MBD2_ARATH
ID MBD2_ARATH Reviewed; 272 AA.
AC Q8LA53; O65234; Q0WRD3; Q84TJ8; Q9FZP7;
DT 08-MAR-2011, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2002, sequence version 1.
DT 03-AUG-2022, entry version 114.
DE RecName: Full=Methyl-CpG-binding domain-containing protein 2;
DE Short=AtMBD2;
DE Short=MBD02;
DE AltName: Full=Methyl-CpG-binding protein MBD2;
GN Name=MBD2; OrderedLocusNames=At5g35330; ORFNames=T26D22.18;
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 NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130714; DOI=10.1038/35048507;
RA Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E.,
RA Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M.,
RA Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.,
RA Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M.,
RA Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L.,
RA O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D.,
RA Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M.,
RA Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L.,
RA Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B.,
RA Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P.,
RA Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M.,
RA Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D.,
RA Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A.,
RA Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I.,
RA Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T.,
RA Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A.,
RA McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U.,
RA Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W.,
RA Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M.,
RA Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S.,
RA Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G.,
RA Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W.,
RA Bevan M., Fransz P.F.;
RT "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana.";
RL Nature 408:823-826(2000).
RN [3]
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 [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
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 NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RA Kim C.J., Chen H., Quinitio C., Shinn P., Ecker J.R.;
RT "Arabidopsis ORF clones.";
RL Submitted (JUN-2006) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1-257.
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 [7]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1-252.
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 [8]
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 [9]
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 [10]
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 [11]
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 [12]
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 [13]
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).
RN [14]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19376835; DOI=10.1104/pp.109.138677;
RA Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A.,
RA Grossmann J., Gruissem W., Baginsky S.;
RT "Large-scale Arabidopsis phosphoproteome profiling reveals novel
RT chloroplast kinase substrates and phosphorylation networks.";
RL Plant Physiol. 150:889-903(2009).
CC -!- FUNCTION: Probable transcriptional regulator. {ECO:0000250}.
CC -!- SUBUNIT: Interacts (via MBD domain) with DDM1.
CC {ECO:0000269|PubMed:15805479}.
CC -!- INTERACTION:
CC Q8LA53; Q9CAV7: At3g04930; NbExp=5; IntAct=EBI-4425826, EBI-15198431;
CC Q8LA53; O81793: At4g35610; NbExp=5; IntAct=EBI-4425826, EBI-15191765;
CC Q8LA53; F4K5T4: At5g28040; NbExp=3; IntAct=EBI-4425826, EBI-15193831;
CC Q8LA53; P46897: ATHB-7; NbExp=3; IntAct=EBI-4425826, EBI-15193277;
CC Q8LA53; Q9LNJ5: BHLH13; NbExp=3; IntAct=EBI-4425826, EBI-4434261;
CC Q8LA53; O81801: DAZ3; NbExp=5; IntAct=EBI-4425826, EBI-4447483;
CC Q8LA53; Q04996: HAT3.1; NbExp=4; IntAct=EBI-4425826, EBI-4457944;
CC Q8LA53; Q38828: IAA10; NbExp=4; IntAct=EBI-4425826, EBI-3946434;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:14605234,
CC ECO:0000269|PubMed:15805479}. Note=Not present in chromocenters and the
CC nucleolus.
CC -!- TISSUE SPECIFICITY: Expressed in buds, flowers, stems, siliques and
CC mature seeds. {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 -!- SEQUENCE CAUTION:
CC Sequence=AAC13602.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=BAB11480.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AB025636; BAB11480.1; ALT_INIT; Genomic_DNA.
DR EMBL; AF058826; AAC13602.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002688; AED93952.1; -; Genomic_DNA.
DR EMBL; CP002688; AED93953.1; -; Genomic_DNA.
DR EMBL; CP002688; AED93954.1; -; Genomic_DNA.
DR EMBL; CP002688; ANM69459.1; -; Genomic_DNA.
DR EMBL; AY088026; AAM65572.1; -; mRNA.
DR EMBL; BT025800; ABF83690.1; -; mRNA.
DR EMBL; BT005718; AAO64137.1; -; mRNA.
DR EMBL; AK228378; BAF00316.1; -; mRNA.
DR PIR; T01176; T01176.
DR RefSeq; NP_001190421.1; NM_001203492.2.
DR RefSeq; NP_001331130.1; NM_001344102.1.
DR RefSeq; NP_198383.1; NM_122924.3.
DR RefSeq; NP_974850.1; NM_203121.3.
DR AlphaFoldDB; Q8LA53; -.
DR SMR; Q8LA53; -.
DR BioGRID; 18742; 29.
DR IntAct; Q8LA53; 28.
DR STRING; 3702.AT5G35330.3; -.
DR iPTMnet; Q8LA53; -.
DR PaxDb; Q8LA53; -.
DR PRIDE; Q8LA53; -.
DR ProteomicsDB; 238688; -.
DR DNASU; 833487; -.
DR EnsemblPlants; AT5G35330.1; AT5G35330.1; AT5G35330.
DR EnsemblPlants; AT5G35330.2; AT5G35330.2; AT5G35330.
DR EnsemblPlants; AT5G35330.3; AT5G35330.3; AT5G35330.
DR EnsemblPlants; AT5G35330.4; AT5G35330.4; AT5G35330.
DR GeneID; 833487; -.
DR Gramene; AT5G35330.1; AT5G35330.1; AT5G35330.
DR Gramene; AT5G35330.2; AT5G35330.2; AT5G35330.
DR Gramene; AT5G35330.3; AT5G35330.3; AT5G35330.
DR Gramene; AT5G35330.4; AT5G35330.4; AT5G35330.
DR KEGG; ath:AT5G35330; -.
DR Araport; AT5G35330; -.
DR TAIR; locus:2182643; AT5G35330.
DR eggNOG; KOG4161; Eukaryota.
DR HOGENOM; CLU_061068_0_0_1; -.
DR InParanoid; Q8LA53; -.
DR OMA; WKPDISC; -.
DR OrthoDB; 986130at2759; -.
DR PhylomeDB; Q8LA53; -.
DR PRO; PR:Q8LA53; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q8LA53; baseline and differential.
DR Genevisible; Q8LA53; AT.
DR GO; GO:0000118; C:histone deacetylase complex; IDA:TAIR.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0019899; F:enzyme binding; IPI:UniProtKB.
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..272
FT /note="Methyl-CpG-binding domain-containing protein 2"
FT /id="PRO_0000405278"
FT DOMAIN 118..192
FT /note="MBD"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00338"
FT ZN_FING 53..112
FT /note="CW-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00454"
FT REGION 1..24
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 236..272
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 62..104
FT /note="MBD-associated domain (MAD)"
FT COMPBIAS 1..20
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 236..265
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 63
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00454"
FT BINDING 66
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00454"
FT BINDING 92
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00454"
FT BINDING 104
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00454"
FT CONFLICT 257
FT /note="T -> K (in Ref. 6; AAO64137)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 272 AA; 30767 MW; A42C598A57797887 CRC64;
MSMSQSRAVQ RSSSPNEDRG ENQLVVYDLK GNDDTEEEVL PVQSQPLSSR TQCPSIGAFT
VQCASCFKWR LMPSMQKYEE IREQLLENPF FCDTAREWKP DISCDVPADI YQDGTRLWAI
DKPNISRPPA GWQRLLRIRG EGGTRFADVY YVAPSGKKLR STVEVQKYLN DNSEYIGEGV
KLSQFSFQIP KPLQDDYVRK RPARLLDSID NTNTPVAKEA NPLAWISPDD HISLQLGTPT
ESGLNNSHYQ PSKKKKTSTL SIFGSNDELA DR
