ID   FDM1_ARATH              Reviewed;         634 AA.
AC   Q9S9P3;
DT   29-OCT-2014, integrated into UniProtKB/Swiss-Prot.
DT   01-MAY-2000, sequence version 1.
DT   03-AUG-2022, entry version 113.
DE   RecName: Full=Factor of DNA methylation 1 {ECO:0000303|PubMed:22302148};
DE   AltName: Full=Protein IDN2 PARALOG 1 {ECO:0000303|PubMed:22570638};
DE   AltName: Full=Protein IDN2-LIKE 1 {ECO:0000303|PubMed:22592791};
GN   Name=FDM1 {ECO:0000303|PubMed:22302148};
GN   Synonyms=IDNL1 {ECO:0000303|PubMed:22592791},
GN   IDP1 {ECO:0000303|PubMed:22570638};
GN   OrderedLocusNames=At1g15910 {ECO:0000312|Araport:AT1G15910};
GN   ORFNames=T24D18.1 {ECO:0000312|EMBL:AAF18488.1};
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=11130712; DOI=10.1038/35048500;
RA   Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA   Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA   Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA   Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA   Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA   Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA   Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA   Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA   Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA   Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA   Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA   Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA   Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA   Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA   Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT   "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL   Nature 408:816-820(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   FUNCTION, INTERACTION WITH AGO4, TISSUE SPECIFICITY, AND DISRUPTION
RP   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   FUNCTION, SUBUNIT, AND INTERACTION WITH IDN2.
RX   PubMed=22757778; DOI=10.1111/j.1365-313x.2012.05092.x;
RA   Xie M., Ren G., Zhang C., Yu B.;
RT   "The DNA- and RNA-binding protein FACTOR of DNA METHYLATION 1 requires XH
RT   domain-mediated complex formation for its function in RNA-directed DNA
RT   methylation.";
RL   Plant J. 72:491-500(2012).
RN   [5]
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   [6]
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 FDM2/IDNL2 that is required for
CC       RNA-directed DNA methylation (RdDM) and that functions at a downstream
CC       step of the RdDM pathway (PubMed:22302148, PubMed:22757778,
CC       PubMed:22570638, PubMed:22592791). Required for de novo DNA methylation
CC       and 24 nucleotide small interfering RNA (siRNA) accumulation
CC       (PubMed:22570638). Binds unmethylated but not methylated DNAs through
CC       its coiled-coil domain (PubMed:22757778). May bind double-stranded RNAs
CC       (dsRNAs) with 5'-overhangs through its XS domain (PubMed:22302148,
CC       PubMed:22757778). However, according to (PubMed:22570638), FMD1 does
CC       not bind dsRNAs. {ECO:0000269|PubMed:22302148,
CC       ECO:0000269|PubMed:22570638, ECO:0000269|PubMed:22592791,
CC       ECO:0000269|PubMed:22757778}.
CC   -!- SUBUNIT: Homodimer (PubMed:22757778). Interacts with IDN2
CC       (PubMed:22757778, PubMed:22592791) and AGO4 (PubMed:22302148). Forms a
CC       complex with IDN2 and FMD2/INDL2 (PubMed:22570638, PubMed:22592791).
CC       {ECO:0000269|PubMed:22302148, ECO:0000269|PubMed:22592791,
CC       ECO:0000269|PubMed:22757778}.
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}.
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DR   EMBL; AC010924; AAF18488.1; -; Genomic_DNA.
DR   EMBL; CP002684; AEE29382.1; -; Genomic_DNA.
DR   PIR; E86293; E86293.
DR   RefSeq; NP_173043.1; NM_101459.4.
DR   AlphaFoldDB; Q9S9P3; -.
DR   SMR; Q9S9P3; -.
DR   BioGRID; 23401; 2.
DR   STRING; 3702.AT1G15910.1; -.
DR   PaxDb; Q9S9P3; -.
DR   PRIDE; Q9S9P3; -.
DR   ProteomicsDB; 222594; -.
DR   EnsemblPlants; AT1G15910.1; AT1G15910.1; AT1G15910.
DR   GeneID; 838161; -.
DR   Gramene; AT1G15910.1; AT1G15910.1; AT1G15910.
DR   KEGG; ath:AT1G15910; -.
DR   Araport; AT1G15910; -.
DR   TAIR; locus:2200487; AT1G15910.
DR   eggNOG; ENOG502QRE8; Eukaryota.
DR   HOGENOM; CLU_021775_1_1_1; -.
DR   InParanoid; Q9S9P3; -.
DR   OMA; AREDDFR; -.
DR   OrthoDB; 635221at2759; -.
DR   PhylomeDB; Q9S9P3; -.
DR   PRO; PR:Q9S9P3; -.
DR   Proteomes; UP000006548; Chromosome 1.
DR   ExpressionAtlas; Q9S9P3; baseline and differential.
DR   Genevisible; Q9S9P3; AT.
DR   GO; GO:0009506; C:plasmodesma; HDA:TAIR.
DR   GO; GO:0003677; F:DNA binding; IDA:TAIR.
DR   GO; GO:0003725; F:double-stranded RNA binding; IDA:TAIR.
DR   GO; GO:0043621; F:protein self-association; IPI:TAIR.
DR   GO; GO:0003723; F:RNA binding; IDA:TAIR.
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; DNA-binding; Reference proteome; RNA-binding;
KW   RNA-mediated gene silencing.
FT   CHAIN           1..634
FT                   /note="Factor of DNA methylation 1"
FT                   /id="PRO_0000430681"
FT   REGION          349..375
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COILED          288..469
FT                   /evidence="ECO:0000255"
FT   COMPBIAS        349..365
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ   SEQUENCE   634 AA;  72635 MW;  0071930DED7F41B0 CRC64;
     MSISDEEAEI SESEIEDYSE TPYRLLRDGT YKVKVNGQLR CPFCAGKKKQ DYKYKELYAH
     ATGVSKGSAT RSALQKANHL ALAMFLENEL AGYAEPVPRP PVVPPQLDET EPNPHNVYVW
     PWMGIVVNPL KEADDKELLL DSAYWLQTLS KFKPIEVNAF WVEQDSIVGV IAKFNGDWSG
     FAGATELEKE FETQGSSKKE WTERSGDSES KAYGWCARAD DFESQGPIGE YLSKEGQLRT
     VSDISQKNVQ DRNTVLEELS DMIAMTNEDL NKVQYSYNRT AMSLQRVLDE KKNLHQAFAD
     ETKKMQQMSL RHIQKILYDK EKLSNELDRK MRDLESRAKQ LEKHEALTEL DRQKLDEDKR
     KSDAMNKSLQ LASREQKKAD ESVLRLVEEH QRQKEDALNK ILLLEKQLDT KQTLEMEIQE
     LKGKLQVMKH LGDDDDEAVQ KKMKEMNDEL DDKKAELEGL ESMNSVLMTK ERQSNDEIQA
     ARKKLIAGLT GLLGAETDIG VKRMGELDEK PFLDVCKLRY SANEAAVEAA TLCSTWQENL
     KNPSWQPFKH EGTGDGAEEV VDEDDEQLKK LKREWGKEVH NAVKTALVEM NEYNASGRYT
     TPELWNFKEG RKATLKEVIT FISNDIKILK RKRT