IDM2_ARATH
ID IDM2_ARATH Reviewed; 349 AA.
AC Q8RWL4; F4HYL2; Q9ZVL2;
DT 01-APR-2015, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2002, sequence version 1.
DT 25-MAY-2022, entry version 112.
DE RecName: Full=Increased DNA methylation 2 {ECO:0000303|PubMed:25002145};
DE AltName: Full=Alpha-crystallin domain-containing protein 39.4 {ECO:0000303|PubMed:16531488};
DE Short=AtAcd39.4 {ECO:0000303|PubMed:16531488};
DE AltName: Full=Protein ROS5 {ECO:0000303|PubMed:24920332};
DE AltName: Full=Repressor of silencing 5 {ECO:0000303|PubMed:24920332};
GN Name=IDM2 {ECO:0000303|PubMed:25002145};
GN Synonyms=ACD39.4 {ECO:0000303|PubMed:16531488},
GN ROS5 {ECO:0000303|PubMed:24920332};
GN OrderedLocusNames=At1g54840 {ECO:0000312|Araport:AT1G54840};
GN ORFNames=F14C21.38 {ECO:0000312|EMBL:AAG51105.1},
GN T22H22.23 {ECO:0000312|EMBL:AAC64893.1};
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:AAM13019.1};
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 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 NOMENCLATURE.
RX PubMed=16531488; DOI=10.1104/pp.105.073841;
RA Ma C., Haslbeck M., Babujee L., Jahn O., Reumann S.;
RT "Identification and characterization of a stress-inducible and a
RT constitutive small heat-shock protein targeted to the matrix of plant
RT peroxisomes.";
RL Plant Physiol. 141:47-60(2006).
RN [5]
RP FUNCTION, DISRUPTION PHENOTYPE, MUTAGENESIS OF ASP-49; GLY-246; GLY-260 AND
RP GLY-276, INDUCTION BY HEAT, SUBCELLULAR LOCATION, AND INTERACTION WITH
RP IDM1.
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 FUNCTION, DISRUPTION PHENOTYPE, MUTAGENESIS OF GLY-246, SUBUNIT,
RP SUBCELLULAR LOCATION, TISSUE SPECIFICITY, INTERACTION WITH IDM1, AND
RP INDUCTION BY HEAT.
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 MBD7; IDM1 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).
RN [8]
RP INTERACTION WITH MBD7, AND SUBCELLULAR LOCATION.
RX PubMed=25593350; DOI=10.1104/pp.114.252106;
RA Wang C., Dong X., Jin D., Zhao Y., Xie S., Li X., He X., Lang Z., Lai J.,
RA Zhu J.K., Gong Z.;
RT "Methyl-CpG-binding domain protein MBD7 is required for active DNA
RT demethylation in Arabidopsis.";
RL Plant Physiol. 167:905-914(2015).
CC -!- FUNCTION: Prevents DNA hypermethylation and transcriptional silencing
CC of transgenes and of some endogenous genes (PubMed:25002145,
CC PubMed:24920332). May act as a molecular chaperone of IDM1, regulating
CC its H3K18 acetylation activity (PubMed:25002145, PubMed:24920332).
CC {ECO:0000269|PubMed:24920332, ECO:0000269|PubMed:25002145}.
CC -!- SUBUNIT: Homodimer or oligomer (PubMed:24920332). May form an 16-mer
CC complex (PubMed:24920332). Interacts with MBD7 (via C-terminus)
CC (PubMed:25684209, PubMed:25593350). Interacts with IDM1 (via N-
CC terminus) (PubMed:25002145, PubMed:24920332, PubMed:25684209).
CC Interacts with IMD3 (PubMed:25684209). Part of a complex made of MBD7,
CC IDM1, IDM2, IDM3 and ROS1 (PubMed:24920332, PubMed:25684209).
CC {ECO:0000269|PubMed:24920332, ECO:0000269|PubMed:25002145,
CC ECO:0000269|PubMed:25593350, ECO:0000269|PubMed:25684209}.
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleoplasm
CC {ECO:0000269|PubMed:24920332, ECO:0000269|PubMed:25002145,
CC ECO:0000269|PubMed:25593350}. Note=Colocalizes with IDM1 within
CC nucleoplasmic and nucleolar foci. {ECO:0000269|PubMed:24920332,
CC ECO:0000269|PubMed:25002145}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1; Synonyms=Acd39.4;
CC IsoId=Q8RWL4-1; Sequence=Displayed;
CC Name=2; Synonyms=Acd30.4;
CC IsoId=Q8RWL4-2; Sequence=VSP_057559, VSP_057560;
CC -!- TISSUE SPECIFICITY: Expressed in cotyledons and hypocotyls in young
CC seedlings. {ECO:0000269|PubMed:24920332}.
CC -!- INDUCTION: Not regulated by heat. {ECO:0000269|PubMed:24920332,
CC ECO:0000269|PubMed:25002145}.
CC -!- DISRUPTION PHENOTYPE: No visible growth or developmental defects under
CC normal growth conditions (PubMed:24920332). DNA hypermethylation
CC (PubMed:25002145). {ECO:0000269|PubMed:24920332,
CC ECO:0000269|PubMed:25002145}.
CC -!- SIMILARITY: Belongs to the small heat shock protein (HSP20) family.
CC {ECO:0000255|PROSITE-ProRule:PRU00285}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAC64893.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
CC Sequence=AAG51105.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AC005388; AAC64893.1; ALT_INIT; Genomic_DNA.
DR EMBL; AC069144; AAG51105.1; ALT_INIT; Genomic_DNA.
DR EMBL; CP002684; AEE33154.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE33155.1; -; Genomic_DNA.
DR EMBL; AY093020; AAM13019.1; -; mRNA.
DR EMBL; AY128943; AAM91343.1; -; mRNA.
DR RefSeq; NP_175881.2; NM_104357.5. [Q8RWL4-1]
DR RefSeq; NP_974031.1; NM_202302.2. [Q8RWL4-2]
DR AlphaFoldDB; Q8RWL4; -.
DR SMR; Q8RWL4; -.
DR IntAct; Q8RWL4; 1.
DR STRING; 3702.AT1G54840.1; -.
DR PaxDb; Q8RWL4; -.
DR PRIDE; Q8RWL4; -.
DR ProteomicsDB; 232125; -. [Q8RWL4-1]
DR EnsemblPlants; AT1G54840.1; AT1G54840.1; AT1G54840. [Q8RWL4-1]
DR EnsemblPlants; AT1G54840.2; AT1G54840.2; AT1G54840. [Q8RWL4-2]
DR GeneID; 841923; -.
DR Gramene; AT1G54840.1; AT1G54840.1; AT1G54840. [Q8RWL4-1]
DR Gramene; AT1G54840.2; AT1G54840.2; AT1G54840. [Q8RWL4-2]
DR KEGG; ath:AT1G54840; -.
DR Araport; AT1G54840; -.
DR TAIR; locus:2010945; AT1G54840.
DR eggNOG; ENOG502QT4Y; Eukaryota.
DR HOGENOM; CLU_043084_0_0_1; -.
DR InParanoid; Q8RWL4; -.
DR OMA; QNVHAVK; -.
DR PhylomeDB; Q8RWL4; -.
DR PRO; PR:Q8RWL4; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q8RWL4; baseline and differential.
DR Genevisible; Q8RWL4; AT.
DR GO; GO:0005654; C:nucleoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; IDA:TAIR.
DR GO; GO:0080111; P:DNA demethylation; IMP:TAIR.
DR GO; GO:0043971; P:histone H3-K18 acetylation; IMP:TAIR.
DR GO; GO:1901537; P:positive regulation of DNA demethylation; IBA:GO_Central.
DR Gene3D; 2.60.40.790; -; 1.
DR InterPro; IPR002068; A-crystallin/Hsp20_dom.
DR InterPro; IPR008978; HSP20-like_chaperone.
DR InterPro; IPR039321; IDM2/3-like.
DR PANTHER; PTHR34661; PTHR34661; 2.
DR SUPFAM; SSF49764; SSF49764; 1.
DR PROSITE; PS01031; SHSP; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Nucleus; Reference proteome; Stress response;
KW Transcription; Transcription regulation.
FT CHAIN 1..349
FT /note="Increased DNA methylation 2"
FT /id="PRO_0000432655"
FT DOMAIN 233..349
FT /note="sHSP"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00285"
FT REGION 210..230
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT VAR_SEQ 266..268
FT /note="RYF -> TVK (in isoform 2)"
FT /id="VSP_057559"
FT VAR_SEQ 269..349
FT /note="Missing (in isoform 2)"
FT /id="VSP_057560"
FT MUTAGEN 49
FT /note="D->E: Loss of function."
FT /evidence="ECO:0000269|PubMed:25002145"
FT MUTAGEN 246
FT /note="G->D: Loss of function, but no effect on the
FT oligomer formation."
FT /evidence="ECO:0000269|PubMed:24920332,
FT ECO:0000269|PubMed:25002145"
FT MUTAGEN 260
FT /note="G->D: Loss of function."
FT /evidence="ECO:0000269|PubMed:25002145"
FT MUTAGEN 276
FT /note="G->E: In idm2-3; DNA hypermethylation and loss of
FT transgenes transcriptional silencing."
FT /evidence="ECO:0000269|PubMed:25002145"
SQ SEQUENCE 349 AA; 39395 MW; 22E6CC55F9B02BBC CRC64;
MSDTMPEIVS PLVAENSQEQ EESVLISLDI EEDKLFLLHF IIGTYFGPDL RKQHHRPKQS
AFQIQALKNV VVDELSGSLM KRAELERVYY HIIRNVDPSL VMKPKKLREY FNAKRNDSNR
DYPLFVDLFP RKLHPETHVR HKFKFIRSIV FINDPDTSCM REECVARFKR LTGLDSFALS
LSVDVTKSNG VVAANEVKVE IDESVEPVKE DNAGTCTSGE ESDVAAKPEV KSEAHGGLMV
GLMDIGECDD AYLFRVSLPG VKRDERYFSC EVEDNGKVLV RGVTTTGGKR VKRYSHVFEM
QTRSLCPPGN FSVSFRLPGP VHPHEFSGNF GTDGILEGVV MKNLQKQTV
