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 27-MAR-2024, entry version 148. 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}; CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- 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 PDB; 8T1U; X-ray; 2.91 A; A=274-626. DR PDBsum; 7L4C; -. DR PDBsum; 7L4F; -. DR PDBsum; 7L4H; -. DR PDBsum; 7L4K; -. DR PDBsum; 7L4M; -. DR PDBsum; 7L4N; -. DR PDBsum; 8T1U; -. DR AlphaFoldDB; Q9M548; -. DR SMR; Q9M548; -. DR BioGRID; 16592; 10. DR DIP; DIP-59279N; -. DR IntAct; Q9M548; 9. DR MINT; Q9M548; -. DR STRING; 3702.Q9M548; -. DR iPTMnet; Q9M548; -. DR PaxDb; 3702-AT5G14620-1; -. 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; AT5G14620; DRM2. DR eggNOG; ENOG502QVZV; Eukaryota. DR HOGENOM; CLU_006805_2_0_1; -. DR InParanoid; Q9M548; -. DR OMA; FMGMGFP; -. DR OrthoDB; 913973at2759; -. DR PhylomeDB; Q9M548; -. DR PRO; PR:Q9M548; -. DR Proteomes; UP000006548; Chromosome 5. DR ExpressionAtlas; Q9M548; baseline and differential. 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; IEA:UniProtKB-EC. 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 formation; IMP:UniProtKB. DR GO; GO:0051567; P:histone H3-K9 methylation; IGI:TAIR. DR CDD; cd14270; UBA; 1. DR CDD; cd14330; UBA_atDRM2_like; 1. DR Gene3D; 1.10.8.10; DNA helicase RuvA subunit, C-terminal domain; 2. DR Gene3D; 3.40.50.150; Vaccinia Virus protein VP39; 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 PANTHER; PTHR23068:SF25; DNA (CYTOSINE-5)-METHYLTRANSFERASE DRM2; 1. DR PANTHER; PTHR23068; DNA CYTOSINE-5- -METHYLTRANSFERASE 3-RELATED; 1. DR Pfam; PF00145; DNA_methylase; 1. DR SMART; SM00165; UBA; 3. DR SUPFAM; SSF53335; S-adenosyl-L-methionine-dependent methyltransferases; 2. DR SUPFAM; SSF46934; UBA-like; 3. DR PROSITE; PS51680; SAM_MT_DRM; 1. DR PROSITE; PS50030; UBA; 2. DR Genevisible; Q9M548; AT. 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 //