MBD4_ARATH
ID MBD4_ARATH Reviewed; 186 AA.
AC Q9LYB9;
DT 08-MAR-2011, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 121.
DE RecName: Full=Methyl-CpG-binding domain-containing protein 4;
DE Short=AtMBD4;
DE Short=MBD04;
DE AltName: Full=Methyl-CpG-binding protein MBD4;
GN Name=MBD4; OrderedLocusNames=At3g63030; ORFNames=T20O10.130;
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=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(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 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 (SEP-2004) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP MAD MOTIF, 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 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 [7]
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 [8]
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 [9]
RP 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).
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.
CC {ECO:0000269|PubMed:14605234}.
CC -!- INTERACTION:
CC Q9LYB9; O81793: At4g35610; NbExp=5; IntAct=EBI-15191715, EBI-15191765;
CC Q9LYB9; F4K5T4: At5g28040; NbExp=3; IntAct=EBI-15191715, EBI-15193831;
CC Q9LYB9; O81801: DAZ3; NbExp=5; IntAct=EBI-15191715, EBI-4447483;
CC Q9LYB9; P49678: IAA2; NbExp=4; IntAct=EBI-15191715, EBI-632343;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:14605234}.
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}.
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DR EMBL; AL163816; CAB87748.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE80426.1; -; Genomic_DNA.
DR EMBL; BT010516; AAQ65139.1; -; mRNA.
DR EMBL; AK176600; BAD44363.1; -; mRNA.
DR PIR; T48092; T48092.
DR RefSeq; NP_191862.1; NM_116168.5.
DR AlphaFoldDB; Q9LYB9; -.
DR SMR; Q9LYB9; -.
DR BioGRID; 10792; 11.
DR IntAct; Q9LYB9; 11.
DR STRING; 3702.AT3G63030.1; -.
DR iPTMnet; Q9LYB9; -.
DR PaxDb; Q9LYB9; -.
DR PRIDE; Q9LYB9; -.
DR ProteomicsDB; 238287; -.
DR EnsemblPlants; AT3G63030.1; AT3G63030.1; AT3G63030.
DR GeneID; 825478; -.
DR Gramene; AT3G63030.1; AT3G63030.1; AT3G63030.
DR KEGG; ath:AT3G63030; -.
DR Araport; AT3G63030; -.
DR TAIR; locus:2099187; AT3G63030.
DR eggNOG; KOG4161; Eukaryota.
DR HOGENOM; CLU_109577_1_0_1; -.
DR InParanoid; Q9LYB9; -.
DR OMA; DIRSKML; -.
DR OrthoDB; 986130at2759; -.
DR PhylomeDB; Q9LYB9; -.
DR PRO; PR:Q9LYB9; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9LYB9; baseline and differential.
DR GO; GO:0000118; C:histone deacetylase complex; IDA:TAIR.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0008327; F:methyl-CpG binding; ISS:TAIR.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR InterPro; IPR016177; DNA-bd_dom_sf.
DR InterPro; IPR001739; Methyl_CpG_DNA-bd.
DR InterPro; IPR011124; Znf_CW.
DR Pfam; PF01429; MBD; 1.
DR Pfam; PF07496; zf-CW; 1.
DR SMART; SM00391; MBD; 1.
DR SUPFAM; SSF54171; SSF54171; 1.
DR PROSITE; PS50982; MBD; 1.
DR PROSITE; PS51050; ZF_CW; 1.
PE 1: Evidence at protein level;
KW DNA-binding; Metal-binding; Nucleus; Reference proteome; Transcription;
KW Transcription regulation; Zinc; Zinc-finger.
FT CHAIN 1..186
FT /note="Methyl-CpG-binding domain-containing protein 4"
FT /id="PRO_0000405280"
FT DOMAIN 83..153
FT /note="MBD"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00338"
FT ZN_FING 22..77
FT /note="CW-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00454"
FT REGION 154..186
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 31..69
FT /note="MBD-associated domain (MAD)"
FT COMPBIAS 167..186
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 32
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00454"
FT BINDING 35
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00454"
FT BINDING 61
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00454"
FT BINDING 69
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00454"
SQ SEQUENCE 186 AA; 21159 MW; 754BED4FF0575A8C CRC64;
MKEEEEIGKP AKPKAKKDVA PGRLIDTYAA QCDNCHKWRV IDSQEEYEDI RSKMLEDPFN
CQKKQGMSCE EPADIDYDSS RTWVIDKPGL PKTPKGFKRS LVLRKDYSKM DTYYFTPTGK
KLRSRNEIAA FVEANPEFRN APLGDFNFTV PKVMEDTVPP DPKLGSPFPS TTTTTSEKSS
VKQSHN
