TRDMT_ARATH
ID TRDMT_ARATH Reviewed; 383 AA.
AC F4JWT7; Q6QPM1; Q8LER4;
DT 10-OCT-2018, integrated into UniProtKB/Swiss-Prot.
DT 28-JUN-2011, sequence version 1.
DT 03-AUG-2022, entry version 74.
DE RecName: Full=tRNA (cytosine(38)-C(5))-methyltransferase 2 {ECO:0000303|PubMed:16424344};
DE Short=AtDNMT2 {ECO:0000303|PubMed:16424344};
DE EC=2.1.1.204 {ECO:0000250|UniProtKB:O14717, ECO:0000255|PROSITE-ProRule:PRU01016};
DE AltName: Full=DNA (cytosine-5)-methyltransferase-like protein 2 {ECO:0000303|PubMed:16424344};
DE Short=Dnmt2 {ECO:0000303|PubMed:16424344};
GN Name=DNMT2 {ECO:0000303|PubMed:16424344};
GN OrderedLocusNames=At5g25480 {ECO:0000312|Araport:AT5G25480};
GN ORFNames=T14C9.10 {ECO:0000312|EMBL:AED93453.1};
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 [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 [2]
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 [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-176.
RC STRAIN=cv. Columbia er-105;
RX PubMed=14871304; DOI=10.1111/j.0960-7412.2003.01999.x;
RA Comai L., Young K., Till B.J., Reynolds S.H., Greene E.A., Codomo C.A.,
RA Enns L.C., Johnson J.E., Burtner C., Odden A.R., Henikoff S.;
RT "Efficient discovery of DNA polymorphisms in natural populations by
RT Ecotilling.";
RL Plant J. 37:778-786(2004).
RN [5]
RP GENE FAMILY, AND NOMENCLATURE.
RX PubMed=16424344; DOI=10.1126/science.1120976;
RA Goll M.G., Kirpekar F., Maggert K.A., Yoder J.A., Hsieh C.L., Zhang X.,
RA Golic K.G., Jacobsen S.E., Bestor T.H.;
RT "Methylation of tRNAAsp by the DNA methyltransferase homolog Dnmt2.";
RL Science 311:395-398(2006).
RN [6]
RP FUNCTION, INTERACTION WITH HDT1; HDT2 AND HDT3, AND SUBCELLULAR LOCATION.
RC STRAIN=cv. Columbia;
RX PubMed=20331964; DOI=10.1016/j.bbrc.2010.03.119;
RA Song Y., Wu K., Dhaubhadel S., An L., Tian L.;
RT "Arabidopsis DNA methyltransferase AtDNMT2 associates with histone
RT deacetylase AtHD2s activity.";
RL Biochem. Biophys. Res. Commun. 396:187-192(2010).
CC -!- FUNCTION: Specifically methylates cytosine 38 in the anticodon loop of
CC tRNA(Asp) (By similarity). Represses gene expression at transcription
CC level, probably by regulating histone deacetylation and epigenetic
CC regulatory network (PubMed:20331964). {ECO:0000250|UniProtKB:O14717,
CC ECO:0000269|PubMed:20331964}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=cytidine(38) in tRNA + S-adenosyl-L-methionine = 5-
CC methylcytidine(38) in tRNA + H(+) + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:42956, Rhea:RHEA-COMP:10299, Rhea:RHEA-COMP:10300,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74483, ChEBI:CHEBI:82748; EC=2.1.1.204;
CC Evidence={ECO:0000250|UniProtKB:O14717};
CC -!- SUBUNIT: Interacts with type-2 histone deacetylases (AtHD2s) HDT1, HDT2
CC and HDT3. {ECO:0000269|PubMed:20331964}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:20331964}.
CC -!- SIMILARITY: Belongs to the class I-like SAM-binding methyltransferase
CC superfamily. C5-methyltransferase family. {ECO:0000255|PROSITE-
CC ProRule:PRU01016}.
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DR EMBL; AC006601; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CP002688; AED93453.1; -; Genomic_DNA.
DR EMBL; AY085281; AAM62513.1; -; mRNA.
DR EMBL; AY530747; AAS45432.1; -; Genomic_DNA.
DR RefSeq; NP_568474.1; NM_122459.3.
DR AlphaFoldDB; F4JWT7; -.
DR SMR; F4JWT7; -.
DR STRING; 3702.AT5G25480.1; -.
DR PaxDb; F4JWT7; -.
DR PRIDE; F4JWT7; -.
DR ProteomicsDB; 228260; -.
DR EnsemblPlants; AT5G25480.1; AT5G25480.1; AT5G25480.
DR GeneID; 832623; -.
DR Gramene; AT5G25480.1; AT5G25480.1; AT5G25480.
DR KEGG; ath:AT5G25480; -.
DR Araport; AT5G25480; -.
DR TAIR; locus:2179469; AT5G25480.
DR eggNOG; KOG0919; Eukaryota.
DR HOGENOM; CLU_049101_0_0_1; -.
DR InParanoid; F4JWT7; -.
DR OMA; VMDIIHP; -.
DR OrthoDB; 1519639at2759; -.
DR PRO; PR:F4JWT7; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; F4JWT7; baseline and differential.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0016428; F:tRNA (cytosine-5-)-methyltransferase activity; IBA:GO_Central.
DR GO; GO:0045814; P:negative regulation of gene expression, epigenetic; IMP:UniProtKB.
DR GO; GO:0002946; P:tRNA C5-cytosine methylation; IBA:GO_Central.
DR Gene3D; 3.40.50.150; -; 1.
DR InterPro; IPR001525; C5_MeTfrase.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR Pfam; PF00145; DNA_methylase; 1.
DR PRINTS; PR00105; C5METTRFRASE.
DR SUPFAM; SSF53335; SSF53335; 1.
DR TIGRFAMs; TIGR00675; dcm; 1.
DR PROSITE; PS51679; SAM_MT_C5; 1.
PE 1: Evidence at protein level;
KW Methyltransferase; Nucleus; Reference proteome; Repressor; RNA-binding;
KW S-adenosyl-L-methionine; Transcription; Transcription regulation;
KW Transferase; tRNA processing.
FT CHAIN 1..383
FT /note="tRNA (cytosine(38)-C(5))-methyltransferase 2"
FT /id="PRO_0000445249"
FT DOMAIN 15..383
FT /note="SAM-dependent MTase C5-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01016"
FT REGION 241..261
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 89
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01016"
FT BINDING 24..26
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:O14717"
FT BINDING 45
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:O14717"
FT BINDING 67..68
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:O14717"
FT BINDING 86
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:O14717"
FT BINDING 367
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:O14717"
FT CONFLICT 107
FT /note="F -> S (in Ref. 3; AAM62513)"
FT /evidence="ECO:0000305"
FT CONFLICT 226
FT /note="K -> E (in Ref. 3; AAM62513)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 383 AA; 43719 MW; 42E15C374867C5CC CRC64;
MAEQELQRIN EKKPWQVLEF YSGIGGMRYS LMASGIVSEV VEAFEINDSA NDVYQHNFKH
RPYQGNIQSL TAADLDKYNA DAWLLSPPCQ PYTRQGLQKH SGDARAFSFL RILELIPHTT
KPPQMLFVEN VVGFETSDTH MEMIGTLTKL DYVTQEFILS PLQFGVPYSR PRYFCLAKRK
PLPFKSQHSN NKLLWSPDPL YGRDDQVEFG KCQAEEGLDK LLEFCKPVEK FLELAAHVDG
EPSSVDDSEN GSKDCCGQEG DSVPDSVHQY LVPVSLIERW GNAMDIVYPD SKRCCCFTKS
YYRYVKGTGS LLATVQPKIK GKESCLKEQR LRYFTPREVA NFHSFPEDFE FPKHISLRQR
YAMLGNSLSV AVVAPLLRYL FDS
