RDM1_ARATH
ID RDM1_ARATH Reviewed; 163 AA.
AC Q9LUJ3; Q84MD0;
DT 30-AUG-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 125.
DE RecName: Full=Protein RDM1;
DE AltName: Full=Protein RNA-directed DNA methylation 1;
GN Name=RDM1; OrderedLocusNames=At3g22680; ORFNames=MWI23.5;
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=10819329; DOI=10.1093/dnares/7.2.131;
RA Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 3. I. Sequence
RT features of the regions of 4,504,864 bp covered by sixty P1 and TAC
RT clones.";
RL DNA Res. 7:131-135(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] OF 1-121.
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 FUNCTION, DISRUPTION PHENOTYPE, AND 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 [5]
RP FUNCTION, MUTAGENESIS OF MET-50 AND 152-TYR--LYS-163, INTERACTION WITH
RP AGO4; RPB205 AND DRM2, SUBCELLULAR LOCATION, SUBUNIT, AND DISRUPTION
RP PHENOTYPE.
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 [6]
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 [7]
RP X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF 8-163.
RX PubMed=16511118; DOI=10.1107/s1744309105019743;
RA Allard S.T., Bingman C.A., Johnson K.A., Wesenberg G.E., Bitto E.,
RA Jeon W.B., Phillips G.N. Jr.;
RT "Structure at 1.6 A resolution of the protein from gene locus At3g22680
RT from Arabidopsis thaliana.";
RL Acta Crystallogr. F 61:647-650(2005).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 8-163.
RG Center for eukaryotic structural genomics (CESG);
RT "Crystal structure of gene product from Arabidopsis thaliana At3g22680 with
RT bound suramin.";
RL Submitted (MAR-2009) to the PDB data bank.
CC -!- FUNCTION: Regulator of RNA-directed DNA methylation (RdDM). Binds to
CC single-stranded methyl DNA. Involved in the assembly of RNA polymerase
CC V (Pol V) transcription initiation or elongation complexes at the
CC chromatin, as a component of the DDR complex.
CC {ECO:0000269|PubMed:20409711, ECO:0000269|PubMed:20410883,
CC ECO:0000269|PubMed:22864289}.
CC -!- SUBUNIT: Homodimer. Interacts with AGO4, RPB205 and DRM2. Part of the
CC chromatin-remodeling complex (DDR complex) that contains at least DRD1,
CC DMS3 and RDM1. The DDR complex recruits/activates the RNA polymerases V
CC and acts during siRNA-directed DNA methylation (RdDM).
CC {ECO:0000269|PubMed:20409711, ECO:0000269|PubMed:20410883}.
CC -!- INTERACTION:
CC Q9LUJ3; Q9ZVD5: AGO4; NbExp=2; IntAct=EBI-15850569, EBI-2352199;
CC Q9LUJ3; Q9M548: DRM2; NbExp=2; IntAct=EBI-15850569, EBI-6923904;
CC Q9LUJ3; P18616: NRPB1; NbExp=2; IntAct=EBI-15850569, EBI-1540537;
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleoplasm
CC {ECO:0000269|PubMed:20410883}. Note=Peri-nucleolar.
CC -!- DISRUPTION PHENOTYPE: Impaired accumulation of siRNAs, reduced DNA
CC methylation, and loss of transcriptional gene silencing at RdDM target
CC loci. Impaired RNA polymerase V-chromatin associations (Pol V).
CC {ECO:0000269|PubMed:20409711, ECO:0000269|PubMed:20410883,
CC ECO:0000269|PubMed:22864289}.
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DR EMBL; AB022223; BAB01243.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE76664.1; -; Genomic_DNA.
DR EMBL; BT006390; AAP21198.1; -; mRNA.
DR RefSeq; NP_188907.2; NM_113167.5.
DR PDB; 1VK5; X-ray; 1.60 A; A=8-163.
DR PDB; 2Q3T; X-ray; 1.60 A; A=8-163.
DR PDB; 3GAN; X-ray; 2.00 A; A=8-163.
DR PDB; 6OIS; EM; 3.60 A; A/B=3-163.
DR PDB; 6OIT; EM; 3.50 A; A/B=3-163.
DR PDBsum; 1VK5; -.
DR PDBsum; 2Q3T; -.
DR PDBsum; 3GAN; -.
DR PDBsum; 6OIS; -.
DR PDBsum; 6OIT; -.
DR AlphaFoldDB; Q9LUJ3; -.
DR SMR; Q9LUJ3; -.
DR BioGRID; 7171; 6.
DR DIP; DIP-59278N; -.
DR IntAct; Q9LUJ3; 3.
DR STRING; 3702.AT3G22680.1; -.
DR PaxDb; Q9LUJ3; -.
DR PRIDE; Q9LUJ3; -.
DR ProteomicsDB; 236344; -.
DR DNASU; 821839; -.
DR EnsemblPlants; AT3G22680.1; AT3G22680.1; AT3G22680.
DR GeneID; 821839; -.
DR Gramene; AT3G22680.1; AT3G22680.1; AT3G22680.
DR KEGG; ath:AT3G22680; -.
DR Araport; AT3G22680; -.
DR TAIR; locus:2094399; AT3G22680.
DR eggNOG; ENOG502RYHT; Eukaryota.
DR HOGENOM; CLU_093312_0_0_1; -.
DR InParanoid; Q9LUJ3; -.
DR OMA; HPRRAES; -.
DR PhylomeDB; Q9LUJ3; -.
DR EvolutionaryTrace; Q9LUJ3; -.
DR PRO; PR:Q9LUJ3; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9LUJ3; baseline and differential.
DR Genevisible; Q9LUJ3; AT.
DR GO; GO:0005654; C:nucleoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0000419; C:RNA polymerase V complex; IMP:UniProtKB.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0043621; F:protein self-association; IDA:UniProtKB.
DR GO; GO:0006306; P:DNA methylation; IGI:TAIR.
DR GO; GO:0044030; P:regulation of DNA methylation; IMP:UniProtKB.
DR GO; GO:0070918; P:small regulatory ncRNA processing; IMP:UniProtKB.
DR Gene3D; 1.20.120.690; -; 1.
DR InterPro; IPR015270; RDM1_plant.
DR InterPro; IPR036319; RDM1_sf.
DR PANTHER; PTHR36366; PTHR36366; 1.
DR Pfam; PF09187; RdDM_RDM1; 1.
DR SUPFAM; SSF109920; SSF109920; 1.
PE 1: Evidence at protein level;
KW 3D-structure; DNA-binding; Nucleus; Reference proteome.
FT CHAIN 1..163
FT /note="Protein RDM1"
FT /id="PRO_0000220605"
FT REGION 1..36
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MUTAGEN 50
FT /note="M->A: Decreased binding to single-stranded methyl
FT DNA."
FT /evidence="ECO:0000269|PubMed:20410883"
FT MUTAGEN 152..163
FT /note="Missing: In rdm1-1; reduced DNA methylation."
FT /evidence="ECO:0000269|PubMed:20410883"
FT CONFLICT 121
FT /note="K -> S (in Ref. 3; AAP21198)"
FT /evidence="ECO:0000305"
FT HELIX 45..56
FT /evidence="ECO:0007829|PDB:2Q3T"
FT HELIX 73..84
FT /evidence="ECO:0007829|PDB:2Q3T"
FT HELIX 90..101
FT /evidence="ECO:0007829|PDB:2Q3T"
FT TURN 102..105
FT /evidence="ECO:0007829|PDB:2Q3T"
FT HELIX 107..110
FT /evidence="ECO:0007829|PDB:6OIT"
FT HELIX 113..115
FT /evidence="ECO:0007829|PDB:2Q3T"
FT HELIX 119..135
FT /evidence="ECO:0007829|PDB:2Q3T"
FT HELIX 139..148
FT /evidence="ECO:0007829|PDB:2Q3T"
FT HELIX 152..155
FT /evidence="ECO:0007829|PDB:2Q3T"
SQ SEQUENCE 163 AA; 18692 MW; 824051FDD1F11DFB CRC64;
MQSSMTMELR PSGDSGSSDV DAEISDGFSP LDTSHRDVAD EGSLLRRAEM YQDYMKQVPI
PTNRGSLIPF TSWVGLSISM KQLYGQPLHY LTNVLLQRWD QSRFGTDSEE QRLDSIIHPT
KAEATIWLVE EIHRLTPSHL HMALLWRSDP MYHSFIDPIF PEK
