MBD7_ARATH
ID MBD7_ARATH Reviewed; 306 AA.
AC Q9FJF4;
DT 08-MAR-2011, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 1.
DT 25-MAY-2022, entry version 126.
DE RecName: Full=Methyl-CpG-binding domain-containing protein 7 {ECO:0000303|PubMed:12954765};
DE Short=AtMBD7 {ECO:0000303|PubMed:12954765};
DE Short=MBD07 {ECO:0000303|PubMed:12954765};
DE AltName: Full=Methyl-CpG-binding protein MBD7;
GN Name=MBD7 {ECO:0000303|PubMed:12954765};
GN OrderedLocusNames=At5g59800 {ECO:0000312|Araport:AT5G59800};
GN ORFNames=MMN10.2 {ECO:0000312|EMBL:BAB08347.1};
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=9872454; DOI=10.1093/dnares/5.5.297;
RA Nakamura Y., Sato S., Asamizu E., Kaneko T., Kotani H., Miyajima N.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. VII. Sequence
RT features of the regions of 1,013,767 bp covered by sixteen physically
RT assigned P1 and TAC clones.";
RL DNA Res. 5:297-308(1998).
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] (ISOFORM 1).
RC STRAIN=cv. Columbia;
RA Kim C.J., Chen H., Cheuk R.F., Shinn P., Ecker J.R.;
RT "Arabidopsis ORF clones.";
RL Submitted (OCT-2004) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 2 AND 3).
RC STRAIN=cv. Columbia;
RX PubMed=14993207; DOI=10.1101/gr.1515604;
RA Castelli V., Aury J.-M., Jaillon O., Wincker P., Clepet C., Menard M.,
RA Cruaud C., Quetier F., Scarpelli C., Schaechter V., Temple G., Caboche M.,
RA Weissenbach J., Salanoubat M.;
RT "Whole genome sequence comparisons and 'full-length' cDNA sequences: a
RT combined approach to evaluate and improve Arabidopsis genome annotation.";
RL Genome Res. 14:406-413(2004).
RN [5]
RP ALTERNATIVE SPLICING, TISSUE SPECIFICITY, GENE FAMILY, AND NOMENCLATURE.
RX PubMed=12954765; DOI=10.1093/nar/gkg735;
RA Berg A., Meza T.J., Mahic M., Thorstensen T., Kristiansen K., Aalen R.B.;
RT "Ten members of the Arabidopsis gene family encoding methyl-CpG-binding
RT domain proteins are transcriptionally active and at least one, AtMBD11, is
RT crucial for normal development.";
RL Nucleic Acids Res. 31:5291-5304(2003).
RN [6]
RP FUNCTION.
RX PubMed=12787239; DOI=10.1046/j.1365-313x.2003.01756.x;
RA Zemach A., Grafi G.;
RT "Characterization of Arabidopsis thaliana methyl-CpG-binding domain (MBD)
RT proteins.";
RL Plant J. 34:565-572(2003).
RN [7]
RP SUBCELLULAR LOCATION.
RX PubMed=14605234; DOI=10.1104/pp.103.026708;
RA Ito M., Koike A., Koizumi N., Sano H.;
RT "Methylated DNA-binding proteins from Arabidopsis.";
RL Plant Physiol. 133:1747-1754(2003).
RN [8]
RP SUBCELLULAR LOCATION.
RX PubMed=15805479; DOI=10.1105/tpc.105.031567;
RA Zemach A., Li Y., Wayburn B., Ben-Meir H., Kiss V., Avivi Y., Kalchenko V.,
RA Jacobsen S.E., Grafi G.;
RT "DDM1 binds Arabidopsis methyl-CpG binding domain proteins and affects
RT their subnuclear localization.";
RL Plant Cell 17:1549-1558(2005).
RN [9]
RP GENE FAMILY.
RX PubMed=15888682; DOI=10.1104/pp.105.060566;
RA Springer N.M., Kaeppler S.M.;
RT "Evolutionary divergence of monocot and dicot methyl-CpG-binding domain
RT proteins.";
RL Plant Physiol. 138:92-104(2005).
RN [10]
RP INTERACTION WITH PRMT11, SUBCELLULAR LOCATION, AND METHYLATION AT ARG-118;
RP ARG-145 AND ARG-174.
RC STRAIN=cv. Columbia, and cv. Landsberg erecta;
RX PubMed=17711414; DOI=10.1111/j.1365-313x.2007.03238.x;
RA Scebba F., De Bastiani M., Bernacchia G., Andreucci A., Galli A., Pitto L.;
RT "PRMT11: a new Arabidopsis MBD7 protein partner with arginine
RT methyltransferase activity.";
RL Plant J. 52:210-222(2007).
RN [11]
RP SUBCELLULAR LOCATION, AND REVIEW.
RX PubMed=17208509; DOI=10.1016/j.tplants.2006.12.004;
RA Zemach A., Grafi G.;
RT "Methyl-CpG-binding domain proteins in plants: interpreters of DNA
RT methylation.";
RL Trends Plant Sci. 12:80-85(2007).
RN [12]
RP FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=18211904; DOI=10.1074/jbc.m706221200;
RA Zemach A., Gaspan O., Grafi G.;
RT "The three methyl-CpG-binding domains of AtMBD7 control its subnuclear
RT localization and mobility.";
RL J. Biol. Chem. 283:8406-8411(2008).
RN [13]
RP DOMAIN, AND MUTAGENESIS OF 263-LYS--LYS-266; ILE-302; GLU-303; ASP-304;
RP ARG-305 AND SER-306.
RX PubMed=19647732; DOI=10.1016/j.yexcr.2009.07.022;
RA Zemach A., Paul L.K., Stambolsky P., Efroni I., Rotter V., Grafi G.;
RT "The C-terminal domain of the Arabidopsis AtMBD7 protein confers strong
RT chromatin binding activity.";
RL Exp. Cell Res. 315:3554-3562(2009).
RN [14]
RP FUNCTION, INTERACTION WITH IDM2 AND IDM3, DISRUPTION PHENOTYPE, AND DOMAIN.
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 [15]
RP FUNCTION, DEVELOPMENTAL STAGE, INTERACTION WITH IDM2, AND SUBCELLULAR
RP 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: Transcriptional regulator that binds CpG islands in promoters
CC where the DNA is methylated at position 5 of cytosine within CpG
CC dinucleotides. May directly affect chromatin structure by inducing
CC intra- and inter- chromatin compaction via bridging over multiple
CC methylated CpG sites. Acts as an anti-silencing factor that prevents
CC DNA hypermethylation and gene repression (PubMed:25684209). Requires
CC high mCG density for binding (PubMed:25684209, PubMed:25593350).
CC Recognizes preferentially mCGs located in transposable elements
CC (PubMed:25684209, PubMed:25593350). Required for active DNA
CC demethylation (PubMed:25593350). Prefers to target genomic loci around
CC chromocenters (PubMed:25593350). {ECO:0000269|PubMed:12787239,
CC ECO:0000269|PubMed:18211904, ECO:0000269|PubMed:25593350,
CC ECO:0000269|PubMed:25684209}.
CC -!- SUBUNIT: Interacts with PRMT11 (PubMed:17711414). Interacts (via C-
CC terminus) with IDM2, but not with IDM1 (PubMed:25684209,
CC PubMed:25593350). Interacts with IDM3 (PubMed:25684209). Part of a
CC complex made of MBD7, IDM1, IDM2 and IDM3 (PubMed:25684209).
CC {ECO:0000269|PubMed:17711414, ECO:0000269|PubMed:25593350,
CC ECO:0000269|PubMed:25684209}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:14605234,
CC ECO:0000269|PubMed:15805479, ECO:0000269|PubMed:17208509,
CC ECO:0000269|PubMed:17711414, ECO:0000269|PubMed:18211904,
CC ECO:0000269|PubMed:25593350}. Chromosome {ECO:0000269|PubMed:14605234,
CC ECO:0000269|PubMed:17208509, ECO:0000269|PubMed:18211904,
CC ECO:0000269|PubMed:25593350}. Note=Associated with heterochromatin, at
CC all chromocenters. Excluded from nucleolus.
CC {ECO:0000269|PubMed:14605234, ECO:0000269|PubMed:17208509,
CC ECO:0000269|PubMed:17711414, ECO:0000269|PubMed:18211904,
CC ECO:0000269|PubMed:25593350}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=3;
CC Name=1; Synonyms=AtMBD7a;
CC IsoId=Q9FJF4-1; Sequence=Displayed;
CC Name=2; Synonyms=AtMBD7b;
CC IsoId=Q9FJF4-2; Sequence=VSP_040659;
CC Name=3; Synonyms=AtMBD7b;
CC IsoId=Q9FJF4-3; Sequence=VSP_040658;
CC -!- TISSUE SPECIFICITY: Expressed in leaves, buds, flowers, stems,
CC siliques, mature seeds and roots. {ECO:0000269|PubMed:12954765}.
CC -!- DEVELOPMENTAL STAGE: Highly expressed at the early seedling stage.
CC {ECO:0000269|PubMed:25593350}.
CC -!- DOMAIN: The methyl-CpG-binding domain (MBD) functions both in binding
CC to methylated DNA and in protein interactions (By similarity). The
CC number of MBD domains may affect binding affinity, mobility within the
CC nucleus, and subnuclear localization (By similarity). The C-terminal
CC domain (232-306) has a very strong chromatin binding affinity and thus
CC is coined 'sticky-C' (StkC) (PubMed:19647732). StkC confers
CC intranuclear immobility, but has no effect on subnuclear localization
CC (PubMed:19647732). It is necessary for the interaction with IDM2 and
CC IDM3, and for the anti-silencing function (PubMed:25684209).
CC {ECO:0000250, ECO:0000269|PubMed:19647732,
CC ECO:0000269|PubMed:25684209}.
CC -!- PTM: Methylated by PRMT11. {ECO:0000269|PubMed:17711414}.
CC -!- DISRUPTION PHENOTYPE: DNA hypermethylation and transgene silencing
CC phenotype. {ECO:0000269|PubMed:25684209}.
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DR EMBL; AB015475; BAB08347.1; -; Genomic_DNA.
DR EMBL; CP002688; AED97235.1; -; Genomic_DNA.
DR EMBL; BT014975; AAT70426.1; -; mRNA.
DR EMBL; BT015848; AAU94411.1; -; mRNA.
DR EMBL; BX829918; -; NOT_ANNOTATED_CDS; mRNA.
DR RefSeq; NP_200788.1; NM_125372.4. [Q9FJF4-1]
DR AlphaFoldDB; Q9FJF4; -.
DR SMR; Q9FJF4; -.
DR BioGRID; 21345; 10.
DR IntAct; Q9FJF4; 6.
DR STRING; 3702.AT5G59800.1; -.
DR iPTMnet; Q9FJF4; -.
DR PaxDb; Q9FJF4; -.
DR PRIDE; Q9FJF4; -.
DR ProteomicsDB; 238353; -. [Q9FJF4-1]
DR EnsemblPlants; AT5G59800.1; AT5G59800.1; AT5G59800. [Q9FJF4-1]
DR GeneID; 836101; -.
DR Gramene; AT5G59800.1; AT5G59800.1; AT5G59800. [Q9FJF4-1]
DR KEGG; ath:AT5G59800; -.
DR Araport; AT5G59800; -.
DR TAIR; locus:2168047; AT5G59800.
DR eggNOG; KOG4161; Eukaryota.
DR HOGENOM; CLU_047890_0_0_1; -.
DR InParanoid; Q9FJF4; -.
DR OMA; KNSHYID; -.
DR OrthoDB; 1373746at2759; -.
DR PhylomeDB; Q9FJF4; -.
DR PRO; PR:Q9FJF4; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q9FJF4; baseline and differential.
DR Genevisible; Q9FJF4; AT.
DR GO; GO:0010369; C:chromocenter; IDA:UniProtKB.
DR GO; GO:0005694; C:chromosome; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0019899; F:enzyme binding; IPI:UniProtKB.
DR GO; GO:0008327; F:methyl-CpG binding; IDA:TAIR.
DR GO; GO:1901537; P:positive regulation of DNA demethylation; IMP:TAIR.
DR InterPro; IPR016177; DNA-bd_dom_sf.
DR InterPro; IPR001739; Methyl_CpG_DNA-bd.
DR Pfam; PF01429; MBD; 2.
DR SUPFAM; SSF54171; SSF54171; 3.
DR PROSITE; PS50982; MBD; 3.
PE 1: Evidence at protein level;
KW Alternative splicing; Chromosome; DNA-binding; Methylation; Nucleus;
KW Reference proteome; Repeat; Transcription; Transcription regulation.
FT CHAIN 1..306
FT /note="Methyl-CpG-binding domain-containing protein 7"
FT /id="PRO_0000405283"
FT DOMAIN 21..92
FT /note="MBD 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00338"
FT DOMAIN 106..171
FT /note="MBD 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00338"
FT DOMAIN 172..242
FT /note="MBD 3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00338"
FT REGION 1..21
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 163..306
FT /note="Required for interaction with PRMT11"
FT /evidence="ECO:0000269|PubMed:17711414"
FT MOD_RES 118
FT /note="Asymmetric dimethylarginine"
FT /evidence="ECO:0000305|PubMed:17711414"
FT MOD_RES 145
FT /note="Asymmetric dimethylarginine"
FT /evidence="ECO:0000305|PubMed:17711414"
FT MOD_RES 174
FT /note="Asymmetric dimethylarginine"
FT /evidence="ECO:0000305|PubMed:17711414"
FT VAR_SEQ 1..101
FT /note="MQTRSSSSPSANHRRETQLQIADPTSFCGKIMPGWTVVNRPRSSNNGVVDTY
FT FIEPGTGRQFSSLEAIHRHLAGEVNDRRLTRAGSFFQDKTRVYEGSRTK -> MLL
FT (in isoform 3)"
FT /evidence="ECO:0000303|PubMed:14993207"
FT /id="VSP_040658"
FT VAR_SEQ 103..306
FT /note="DHCGVEYASKGFRLPRGWSVEEVPRKNSHYIDKYYVERKTGKRFRSLVSVER
FT YLRESRNSIEQQLRVLQNRRGHSKDFRLPDGWIVEEKPRRSSSHIDRSYIEPGTGNKFR
FT SMAAVERYLISVGNITLDSVSMVHSERLPLLMNRNGIRFQSEVIDPNPPKKVKWVLTGS
FT GGNMFTANVRGSNVSSLVKHTWSEAFVSLIEDRS -> VLCSDLKLQKHMVLLGSNT
FT (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14993207"
FT /id="VSP_040659"
FT MUTAGEN 263..266
FT /note="KKVK->AAVA: No effect on intranuclear immobility."
FT /evidence="ECO:0000269|PubMed:19647732"
FT MUTAGEN 302
FT /note="I->A: Slight increase in intranuclear mobility."
FT /evidence="ECO:0000269|PubMed:19647732"
FT MUTAGEN 303
FT /note="E->A: Loss of intranuclear immobility."
FT /evidence="ECO:0000269|PubMed:19647732"
FT MUTAGEN 304
FT /note="D->A: Slight increase in intranuclear mobility."
FT /evidence="ECO:0000269|PubMed:19647732"
FT MUTAGEN 305
FT /note="R->A: No effect on intranuclear immobility."
FT /evidence="ECO:0000269|PubMed:19647732"
FT MUTAGEN 306
FT /note="S->A: No effect on intranuclear immobility."
FT /evidence="ECO:0000269|PubMed:19647732"
SQ SEQUENCE 306 AA; 35034 MW; 2E362F9FA6543660 CRC64;
MQTRSSSSPS ANHRRETQLQ IADPTSFCGK IMPGWTVVNR PRSSNNGVVD TYFIEPGTGR
QFSSLEAIHR HLAGEVNDRR LTRAGSFFQD KTRVYEGSRT KQDHCGVEYA SKGFRLPRGW
SVEEVPRKNS HYIDKYYVER KTGKRFRSLV SVERYLRESR NSIEQQLRVL QNRRGHSKDF
RLPDGWIVEE KPRRSSSHID RSYIEPGTGN KFRSMAAVER YLISVGNITL DSVSMVHSER
LPLLMNRNGI RFQSEVIDPN PPKKVKWVLT GSGGNMFTAN VRGSNVSSLV KHTWSEAFVS
LIEDRS
