FT /evidence="ECO:0007829|PDB:7L4C"
FT TURN 510..512
FT /evidence="ECO:0007829|PDB:7L4C"
FT HELIX 513..520
FT /evidence="ECO:0007829|PDB:7L4C"
FT STRAND 525..531
FT /evidence="ECO:0007829|PDB:7L4C"
FT HELIX 535..547
FT /evidence="ECO:0007829|PDB:7L4C"
FT STRAND 552..557
FT /evidence="ECO:0007829|PDB:7L4C"
FT HELIX 560..562
FT /evidence="ECO:0007829|PDB:7L4C"
FT HELIX 565..575
FT /evidence="ECO:0007829|PDB:7L4C"
FT STRAND 579..584
FT /evidence="ECO:0007829|PDB:7L4C"
FT TURN 588..590
FT /evidence="ECO:0007829|PDB:7L4C"
FT HELIX 600..602
FT /evidence="ECO:0007829|PDB:7L4F"
FT HELIX 606..608
FT /evidence="ECO:0007829|PDB:7L4C"
FT HELIX 609..623
FT /evidence="ECO:0007829|PDB:7L4C"
SQ SEQUENCE 626 AA; 70431 MW; 10A38FC068636DB7 CRC64;
MVIWNNDDDD FLEIDNFQSS PRSSPIHAMQ CRVENLAGVA VTTSSLSSPT ETTDLVQMGF
SDEVFATLFD MGFPVEMISR AIKETGPNVE TSVIIDTISK YSSDCEAGSS KSKAIDHFLA
MGFDEEKVVK AIQEHGEDNM EAIANALLSC PEAKKLPAAV EEEDGIDWSS SDDDTNYTDM
LNSDDEKDPN SNENGSKIRS LVKMGFSELE ASLAVERCGE NVDIAELTDF LCAAQMAREF
SEFYTEHEEQ KPRHNIKKRR FESKGEPRSS VDDEPIRLPN PMIGFGVPNE PGLITHRSLP
ELARGPPFFY YENVALTPKG VWETISRHLF EIPPEFVDSK YFCVAARKRG YIHNLPINNR
FQIQPPPKYT IHDAFPLSKR WWPEWDKRTK LNCILTCTGS AQLTNRIRVA LEPYNEEPEP
PKHVQRYVID QCKKWNLVWV GKNKAAPLEP DEMESILGFP KNHTRGGGMS RTERFKSLGN
SFQVDTVAYH LSVLKPIFPH GINVLSLFTG IGGGEVALHR LQIKMKLVVS VEISKVNRNI
LKDFWEQTNQ TGELIEFSDI QHLTNDTIEG LMEKYGGFDL VIGGSPCNNL AGGNRVSRVG
LEGDQSSLFF EYCRILEVVR ARMRGS
