MBD5_ARATH
ID MBD5_ARATH Reviewed; 182 AA.
AC Q9SNC0; Q8LCG6;
DT 08-MAR-2011, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 129.
DE RecName: Full=Methyl-CpG-binding domain-containing protein 5;
DE Short=AtMBD5;
DE Short=MBD05;
DE AltName: Full=Methyl-CpG-binding protein MBD5;
GN Name=MBD5; OrderedLocusNames=At3g46580; ORFNames=F12A12.100;
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].
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) 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, SUBCELLULAR LOCATION, AND TISSUE SPECIFICITY.
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 MBD6.
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).
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. In addition, binds specifically methylated m(5)CpNpN but
CC not m(5)CpNpG (N is A, T or C). Plays probably a role in gene
CC silencing. {ECO:0000269|PubMed:12787239, ECO:0000269|PubMed:14605234,
CC ECO:0000269|PubMed:15010609}.
CC -!- SUBUNIT: Homodimer and heterodimer with MBD6. Interacts with DDM1 via
CC its MBD domain. {ECO:0000269|PubMed:15805479,
CC ECO:0000269|PubMed:18211904}.
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}. Chromosome
CC {ECO:0000269|PubMed:15010609, ECO:0000269|PubMed:15805479,
CC ECO:0000269|PubMed:17208509}. Note=Associated with heterochromatin, and
CC particularly at perinucleolar chromocenters.
CC {ECO:0000269|PubMed:15010609, ECO:0000269|PubMed:15805479,
CC ECO:0000269|PubMed:17208509}.
CC -!- TISSUE SPECIFICITY: Mostly expressed in flowers, and, to a lower
CC extent, in seedlings, buds, stems and mature seeds, but barely in
CC roots, exclusively in root meristem cells at tips (at protein level).
CC {ECO:0000269|PubMed:12954765, ECO:0000269|PubMed:14605234,
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; AL133314; CAB62328.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE78174.1; -; Genomic_DNA.
DR EMBL; AY063849; AAL36205.1; -; mRNA.
DR EMBL; AY142653; AAN13191.1; -; mRNA.
DR EMBL; AY086606; AAM63666.1; -; mRNA.
DR PIR; T45595; T45595.
DR RefSeq; NP_190242.1; NM_114525.3.
DR PDB; 7FEO; X-ray; 2.20 A; A/B=28-98.
DR PDBsum; 7FEO; -.
DR AlphaFoldDB; Q9SNC0; -.
DR SMR; Q9SNC0; -.
DR BioGRID; 9131; 10.
DR IntAct; Q9SNC0; 7.
DR STRING; 3702.AT3G46580.1; -.
DR iPTMnet; Q9SNC0; -.
DR PaxDb; Q9SNC0; -.
DR PRIDE; Q9SNC0; -.
DR ProteomicsDB; 238352; -.
DR EnsemblPlants; AT3G46580.1; AT3G46580.1; AT3G46580.
DR GeneID; 823811; -.
DR Gramene; AT3G46580.1; AT3G46580.1; AT3G46580.
DR KEGG; ath:AT3G46580; -.
DR Araport; AT3G46580; -.
DR TAIR; locus:2075135; AT3G46580.
DR eggNOG; KOG4161; Eukaryota.
DR HOGENOM; CLU_113092_0_0_1; -.
DR InParanoid; Q9SNC0; -.
DR OMA; TVDKFYY; -.
DR OrthoDB; 1329208at2759; -.
DR PhylomeDB; Q9SNC0; -.
DR PRO; PR:Q9SNC0; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9SNC0; baseline and differential.
DR Genevisible; Q9SNC0; AT.
DR GO; GO:0000792; C:heterochromatin; IDA:UniProtKB.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0010370; C:perinucleolar chromocenter; IDA: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 InterPro; IPR016177; DNA-bd_dom_sf.
DR InterPro; IPR001739; Methyl_CpG_DNA-bd.
DR Pfam; PF01429; 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 Transcription; Transcription regulation.
FT CHAIN 1..182
FT /note="Methyl-CpG-binding domain-containing protein 5"
FT /id="PRO_0000405281"
FT DOMAIN 25..101
FT /note="MBD"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00338"
FT REGION 1..56
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 80..126
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 80..116
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT CONFLICT 147
FT /note="A -> T (in Ref. 4; AAM63666)"
FT /evidence="ECO:0000305"
FT STRAND 40..46
FT /evidence="ECO:0007829|PDB:7FEO"
FT TURN 50..53
FT /evidence="ECO:0007829|PDB:7FEO"
FT STRAND 55..60
FT /evidence="ECO:0007829|PDB:7FEO"
FT TURN 62..64
FT /evidence="ECO:0007829|PDB:7FEO"
FT STRAND 67..70
FT /evidence="ECO:0007829|PDB:7FEO"
FT HELIX 71..80
FT /evidence="ECO:0007829|PDB:7FEO"
SQ SEQUENCE 182 AA; 20558 MW; E0E99E21382275D1 CRC64;
MSNGTDQAQP PPENPATPVD SKSRKRATPG DDNWLPPDWR TEIRVRTSGT KAGTVDKFYY
EPITGRKFRS KNEVLYYLEH GTPKKKSVKT AENGDSHSEH SEGRGSARRQ TKSNKKVTEP
PPKPLNFDFL NVPEKVTWTG INGSEEAWLP FIGDYKIQES VSQDWDRVFT LVTSQNAGKT
MF
