MBD6_ARATH
ID MBD6_ARATH Reviewed; 225 AA.
AC Q9LTJ1;
DT 08-MAR-2011, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 124.
DE RecName: Full=Methyl-CpG-binding domain-containing protein 6 {ECO:0000303|PubMed:12954765};
DE Short=AtMBD6 {ECO:0000303|PubMed:12954765};
DE Short=MBD06 {ECO:0000303|PubMed:12954765};
DE AltName: Full=Methyl-CpG-binding protein MBD6 {ECO:0000303|PubMed:12954765};
GN Name=MBD6 {ECO:0000303|PubMed:12954765};
GN OrderedLocusNames=At5g59380 {ECO:0000312|Araport:AT5G59380};
GN ORFNames=F2O15.4 {ECO:0000312|EMBL:BAA97474.1};
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;
RA Kaneko T., Katoh T., Asamizu E., Sato S., Nakamura Y., Kotani H.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. XI.";
RL Submitted (APR-1999) to the EMBL/GenBank/DDBJ databases.
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 NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP 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 FUNCTION, SUBCELLULAR LOCATION, AND TISSUE SPECIFICITY.
RC STRAIN=cv. Columbia;
RX PubMed=15010609; DOI=10.1023/b:plan.0000019118.56822.a9;
RA Scebba F., Bernacchia G., De Bastiani M., Evangelista M., Cantoni R.M.,
RA Cella R., Locci M.T., Pitto L.;
RT "Arabidopsis MBD proteins show different binding specificities and nuclear
RT localization.";
RL Plant Mol. Biol. 53:715-731(2003).
RN [8]
RP FUNCTION, AND 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 [9]
RP SUBCELLULAR LOCATION, AND INTERACTION WITH DDM1.
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 [10]
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 [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 SUBCELLULAR LOCATION, DIMERIZATION, AND INTERACTION WITH MBD5.
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 FUNCTION, DISRUPTION PHENOTYPE, AND SUBCELLULAR LOCATION.
RX PubMed=19061642; DOI=10.1016/j.molcel.2008.11.009;
RA Preuss S.B., Costa-Nunes P., Tucker S., Pontes O., Lawrence R.J.,
RA Mosher R., Kasschau K.D., Carrington J.C., Baulcombe D.C., Viegas W.,
RA Pikaard C.S.;
RT "Multimegabase silencing in nucleolar dominance involves siRNA-directed DNA
RT methylation and specific methylcytosine-binding proteins.";
RL Mol. Cell 32:673-684(2008).
RN [14]
RP FUNCTION, DISRUPTION PHENOTYPE, AND INTERACTION WITH NTF2; RPS2C; HDA6 AND
RP AGO4.
RX PubMed=28229965; DOI=10.1007/s12038-016-9658-1;
RA Parida A.P., Sharma A., Sharma A.K.;
RT "AtMBD6, a methyl CpG binding domain protein, maintains gene silencing in
RT Arabidopsis by interacting with RNA binding proteins.";
RL J. Biosci. 42:57-68(2017).
CC -!- FUNCTION: Transcriptional regulator that binds CpG, CpNpN and CpNpG (N
CC is A, T, or C) islands in promoters regardless the DNA methylation
CC status. Plays probably a role in gene silencing. May associate with
CC histone deacetylase proteins (HDAC). Required for nucleolar dominance
CC that consist in the silencing of rRNA genes inherited from one
CC progenitor in genetic hybrids. Recruited to rRNA genes in a DRM2-
CC dependent manner. Maintains gene silencing by interacting with RNA
CC binding proteins (e.g. NTF2, RPS2C, HDA6 and AGO4) and by regulating
CC DNA methylation status (PubMed:28229965). {ECO:0000269|PubMed:12787239,
CC ECO:0000269|PubMed:14605234, ECO:0000269|PubMed:15010609,
CC ECO:0000269|PubMed:19061642, ECO:0000269|PubMed:28229965}.
CC -!- SUBUNIT: Homodimer and heterodimer with MBD5 (PubMed:18211904).
CC Interacts with DDM1 via its MBD domain (PubMed:15805479). Interacts
CC with NTF2, RPS2C, HDA6 and AGO4 (PubMed:28229965).
CC {ECO:0000269|PubMed:15805479, ECO:0000269|PubMed:18211904,
CC ECO:0000269|PubMed:28229965}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:14605234,
CC ECO:0000269|PubMed:15010609, ECO:0000269|PubMed:15805479,
CC ECO:0000269|PubMed:17208509, ECO:0000269|PubMed:18211904,
CC ECO:0000269|PubMed:19061642}. Chromosome {ECO:0000269|PubMed:15010609,
CC ECO:0000269|PubMed:15805479, ECO:0000269|PubMed:17208509,
CC ECO:0000269|PubMed:18211904, ECO:0000269|PubMed:19061642}. Nucleus,
CC nucleolus {ECO:0000269|PubMed:19061642}. Note=Associated with
CC heterochromatin, and particularly at perinucleolar chromocenters and
CC nucleolus organizer regions (NORs) in a DRM2-dependent manner.
CC {ECO:0000269|PubMed:15010609, ECO:0000269|PubMed:15805479,
CC ECO:0000269|PubMed:17208509, ECO:0000269|PubMed:18211904,
CC ECO:0000269|PubMed:19061642}.
CC -!- TISSUE SPECIFICITY: Expressed in rosette leaves, buds, flowers, stems,
CC mature seeds and roots. {ECO:0000269|PubMed:12954765,
CC ECO:0000269|PubMed:15010609}.
CC -!- DOMAIN: The methyl-CpG-binding domain (MBD) functions both in binding
CC to methylated DNA and in protein interactions. {ECO:0000250}.
CC -!- DISRUPTION PHENOTYPE: Impaired nucleolar dominance (PubMed:19061642).
CC Reduced DNA methylation in some of the targets of RNA-directed DNA
CC methylation (RdDM) and loss of DNA methylation in 180 bp centromeric
CC repeats (PubMed:28229965). {ECO:0000269|PubMed:19061642,
CC ECO:0000269|PubMed:28229965}.
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DR EMBL; AB025604; BAA97474.1; -; Genomic_DNA.
DR EMBL; CP002688; AED97178.1; -; Genomic_DNA.
DR EMBL; BT004606; AAO42852.1; -; mRNA.
DR EMBL; AK227565; BAE99559.1; -; mRNA.
DR RefSeq; NP_200746.1; NM_125329.4.
DR PDB; 7D8K; NMR; -; A=78-140.
DR PDB; 7FEF; X-ray; 2.39 A; A=67-137.
DR PDBsum; 7D8K; -.
DR PDBsum; 7FEF; -.
DR AlphaFoldDB; Q9LTJ1; -.
DR SMR; Q9LTJ1; -.
DR BioGRID; 21301; 21.
DR IntAct; Q9LTJ1; 16.
DR STRING; 3702.AT5G59380.1; -.
DR iPTMnet; Q9LTJ1; -.
DR PaxDb; Q9LTJ1; -.
DR PRIDE; Q9LTJ1; -.
DR ProteomicsDB; 250924; -.
DR EnsemblPlants; AT5G59380.1; AT5G59380.1; AT5G59380.
DR GeneID; 836057; -.
DR Gramene; AT5G59380.1; AT5G59380.1; AT5G59380.
DR KEGG; ath:AT5G59380; -.
DR Araport; AT5G59380; -.
DR TAIR; locus:2148308; AT5G59380.
DR eggNOG; KOG4161; Eukaryota.
DR HOGENOM; CLU_113092_0_0_1; -.
DR InParanoid; Q9LTJ1; -.
DR OMA; DWATAFT; -.
DR OrthoDB; 1329208at2759; -.
DR PhylomeDB; Q9LTJ1; -.
DR PRO; PR:Q9LTJ1; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q9LTJ1; baseline and differential.
DR Genevisible; Q9LTJ1; AT.
DR GO; GO:0000792; C:heterochromatin; IDA:UniProtKB.
DR GO; GO:0005731; C:nucleolus organizer region; IDA:UniProtKB.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0010370; C:perinucleolar chromocenter; IDA:TAIR.
DR GO; GO:0009536; C:plastid; HDA:TAIR.
DR GO; GO:0019899; F:enzyme binding; IPI:UniProtKB.
DR GO; GO:0008327; F:methyl-CpG binding; IDA:TAIR.
DR GO; GO:0043621; F:protein self-association; IDA:UniProtKB.
DR GO; GO:0031047; P:gene silencing by RNA; IEA:UniProtKB-KW.
DR InterPro; IPR016177; DNA-bd_dom_sf.
DR InterPro; IPR001739; Methyl_CpG_DNA-bd.
DR Pfam; PF01429; MBD; 1.
DR SMART; SM00391; MBD; 1.
DR SUPFAM; SSF54171; SSF54171; 1.
DR PROSITE; PS50982; MBD; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Chromosome; DNA-binding; Nucleus; Reference proteome;
KW RNA-mediated gene silencing; Transcription; Transcription regulation.
FT CHAIN 1..225
FT /note="Methyl-CpG-binding domain-containing protein 6"
FT /id="PRO_0000405282"
FT DOMAIN 71..146
FT /note="MBD"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00338"
FT REGION 25..92
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT TURN 78..80
FT /evidence="ECO:0007829|PDB:7D8K"
FT STRAND 86..91
FT /evidence="ECO:0007829|PDB:7FEF"
FT TURN 96..99
FT /evidence="ECO:0007829|PDB:7FEF"
FT STRAND 101..106
FT /evidence="ECO:0007829|PDB:7FEF"
FT TURN 108..110
FT /evidence="ECO:0007829|PDB:7FEF"
FT STRAND 113..116
FT /evidence="ECO:0007829|PDB:7FEF"
FT HELIX 117..125
FT /evidence="ECO:0007829|PDB:7FEF"
SQ SEQUENCE 225 AA; 24450 MW; 3DAF03A0A89AF5C0 CRC64;
MSDSVAGDFP PDPLLASGAF ISSAGDGTLD SSAKRRPIQG GIGISGSGES VRIGMANGTD
QVNHQTESKS RKRAAPGDNW LPPGWRVEDK IRTSGATAGS VDKYYYEPNT GRKFRSRTEV
LYYLEHGTSK RGTKKAENTY FNPDHFEGQG SNRVTRTATV PPPPPPPLDF DFKNPPDKVS
WSMANAGEEG WIPNIGDVKV QDSVRRDWST AFTFITSRNP SKVSA
