IDN2_ARATH
ID IDN2_ARATH Reviewed; 647 AA.
AC Q8VZ79; Q9SMN2;
DT 29-OCT-2014, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2002, sequence version 1.
DT 03-AUG-2022, entry version 118.
DE RecName: Full=Protein INVOLVED IN DE NOVO 2 {ECO:0000303|PubMed:19915591};
DE AltName: Full=Protein RNA-DIRECTED DNA METHYLATION 12 {ECO:0000303|PubMed:20059743};
GN Name=IDN2 {ECO:0000303|PubMed:19915591};
GN Synonyms=RDM12 {ECO:0000303|PubMed:20059743};
GN OrderedLocusNames=At3g48670 {ECO:0000312|Araport:AT3G48670};
GN ORFNames=T8P19.180 {ECO:0000312|EMBL:CAB62356.1};
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 {ECO:0000312|EMBL:AAL38360.1};
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 FUNCTION, DISRUPTION PHENOTYPE, AND MUTAGENESIS OF ASN-116 AND PHE-165.
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 [5]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=20059743; DOI=10.1111/j.1365-313x.2010.04130.x;
RA Zheng Z., Xing Y., He X.J., Li W., Hu Y., Yadav S.K., Oh J., Zhu J.K.;
RT "An SGS3-like protein functions in RNA-directed DNA methylation and
RT transcriptional gene silencing in Arabidopsis.";
RL Plant J. 62:92-99(2010).
RN [6]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=22810086; DOI=10.4161/epi.21237;
RA Finke A., Kuhlmann M., Mette M.F.;
RT "IDN2 has a role downstream of siRNA formation in RNA-directed DNA
RT methylation.";
RL Epigenetics 7:950-960(2012).
RN [7]
RP IDENTIFICATION BY MASS SPECTROMETRY, FUNCTION, SUBUNIT, AND DISRUPTION
RP PHENOTYPE.
RX PubMed=22570638; DOI=10.1371/journal.pgen.1002693;
RA Zhang C.J., Ning Y.Q., Zhang S.W., Chen Q., Shao C.R., Guo Y.W., Zhou J.X.,
RA Li L., Chen S., He X.J.;
RT "IDN2 and its paralogs form a complex required for RNA-directed DNA
RT methylation.";
RL PLoS Genet. 8:E1002693-E1002693(2012).
RN [8]
RP FUNCTION, AND HOMODIMERIZATION.
RX PubMed=23246435; DOI=10.1016/j.molcel.2012.11.011;
RA Zhu Y., Rowley M.J., Bohmdorfer G., Wierzbicki A.T.;
RT "A SWI/SNF chromatin-remodeling complex acts in noncoding RNA-mediated
RT transcriptional silencing.";
RL Mol. Cell 49:298-309(2013).
RN [9]
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).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (2.70 ANGSTROMS) OF 120-290, IDENTIFICATION BY MASS
RP SPECTROMETRY, FUNCTION, SUBUNIT, AND DISRUPTION PHENOTYPE.
RX PubMed=22592791; DOI=10.1073/pnas.1206638109;
RA Ausin I., Greenberg M.V., Simanshu D.K., Hale C.J., Vashisht A.A.,
RA Simon S.A., Lee T.F., Feng S., Espanola S.D., Meyers B.C.,
RA Wohlschlegel J.A., Patel D.J., Jacobsen S.E.;
RT "INVOLVED IN DE NOVO 2-containing complex involved in RNA-directed DNA
RT methylation in Arabidopsis.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:8374-8381(2012).
RN [11]
RP FUNCTION, AND INTERACTION WITH MORC6.
RX PubMed=27171427; DOI=10.1371/journal.pgen.1006026;
RA Liu Z.-W., Zhou J.-X., Huang H.-W., Li Y.-Q., Shao C.-R., Li L., Cai T.,
RA Chen S., He X.-J.;
RT "Two components of the RNA-Directed DNA methylation pathway associate with
RT MORC6 and silence loci targeted by MORC6 in Arabidopsis.";
RL PLoS Genet. 12:E1006026-E1006026(2016).
CC -!- FUNCTION: Forms a complex with FDM1/IDNL1 and FDM2/IDNL2 that is
CC required for RNA-directed DNA methylation (RdDM) and that functions at
CC a downstream step of the RdDM pathway (PubMed:22570638,
CC PubMed:22592791) and downstream of small interfering RNA (siRNA)
CC formation (PubMed:22810086). Required for de novo DNA methylation,
CC siRNA accumulation and siRNA-mediated maintenance methylation
CC (PubMed:19915591). Required for several post-transcriptional gene
CC silencing pathways (PubMed:20059743). Binds double-stranded RNAs
CC (dsRNAs) with 5'-overhangs through its XS domain (PubMed:19915591,
CC PubMed:20059743). Binds long non-coding RNA (lncRNA) in an AGO4-
CC dependent manner and associates with DRM2, resulting in DNA methylation
CC of RdDM target loci (PubMed:23246435, PubMed:24862207). Mediates the
CC silencing of a subset of MORC6 target loci (PubMed:27171427).
CC {ECO:0000269|PubMed:19915591, ECO:0000269|PubMed:20059743,
CC ECO:0000269|PubMed:22570638, ECO:0000269|PubMed:22592791,
CC ECO:0000269|PubMed:22810086, ECO:0000269|PubMed:23246435,
CC ECO:0000269|PubMed:24862207, ECO:0000269|PubMed:27171427}.
CC -!- SUBUNIT: Interacts with FMD1/IDNL1 (PubMed:22592791). Forms a complex
CC with FMD1/IDNL1 and FMD2/INDL2 (PubMed:22570638, PubMed:22592791). Can
CC form homodimers (PubMed:22570638, PubMed:23246435). Interacts with
CC MORC6 (PubMed:27171427). {ECO:0000269|PubMed:22570638,
CC ECO:0000269|PubMed:22592791, ECO:0000269|PubMed:23246435,
CC ECO:0000269|PubMed:27171427}.
CC -!- DISRUPTION PHENOTYPE: Late flowering phenotype (PubMed:22592791) and
CC reduction of DNA methylation at RNA-directed DNA methylation (RdDM)
CC target loci (PubMed:19915591, PubMed:20059743, PubMed:22810086,
CC PubMed:22570638, PubMed:22592791). {ECO:0000269|PubMed:19915591,
CC ECO:0000269|PubMed:20059743, ECO:0000269|PubMed:22570638,
CC ECO:0000269|PubMed:22592791, ECO:0000269|PubMed:22810086}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAB62356.1; Type=Erroneous gene model prediction;
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DR EMBL; AL133315; CAB62356.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002686; AEE78442.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE78443.1; -; Genomic_DNA.
DR EMBL; CP002686; ANM65088.1; -; Genomic_DNA.
DR EMBL; AY065184; AAL38360.1; -; mRNA.
DR EMBL; BT000136; AAN15455.1; -; mRNA.
DR PIR; T46211; T46211.
DR RefSeq; NP_001327083.1; NM_001339377.1.
DR RefSeq; NP_190436.2; NM_114726.6.
DR RefSeq; NP_974403.1; NM_202674.3.
DR PDB; 4E8U; X-ray; 2.70 A; A/C=120-290.
DR PDBsum; 4E8U; -.
DR AlphaFoldDB; Q8VZ79; -.
DR SMR; Q8VZ79; -.
DR BioGRID; 9345; 3.
DR STRING; 3702.AT3G48670.1; -.
DR PaxDb; Q8VZ79; -.
DR PRIDE; Q8VZ79; -.
DR ProteomicsDB; 232181; -.
DR EnsemblPlants; AT3G48670.1; AT3G48670.1; AT3G48670.
DR EnsemblPlants; AT3G48670.2; AT3G48670.2; AT3G48670.
DR EnsemblPlants; AT3G48670.3; AT3G48670.3; AT3G48670.
DR GeneID; 824027; -.
DR Gramene; AT3G48670.1; AT3G48670.1; AT3G48670.
DR Gramene; AT3G48670.2; AT3G48670.2; AT3G48670.
DR Gramene; AT3G48670.3; AT3G48670.3; AT3G48670.
DR KEGG; ath:AT3G48670; -.
DR Araport; AT3G48670; -.
DR TAIR; locus:2114560; AT3G48670.
DR eggNOG; ENOG502QRE8; Eukaryota.
DR HOGENOM; CLU_021775_1_1_1; -.
DR InParanoid; Q8VZ79; -.
DR OMA; NVMKHIE; -.
DR OrthoDB; 635221at2759; -.
DR PhylomeDB; Q8VZ79; -.
DR PRO; PR:Q8VZ79; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q8VZ79; baseline and differential.
DR Genevisible; Q8VZ79; AT.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0006306; P:DNA methylation; IMP:TAIR.
DR GO; GO:0080188; P:gene silencing by RNA-directed DNA methylation; IEA:InterPro.
DR GO; GO:0010569; P:regulation of double-strand break repair via homologous recombination; IEP:TAIR.
DR GO; GO:0046686; P:response to cadmium ion; IEP:TAIR.
DR CDD; cd12266; RRM_like_XS; 1.
DR Gene3D; 3.30.70.2890; -; 1.
DR InterPro; IPR045177; FDM1-5/IDN2.
DR InterPro; IPR005379; FDM1-5/IDN2_XH.
DR InterPro; IPR005380; XS_domain.
DR InterPro; IPR038588; XS_domain_sf.
DR InterPro; IPR005381; Znf-XS_domain.
DR PANTHER; PTHR21596; PTHR21596; 1.
DR Pfam; PF03469; XH; 1.
DR Pfam; PF03468; XS; 1.
DR Pfam; PF03470; zf-XS; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Coiled coil; Reference proteome; RNA-binding;
KW RNA-mediated gene silencing.
FT CHAIN 1..647
FT /note="Protein INVOLVED IN DE NOVO 2"
FT /id="PRO_0000430686"
FT REGION 1..20
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 101..123
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 253..508
FT /evidence="ECO:0000255"
FT COMPBIAS 101..115
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MUTAGEN 116
FT /note="N->A: Loss of RNA binding."
FT MUTAGEN 165
FT /note="F->A: Loss of RNA binding."
FT STRAND 126..130
FT /evidence="ECO:0007829|PDB:4E8U"
FT STRAND 132..136
FT /evidence="ECO:0007829|PDB:4E8U"
FT HELIX 154..162
FT /evidence="ECO:0007829|PDB:4E8U"
FT STRAND 168..174
FT /evidence="ECO:0007829|PDB:4E8U"
FT STRAND 176..186
FT /evidence="ECO:0007829|PDB:4E8U"
FT HELIX 191..206
FT /evidence="ECO:0007829|PDB:4E8U"
FT HELIX 211..214
FT /evidence="ECO:0007829|PDB:4E8U"
FT STRAND 217..219
FT /evidence="ECO:0007829|PDB:4E8U"
FT STRAND 225..228
FT /evidence="ECO:0007829|PDB:4E8U"
FT HELIX 231..235
FT /evidence="ECO:0007829|PDB:4E8U"
FT STRAND 236..238
FT /evidence="ECO:0007829|PDB:4E8U"
FT HELIX 239..245
FT /evidence="ECO:0007829|PDB:4E8U"
FT STRAND 249..252
FT /evidence="ECO:0007829|PDB:4E8U"
FT HELIX 253..288
FT /evidence="ECO:0007829|PDB:4E8U"
SQ SEQUENCE 647 AA; 74824 MW; 4AE83BE6376279D0 CRC64;
MGSTVILSSD DEDSDISESE MDEYGDKMYL NLKGGKLKVR LSPQAFICPY CPNKKKTSFQ
YKDLLQHASG VGNSNSDKRS AKEKASHLAL VKYLQQDLAD SASEAEPSSK RQKNGNPIQD
CDHDEKLVYP WKGIVVNIPT TKAQDGRSAG ESGSKLRDEY ILRGFNPTRV RPLWNYLGHS
GTAIVEFNKD WNGLHNGLLF DKAYTVDGHG KKDWLKKDGP KLGLYGWIAR ADDYNGNNII
GENLRKTGDL KTIAELTEEE ARKQELLVQN LRQLVEEKKK DMKEIEELCS VKSEELNQLM
EEKEKNQQKH YRELNAIQER TMSHIQKIVD DHEKLKRLLE SERKKLEIKC NELAKREVHN
GTERMKLSED LEQNASKNSS LELAAMEQQK ADEEVKKLAE DQRRQKEELH EKIIRLERQR
DQKQAIELEV EQLKGQLNVM KHMASDGDAE VVKEVDIIFK DLGEKEAQLA DLDKFNQTLI
LRERRTNDEL QEAHKELVNI MKEWNTNIGV KRMGELVTKP FVDAMQQKYC QQDVEDRAVE
VLQLWEHYLK DSDWHPFKRV KLENEDREVE VIDDRDEKLR ELKADLGDGP YNAVTKALLE
INEYNPSGRY ITTELWNFKA DKKATLEEGV TCLLDQWEKA KRKRGMA
