IDM1_ARATH
ID IDM1_ARATH Reviewed; 1189 AA.
AC F4IXE7; Q9LKA7;
DT 01-APR-2015, integrated into UniProtKB/Swiss-Prot.
DT 28-JUN-2011, sequence version 1.
DT 03-AUG-2022, entry version 73.
DE RecName: Full=Increased DNA methylation 1 {ECO:0000303|PubMed:22700931};
DE AltName: Full=Histone H3 acetyltransferase IDM1 {ECO:0000305};
DE EC=2.3.1.- {ECO:0000255|PROSITE-ProRule:PRU00532};
DE AltName: Full=Protein ROS4 {ECO:0000303|PubMed:22733760};
DE AltName: Full=Repressor of silencing 4 {ECO:0000303|PubMed:22733760};
GN Name=IDM1 {ECO:0000303|PubMed:22700931};
GN Synonyms=ROS4 {ECO:0000303|PubMed:22733760};
GN OrderedLocusNames=At3g14980 {ECO:0000312|Araport:AT3G14980};
GN ORFNames=K15M2.12 {ECO:0000312|EMBL:BAA97061.1};
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|Proteomes:UP000006548};
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10907853; DOI=10.1093/dnares/7.3.217;
RA Kaneko T., Katoh T., Sato S., Nakamura Y., Asamizu E., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 3. II. Sequence
RT features of the 4,251,695 bp regions covered by 90 P1, TAC and BAC
RT clones.";
RL DNA Res. 7:217-221(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, SUBCELLULAR LOCATION, AND TISSUE SPECIFICITY.
RX PubMed=22733760; DOI=10.1073/pnas.1208557109;
RA Li X., Qian W., Zhao Y., Wang C., Shen J., Zhu J.K., Gong Z.;
RT "Antisilencing role of the RNA-directed DNA methylation pathway and a
RT histone acetyltransferase in Arabidopsis.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:11425-11430(2012).
RN [4]
RP FUNCTION, DISRUPTION PHENOTYPE, DOMAIN, MUTAGENESIS OF CYS-732; CYS-740;
RP ASP-924; GLU-941 AND MET-942, AND SUBCELLULAR LOCATION.
RX PubMed=22700931; DOI=10.1126/science.1219416;
RA Qian W., Miki D., Zhang H., Liu Y., Zhang X., Tang K., Kan Y., La H.,
RA Li X., Li S., Zhu X., Shi X., Zhang K., Pontes O., Chen X., Liu R.,
RA Gong Z., Zhu J.K.;
RT "A histone acetyltransferase regulates active DNA demethylation in
RT Arabidopsis.";
RL Science 336:1445-1448(2012).
RN [5]
RP FUNCTION, INTERACTION WITH IDM2, AND SUBCELLULAR LOCATION.
RX PubMed=25002145; DOI=10.1016/j.molcel.2014.06.008;
RA Qian W., Miki D., Lei M., Zhu X., Zhang H., Liu Y., Li Y., Lang Z.,
RA Wang J., Tang K., Liu R., Zhu J.K.;
RT "Regulation of active DNA demethylation by an alpha-crystallin domain
RT protein in Arabidopsis.";
RL Mol. Cell 55:361-371(2014).
RN [6]
RP INTERACTION WITH IDM2, DOMAIN, AND SUBCELLULAR LOCATION.
RX PubMed=24920332; DOI=10.1105/tpc.114.126730;
RA Zhao Y., Xie S., Li X., Wang C., Chen Z., Lai J., Gong Z.;
RT "REPRESSOR OF SILENCING5 encodes a member of the small heat shock protein
RT family and is required for DNA demethylation in Arabidopsis.";
RL Plant Cell 26:2660-2675(2014).
RN [7]
RP INTERACTION WITH IDM2 AND IDM3.
RX PubMed=25684209; DOI=10.1016/j.molcel.2015.01.009;
RA Lang Z., Lei M., Wang X., Tang K., Miki D., Zhang H., Mangrauthia S.K.,
RA Liu W., Nie W., Ma G., Yan J., Duan C.G., Hsu C.C., Wang C., Tao W.A.,
RA Gong Z., Zhu J.K.;
RT "The methyl-CpG-binding protein MBD7 facilitates active DNA demethylation
RT to limit DNA hyper-methylation and transcriptional gene silencing.";
RL Mol. Cell 57:971-983(2015).
CC -!- FUNCTION: Histone H3 acetyltransferase that binds methylated DNA at
CC chromatin sites lacking histone H3K4 di- or trimethylation and
CC catalyzes H3K18 and H3K23 acetylation (PubMed:22733760,
CC PubMed:22700931). Prevents the transcriptional silencing of transgenes
CC and of some endogenous genes (PubMed:22733760, PubMed:22700931).
CC Requires the presence of IDM2 for efficient H3K18 acetylation, but not
CC for H3K23 acetylation (PubMed:25002145). {ECO:0000269|PubMed:22700931,
CC ECO:0000269|PubMed:22733760, ECO:0000269|PubMed:25002145}.
CC -!- SUBUNIT: Interacts (via N-terminus) with IDM2 (PubMed:25002145,
CC PubMed:24920332, PubMed:25684209). Interacts with IMD3
CC (PubMed:25684209). Part of a complex made of MBD7, IDM1, IDM2 and IDM3
CC (PubMed:25684209). {ECO:0000269|PubMed:24920332,
CC ECO:0000269|PubMed:25002145, ECO:0000269|PubMed:25684209}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:22700931,
CC ECO:0000269|PubMed:22733760, ECO:0000269|PubMed:24920332,
CC ECO:0000269|PubMed:25002145}. Note=Colocalizes with IDM2 within
CC nucleoplasmic and nucleolar foci. {ECO:0000269|PubMed:24920332,
CC ECO:0000269|PubMed:25002145}.
CC -!- TISSUE SPECIFICITY: Expressed in cotyledons and hypocotyls in young
CC seedlings. {ECO:0000269|PubMed:22733760}.
CC -!- DOMAIN: The PHD finger domain specifically binds the N-terminal tail of
CC histone H3 and this binding is inhibited by H3K4 di- or trimethylation
CC (PubMed:22700931). No effect of H3K9 methylation on the binding
CC (PubMed:22700931). The N-terminal domain (1-592) is required for
CC interactions with IDM2 (PubMed:24920332). {ECO:0000269|PubMed:22700931,
CC ECO:0000269|PubMed:24920332}.
CC -!- DISRUPTION PHENOTYPE: DNA hypermethylation.
CC {ECO:0000269|PubMed:22700931}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAA97061.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AP000370; BAA97061.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002686; AEE75596.1; -; Genomic_DNA.
DR EMBL; CP002686; ANM64196.1; -; Genomic_DNA.
DR EMBL; CP002686; ANM64199.1; -; Genomic_DNA.
DR RefSeq; NP_001326242.1; NM_001338147.1.
DR RefSeq; NP_001326245.1; NM_001338143.1.
DR RefSeq; NP_188116.1; NM_112360.3.
DR AlphaFoldDB; F4IXE7; -.
DR SMR; F4IXE7; -.
DR DIP; DIP-60052N; -.
DR STRING; 3702.AT3G14980.1; -.
DR PaxDb; F4IXE7; -.
DR PRIDE; F4IXE7; -.
DR EnsemblPlants; AT3G14980.1; AT3G14980.1; AT3G14980.
DR EnsemblPlants; AT3G14980.2; AT3G14980.2; AT3G14980.
DR EnsemblPlants; AT3G14980.6; AT3G14980.6; AT3G14980.
DR GeneID; 820727; -.
DR Gramene; AT3G14980.1; AT3G14980.1; AT3G14980.
DR Gramene; AT3G14980.2; AT3G14980.2; AT3G14980.
DR Gramene; AT3G14980.6; AT3G14980.6; AT3G14980.
DR KEGG; ath:AT3G14980; -.
DR Araport; AT3G14980; -.
DR TAIR; locus:2086395; AT3G14980.
DR eggNOG; ENOG502QTVY; Eukaryota.
DR HOGENOM; CLU_004098_0_0_1; -.
DR InParanoid; F4IXE7; -.
DR OrthoDB; 406167at2759; -.
DR BRENDA; 2.3.1.48; 399.
DR PRO; PR:F4IXE7; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; F4IXE7; baseline and differential.
DR Genevisible; F4IXE7; AT.
DR GO; GO:0005634; C:nucleus; IDA:TAIR.
DR GO; GO:0009506; C:plasmodesma; HDA:TAIR.
DR GO; GO:0010385; F:double-stranded methylated DNA binding; IPI:TAIR.
DR GO; GO:0004402; F:histone acetyltransferase activity; IDA:TAIR.
DR GO; GO:0042393; F:histone binding; IDA:TAIR.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0080188; P:gene silencing by RNA-directed DNA methylation; IMP:TAIR.
DR GO; GO:0044154; P:histone H3-K14 acetylation; IDA:TAIR.
DR GO; GO:0043971; P:histone H3-K18 acetylation; IDA:TAIR.
DR GO; GO:0043972; P:histone H3-K23 acetylation; IDA:TAIR.
DR GO; GO:0044030; P:regulation of DNA methylation; IMP:TAIR.
DR Gene3D; 3.30.40.10; -; 1.
DR InterPro; IPR016181; Acyl_CoA_acyltransferase.
DR InterPro; IPR000182; GNAT_dom.
DR InterPro; IPR031086; IDM1.
DR InterPro; IPR032308; TDBD.
DR InterPro; IPR011011; Znf_FYVE_PHD.
DR InterPro; IPR001965; Znf_PHD.
DR InterPro; IPR019787; Znf_PHD-finger.
DR InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR PANTHER; PTHR46508:SF2; PTHR46508:SF2; 2.
DR Pfam; PF00628; PHD; 1.
DR Pfam; PF16135; TDBD; 1.
DR SMART; SM00249; PHD; 2.
DR SUPFAM; SSF55729; SSF55729; 1.
DR SUPFAM; SSF57903; SSF57903; 1.
DR PROSITE; PS51186; GNAT; 1.
DR PROSITE; PS01359; ZF_PHD_1; 1.
DR PROSITE; PS50016; ZF_PHD_2; 1.
PE 1: Evidence at protein level;
KW Acyltransferase; Metal-binding; Nucleus; Reference proteome; Repeat;
KW Transcription; Transcription regulation; Transferase; Zinc; Zinc-finger.
FT CHAIN 1..1189
FT /note="Increased DNA methylation 1"
FT /id="PRO_0000432653"
FT DOMAIN 879..1024
FT /note="N-acetyltransferase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00532"
FT ZN_FING 726..771
FT /note="PHD-type 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT ZN_FING 767..823
FT /note="PHD-type 2; degenerate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT REGION 475..498
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 523..597
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1031..1157
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 569..593
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1093..1117
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1129..1143
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MUTAGEN 732
FT /note="C->W: Loss of binding to histone H3 and loss of
FT acetyltransferase activity."
FT /evidence="ECO:0000269|PubMed:22700931"
FT MUTAGEN 740
FT /note="C->W: Loss of binding to histone H3, but no effect
FT on acetyltransferase activity."
FT /evidence="ECO:0000269|PubMed:22700931"
FT MUTAGEN 924
FT /note="D->A: Strongly decreased acetyltransferase
FT activity."
FT /evidence="ECO:0000269|PubMed:22700931"
FT MUTAGEN 941
FT /note="E->Q: Loss of acetyltransferase activity."
FT /evidence="ECO:0000269|PubMed:22700931"
FT MUTAGEN 942
FT /note="M->A: Decreased acetyltransferase activity."
FT /evidence="ECO:0000269|PubMed:22700931"
SQ SEQUENCE 1189 AA; 131329 MW; 2525874DB1831D2A CRC64;
MLPGAEIEML GGDCFEGSYE DHQIFREVFF GSDPGNTTKR CLVTGAINFE CDSSKNVNSS
LSSNSVVTSG YACPQGFEAS ASRDGSDFNT KAKRVKLSGN KHLDARDEKG SALHGFPTSD
IARETIPLHL VESSNKGVST SSYLLKHSIV KGREVYLGGI VSGKCKSLNL DKCDGKEFKA
IASPVSQESF ATRMISVGAS TPHSEKACFP LQLNNGSKVS PNELIMSKTC LKIDPKEDPR
PLLYKYVCKV LTAARWKIEK RERSAGRKHV DTFYISPEGR KFREFGSAWK ALGGILLADR
KLMDTGTKKW TGINDFWSDL SLTLLDIEEN MKNLNLANTR ALWWSALEPF VVVVFISKQV
GSLRKGNKVE VARNSNPDKL KKEDTICLNL ISGCPESVLT VSEGSHLVHD VDANQEIHSD
LEVQTKISSQ KVSSRLERQS IIGKEISGTH EQEASKGIVA SKLIAEDMHE SVMRKNLHRR
SKKISDIKPA SLDQHDSLDS NSLNSFEFQD KEMGNIHLVS KGSRDERLRN EKMNNSCCNS
KKGRKKARKH YTQDDDLMGS TITRNKGKFS RSSQKKKTQK PKARTKKRNN RGGCRLLPRS
SSNVENHFFQ GNWSILGPRT VLSWLIATKV ISRDEVIQLR DPDDDTVVKT GLVTKDGVVC
TCCNKTVSLS EFKNHAGFNQ NCPCLNLFMG SGKPFASCQL EAWSAEYKAR RNGWRLEKAS
DDDPNDDSCG VCGDGGELIC CDNCPSTFHQ ACLSMQVLPE GSWYCSSCTC WICSELVSDN
AERSQDFKCS QCAHKYHGTC LQGISKRRKL FPETYFCGKN CEKVYNGLSS RVGIINPNAD
GLSWSILKCF QEDGMVHSAR RLALKAECNS KLAVALSIME ESFLSMVDPR TGIDMIPHVL
YNWGSTFARL DFDGFYTVVV EKDDVMISVA SIRVHGVTIA EMPLVATCSK YRRQGMCRIL
VAAIEEMLMS LKVEKLVVAA LPSLVETWTE GFGFKPMDDE ERDALKRINL MVFPGTTLLK
KTLYESTKPS TMKGVCLSKE RNNPSNKEAD LEPGLDKAGS PMSTQVESCD QMVPAGSDDE
PSPGFPVPLG ADQTEPTSET ENPSRDSNAN DRPNKTTVVS IGEEEEEECL QKDVSKLSEE
GKETTRASSS SAALEEVSGL GLGVVNNVSD EMLLCVDEQL DSDSSQDSE
