FDM2_ARATH
ID FDM2_ARATH Reviewed; 635 AA.
AC F4JH53; O23064;
DT 29-OCT-2014, integrated into UniProtKB/Swiss-Prot.
DT 28-JUN-2011, sequence version 1.
DT 25-MAY-2022, entry version 57.
DE RecName: Full=Factor of DNA methylation 2 {ECO:0000303|PubMed:22302148};
DE AltName: Full=Protein IDN2 PARALOG 2 {ECO:0000303|PubMed:22570638};
DE AltName: Full=Protein IDN2-LIKE 2;
GN Name=FDM2 {ECO:0000303|PubMed:22302148};
GN Synonyms=IDNL2 {ECO:0000303|PubMed:22592791},
GN IDP2 {ECO:0000303|PubMed:22570638};
GN OrderedLocusNames=At4g00380 {ECO:0000312|Araport:AT4G00380};
GN ORFNames=A_IG005I10.22 {ECO:0000312|EMBL:AAB62840.1},
GN F5I10.22 {ECO:0000312|EMBL:AAF02798.1};
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:AEE81871.1};
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(1999).
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 FUNCTION, TISSUE SPECIFICITY, AND DISRUPTION PHENOTYPE.
RX PubMed=22302148; DOI=10.1093/nar/gks034;
RA Xie M., Ren G., Costa-Nunes P., Pontes O., Yu B.;
RT "A subgroup of SGS3-like proteins act redundantly in RNA-directed DNA
RT methylation.";
RL Nucleic Acids Res. 40:4422-4431(2012).
RN [4]
RP IDENTIFICATION BY MASS SPECTROMETRY, FUNCTION, AND SUBUNIT.
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 [5]
RP IDENTIFICATION BY MASS SPECTROMETRY, FUNCTION, SUBUNIT, AND DISRUPTION
RP 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).
CC -!- FUNCTION: Forms a complex with IDN2 and FDM1/IDNL1 that is required for
CC RNA-directed DNA methylation (RdDM) and that functions at a downstream
CC step of the RdDM pathway. {ECO:0000269|PubMed:22302148,
CC ECO:0000269|PubMed:22570638, ECO:0000269|PubMed:22592791}.
CC -!- SUBUNIT: Forms a complex with IDN2 and FMD1/INDL1.
CC {ECO:0000269|PubMed:22570638, ECO:0000269|PubMed:22592791}.
CC -!- TISSUE SPECIFICITY: Highly expressed in flowers and at lower levels in
CC roots, leaves and stems. {ECO:0000269|PubMed:22302148}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype under normal growth
CC conditions. The double mutants idnl1-1 and idnl2-1 show a late-
CC flowering phenotype and reduced level of DNA methylation
CC (PubMed:22592791). The double mutants fdm1-1 and fdm2-1 show reduced
CC level of DNA methylation and repeat-associated small interfering RNAs
CC (ra-siRNAs) (PubMed:22302148). {ECO:0000269|PubMed:22302148,
CC ECO:0000269|PubMed:22592791}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAB62840.1; Type=Erroneous gene model prediction;
CC Sequence=AAF02798.1; Type=Erroneous gene model prediction;
CC Sequence=CAB80796.1; Type=Erroneous gene model prediction;
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DR EMBL; AF013293; AAB62840.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AF195115; AAF02798.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL161471; CAB80796.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002687; AEE81871.1; -; Genomic_DNA.
DR EMBL; CP002687; ANM67981.1; -; Genomic_DNA.
DR PIR; T01533; T01533.
DR RefSeq; NP_001319829.1; NM_001340242.1.
DR RefSeq; NP_567176.2; NM_116262.3.
DR AlphaFoldDB; F4JH53; -.
DR SMR; F4JH53; -.
DR BioGRID; 13307; 1.
DR STRING; 3702.AT4G00380.1; -.
DR PaxDb; F4JH53; -.
DR PRIDE; F4JH53; -.
DR ProteomicsDB; 232077; -.
DR EnsemblPlants; AT4G00380.1; AT4G00380.1; AT4G00380.
DR EnsemblPlants; AT4G00380.3; AT4G00380.3; AT4G00380.
DR GeneID; 828016; -.
DR Gramene; AT4G00380.1; AT4G00380.1; AT4G00380.
DR Gramene; AT4G00380.3; AT4G00380.3; AT4G00380.
DR KEGG; ath:AT4G00380; -.
DR Araport; AT4G00380; -.
DR TAIR; locus:2126081; AT4G00380.
DR eggNOG; ENOG502QRE8; Eukaryota.
DR HOGENOM; CLU_021775_1_1_1; -.
DR InParanoid; F4JH53; -.
DR OMA; YMASMEL; -.
DR OrthoDB; 635221at2759; -.
DR PRO; PR:F4JH53; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; F4JH53; baseline and differential.
DR Genevisible; F4JH53; AT.
DR GO; GO:0080188; P:gene silencing by RNA-directed DNA methylation; IGI:TAIR.
DR GO; GO:0010569; P:regulation of double-strand break repair via homologous recombination; 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 Coiled coil; Reference proteome; RNA-mediated gene silencing.
FT CHAIN 1..635
FT /note="Factor of DNA methylation 2"
FT /id="PRO_0000430682"
FT REGION 350..376
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 289..471
FT /evidence="ECO:0000255"
FT COMPBIAS 350..366
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 635 AA; 73165 MW; 43124190F21B6144 CRC64;
MDISDEESEI SESEIEEYSK TPYHLLRSET YYKVKVNGRL RCPFCVGKKK QDYKYKELHA
HATGVSKGSA TRSALQKSNH LALAKFLEND LAGYAEPLPR PPVVPPLLDE TEPNPHNVYV
WPWMGIVVNP LKETDDKELL LDSVYWLQTL SKFKPVEVNA FWVEQDSIVG VIAKFDSDWS
GFAAATELEK EFETQGSCKK EWTERSGDSE SKAYGWCARA DDFQSQGPIG EYLSKEGTLR
TVSDILQNNV QDRNTLLDVL SNMIDMTNED LNKAQHSYNR TAMSLQRVLD EKKNLHQAFA
EETKKMQQMS LRHIQRILYD KEKLRNELDR KMRDLESRAK QLEKHEALTE LERQKLDEDK
RKSDAMNKSL QLASREQKKA DESVLRLVEE HQRQKEDALN KILLLEKQLD TKQTLEMEIQ
ELKGKLQVMK HLGDDDDEAV QTKMKEMNDE LDDKKAELED LESMNSVLMT KERQSNDEIQ
AARQKMIAGL TGLLGAESDI GVKRMGELDE KPFLDVCKLR YSANEARVEA ATLCSTWKEN
LKNPSWQPFK REGTGDGAEE VVDEDDEQLK KLKREWGKEV HNAVKAALVE MNEYNASGRY
PTSELWNFKE GRKATLKEVI TFISTDIKNL KRKRT
