DMS3_ARATH
ID DMS3_ARATH Reviewed; 420 AA.
AC Q94A79; Q9M3A7;
DT 03-SEP-2014, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 114.
DE RecName: Full=Protein DEFECTIVE IN MERISTEM SILENCING 3;
DE AltName: Full=Protein INVOLVED IN DE NOVO 1;
GN Name=DMS3; Synonyms=IDN1; OrderedLocusNames=At3g49250; ORFNames=F2K15.110;
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=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(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].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [4]
RP INTERACTION WITH CPL1.
RX PubMed=18541146; DOI=10.1016/j.bbrc.2008.05.161;
RA Bang W.Y., Kim S.W., Jeong I.S., Koiwa H., Bahk J.D.;
RT "The C-terminal region (640-967) of Arabidopsis CPL1 interacts with the
RT abiotic stress- and ABA-responsive transcription factors.";
RL Biochem. Biophys. Res. Commun. 372:907-912(2008).
RN [5]
RP FUNCTION, HOMODIMERIZATION, AND DISRUPTION PHENOTYPE.
RX PubMed=18425128; DOI=10.1038/ng.119;
RA Kanno T., Bucher E., Daxinger L., Huettel B., Boehmdorfer G., Gregor W.,
RA Kreil D.P., Matzke M., Matzke A.J.;
RT "A structural-maintenance-of-chromosomes hinge domain-containing protein is
RT required for RNA-directed DNA methylation.";
RL Nat. Genet. 40:670-675(2008).
RN [6]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=19377477; DOI=10.1038/ng.365;
RA Wierzbicki A.T., Ream T.S., Haag J.R., Pikaard C.S.;
RT "RNA polymerase V transcription guides ARGONAUTE4 to chromatin.";
RL Nat. Genet. 41:630-634(2009).
RN [7]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=19915591; DOI=10.1038/nsmb.1690;
RA Ausin I., Mockler T.C., Chory J., Jacobsen S.E.;
RT "IDN1 and IDN2 are required for de novo DNA methylation in Arabidopsis
RT thaliana.";
RL Nat. Struct. Mol. Biol. 16:1325-1327(2009).
RN [8]
RP SUBUNIT.
RX PubMed=20409711; DOI=10.1016/j.cub.2010.03.062;
RA Law J.A., Ausin I., Johnson L.M., Vashisht A.A., Zhu J.-K.,
RA Wohlschlegel J.A., Jacobsen S.E.;
RT "A protein complex required for polymerase V transcripts and RNA-directed
RT DNA methylation in Arabidopsis.";
RL Curr. Biol. 20:951-956(2010).
RN [9]
RP INTERACTION WITH DMS11.
RX PubMed=22560611; DOI=10.1016/j.cub.2012.03.061;
RA Lorkovic Z.J., Naumann U., Matzke A.J., Matzke M.;
RT "Involvement of a GHKL ATPase in RNA-directed DNA methylation in
RT Arabidopsis thaliana.";
RL Curr. Biol. 22:933-938(2012).
RN [10]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=22647529; DOI=10.4161/epi.20290;
RA Lee T.F., Gurazada S.G., Zhai J., Li S., Simon S.A., Matzke M.A., Chen X.,
RA Meyers B.C.;
RT "RNA polymerase V-dependent small RNAs in Arabidopsis originate from small,
RT intergenic loci including most SINE repeats.";
RL Epigenetics 7:781-795(2012).
RN [11]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=22864289; DOI=10.1038/nsmb.2354;
RA Zhong X., Hale C.J., Law J.A., Johnson L.M., Feng S., Tu A., Jacobsen S.E.;
RT "DDR complex facilitates global association of RNA polymerase V to
RT promoters and evolutionarily young transposons.";
RL Nat. Struct. Mol. Biol. 19:870-875(2012).
RN [12]
RP INTERACTION WITH SUVH2.
RC STRAIN=cv. Columbia;
RX PubMed=24465213; DOI=10.1371/journal.pgen.1003948;
RA Liu Z.-W., Shao C.-R., Zhang C.-J., Zhou J.-X., Zhang S.-W., Li L.,
RA Chen S., Huang H.-W., Cai T., He X.-J.;
RT "The SET domain proteins SUVH2 and SUVH9 are required for Pol V occupancy
RT at RNA-directed DNA methylation loci.";
RL PLoS Genet. 10:E1003948-E1003948(2014).
CC -!- FUNCTION: Component of the RNA-directed DNA methylation (RdDM)
CC machinery, probably by facilitating an RNAi-mediated epigenetic
CC modification involving secondary siRNAs and spreading of DNA
CC methylation, thus leading to gene silencing. Involved in the assembly
CC of RNA polymerase V (Pol V) transcription initiation or elongation
CC complexes at the chromatin, as a component of the DDR complex. Required
CC for de novo DNA methylation. {ECO:0000269|PubMed:18425128,
CC ECO:0000269|PubMed:19377477, ECO:0000269|PubMed:19915591,
CC ECO:0000269|PubMed:22647529, ECO:0000269|PubMed:22864289}.
CC -!- SUBUNIT: Homodimer. Part of the chromatin-remodeling complex (DDR
CC complex) that contains at least DRD1, DMS3 and RDM1. Interacts with
CC CPL1. The DDR complex recruits/activates the RNA polymerases V and acts
CC during siRNA-directed DNA methylation (RdDM) (PubMed:18541146,
CC PubMed:20409711, PubMed:22560611). Interacts with SUVH2
CC (PubMed:24465213). Binds to DMS11 and stimulates its ATPase activity
CC (PubMed:22560611). {ECO:0000269|PubMed:18541146,
CC ECO:0000269|PubMed:20409711, ECO:0000269|PubMed:22560611,
CC ECO:0000269|PubMed:24465213}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305}.
CC -!- DISRUPTION PHENOTYPE: Very low levels of RNAi-mediated methylation and
CC derepression of silenced genes. Impaired RNA polymerase V-chromatin
CC associations (Pol V). The mutant idn1-1 fails to establish DNA
CC methylation and exhibits a late-flowering phenotype.
CC {ECO:0000269|PubMed:18425128, ECO:0000269|PubMed:19377477,
CC ECO:0000269|PubMed:19915591, ECO:0000269|PubMed:22647529,
CC ECO:0000269|PubMed:22864289}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAB66404.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AL132956; CAB66404.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002686; AEE78515.1; -; Genomic_DNA.
DR EMBL; AY049288; AAK83630.1; -; mRNA.
DR EMBL; AY090286; AAL90947.1; -; mRNA.
DR PIR; T45830; T45830.
DR RefSeq; NP_566916.1; NM_114784.3.
DR PDB; 6OIS; EM; 3.60 A; C/D/E/F=2-420.
DR PDB; 6OIT; EM; 3.50 A; C/D/E/F=2-420.
DR PDBsum; 6OIS; -.
DR PDBsum; 6OIT; -.
DR AlphaFoldDB; Q94A79; -.
DR SMR; Q94A79; -.
DR BioGRID; 9404; 12.
DR IntAct; Q94A79; 6.
DR STRING; 3702.AT3G49250.1; -.
DR iPTMnet; Q94A79; -.
DR PaxDb; Q94A79; -.
DR PRIDE; Q94A79; -.
DR ProteomicsDB; 224107; -.
DR EnsemblPlants; AT3G49250.1; AT3G49250.1; AT3G49250.
DR GeneID; 824086; -.
DR Gramene; AT3G49250.1; AT3G49250.1; AT3G49250.
DR KEGG; ath:AT3G49250; -.
DR Araport; AT3G49250; -.
DR TAIR; locus:2082876; AT3G49250.
DR eggNOG; ENOG502QS96; Eukaryota.
DR HOGENOM; CLU_046782_0_0_1; -.
DR InParanoid; Q94A79; -.
DR OMA; TPRSENC; -.
DR PhylomeDB; Q94A79; -.
DR PRO; PR:Q94A79; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q94A79; baseline and differential.
DR Genevisible; Q94A79; AT.
DR GO; GO:0000419; C:RNA polymerase V complex; IMP:UniProtKB.
DR GO; GO:0042803; F:protein homodimerization activity; IDA:UniProtKB.
DR GO; GO:0006306; P:DNA methylation; IMP:TAIR.
DR GO; GO:0031047; P:gene silencing by RNA; IMP:TAIR.
DR GO; GO:0080188; P:gene silencing by RNA-directed DNA methylation; IMP:UniProtKB.
PE 1: Evidence at protein level;
KW 3D-structure; Coiled coil; Nucleus; Reference proteome;
KW RNA-mediated gene silencing.
FT CHAIN 1..420
FT /note="Protein DEFECTIVE IN MERISTEM SILENCING 3"
FT /id="PRO_0000430150"
FT COILED 52..93
FT /evidence="ECO:0000255"
FT COILED 353..386
FT /evidence="ECO:0000255"
FT HELIX 47..51
FT /evidence="ECO:0007829|PDB:6OIT"
FT HELIX 53..98
FT /evidence="ECO:0007829|PDB:6OIT"
FT HELIX 118..123
FT /evidence="ECO:0007829|PDB:6OIT"
FT STRAND 126..128
FT /evidence="ECO:0007829|PDB:6OIT"
FT HELIX 129..138
FT /evidence="ECO:0007829|PDB:6OIT"
FT HELIX 149..152
FT /evidence="ECO:0007829|PDB:6OIT"
FT HELIX 157..160
FT /evidence="ECO:0007829|PDB:6OIT"
FT HELIX 166..181
FT /evidence="ECO:0007829|PDB:6OIT"
FT STRAND 184..188
FT /evidence="ECO:0007829|PDB:6OIT"
FT HELIX 189..195
FT /evidence="ECO:0007829|PDB:6OIT"
FT HELIX 209..215
FT /evidence="ECO:0007829|PDB:6OIT"
FT STRAND 225..229
FT /evidence="ECO:0007829|PDB:6OIT"
FT TURN 230..232
FT /evidence="ECO:0007829|PDB:6OIT"
FT STRAND 265..268
FT /evidence="ECO:0007829|PDB:6OIT"
FT TURN 269..271
FT /evidence="ECO:0007829|PDB:6OIT"
FT STRAND 272..275
FT /evidence="ECO:0007829|PDB:6OIT"
FT HELIX 277..279
FT /evidence="ECO:0007829|PDB:6OIT"
FT STRAND 280..282
FT /evidence="ECO:0007829|PDB:6OIT"
FT TURN 291..293
FT /evidence="ECO:0007829|PDB:6OIT"
FT HELIX 294..298
FT /evidence="ECO:0007829|PDB:6OIT"
FT STRAND 303..307
FT /evidence="ECO:0007829|PDB:6OIT"
FT HELIX 308..313
FT /evidence="ECO:0007829|PDB:6OIT"
FT HELIX 315..317
FT /evidence="ECO:0007829|PDB:6OIT"
FT STRAND 322..327
FT /evidence="ECO:0007829|PDB:6OIT"
FT STRAND 335..339
FT /evidence="ECO:0007829|PDB:6OIT"
FT HELIX 357..406
FT /evidence="ECO:0007829|PDB:6OIT"
SQ SEQUENCE 420 AA; 46767 MW; 8DB3D4E3429FEBAE CRC64;
MYPTGQQISF QTTPLNVQDP TRMMNLDQSS PVARNETQNG GGIAHAEFAM FNSKRLESDL
EAMGNKIKQH EDNLKFLKSQ KNKMDEAIVD LQVHMSKLNS SPTPRSENSD NSLQGEDINA
QILRHENSAA GVLSLVETLH GAQASQLMLT KGVVGVVAKL GKVNDENLSQ ILSNYLGTRS
MLAVVCRNYE SVTALEAYDN HGNIDINAGL HCLGSSIGRE IGDSFDAICL ENLRPYVGQH
IADDLQRRLD LLKPKLPNGE CPPGFLGFAV NMIQIDPAYL LCVTSYGYGL RETLFYNLFS
RLQVYKTRAD MISALPCISD GAVSLDGGII RKTGIFNLGN RDEVNVRFAK PTASRTMDNY
SEAEKKMKEL KWKKEKTLED IKREQVLREH AVFNFGKKKE EFVRCLAQSS CTNQPMNTPR
