1ig4

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==Solution Structure of the Methyl-CpG-Binding Domain of Human MBD1 in Complex with Methylated DNA==
==Solution Structure of the Methyl-CpG-Binding Domain of Human MBD1 in Complex with Methylated DNA==
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<StructureSection load='1ig4' size='340' side='right'caption='[[1ig4]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
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<StructureSection load='1ig4' size='340' side='right'caption='[[1ig4]]' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[1ig4]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IG4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IG4 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[1ig4]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IG4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IG4 FirstGlance]. <br>
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</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MBD1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ig4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ig4 OCA], [https://pdbe.org/1ig4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ig4 RCSB], [https://www.ebi.ac.uk/pdbsum/1ig4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ig4 ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ig4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ig4 OCA], [https://pdbe.org/1ig4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ig4 RCSB], [https://www.ebi.ac.uk/pdbsum/1ig4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ig4 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[https://www.uniprot.org/uniprot/MBD1_HUMAN MBD1_HUMAN]] Transcriptional repressor that binds CpG islands in promoters where the DNA is methylated at position 5 of cytosine within CpG dinucleotides. Binding is abolished by the presence of 7-mG that is produced by DNA damage by methylmethanesulfonate (MMS). Acts as transcriptional repressor and plays a role in gene silencing by recruiting AFT7IP, which in turn recruits factors such as the histone methyltransferase SETDB1. Probably forms a complex with SETDB1 and ATF7IP that represses transcription and couples DNA methylation and histone 'Lys-9' trimethylation. Isoform 1 and isoform 2 can also repress transcription from unmethylated promoters.<ref>PMID:9207790</ref> <ref>PMID:10454587</ref> <ref>PMID:9774669</ref> <ref>PMID:10648624</ref> <ref>PMID:12711603</ref> <ref>PMID:12665582</ref> <ref>PMID:12697822</ref> <ref>PMID:14610093</ref> <ref>PMID:15327775</ref> <ref>PMID:14555760</ref>
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[https://www.uniprot.org/uniprot/MBD1_HUMAN MBD1_HUMAN] Transcriptional repressor that binds CpG islands in promoters where the DNA is methylated at position 5 of cytosine within CpG dinucleotides. Binding is abolished by the presence of 7-mG that is produced by DNA damage by methylmethanesulfonate (MMS). Acts as transcriptional repressor and plays a role in gene silencing by recruiting AFT7IP, which in turn recruits factors such as the histone methyltransferase SETDB1. Probably forms a complex with SETDB1 and ATF7IP that represses transcription and couples DNA methylation and histone 'Lys-9' trimethylation. Isoform 1 and isoform 2 can also repress transcription from unmethylated promoters.<ref>PMID:9207790</ref> <ref>PMID:10454587</ref> <ref>PMID:9774669</ref> <ref>PMID:10648624</ref> <ref>PMID:12711603</ref> <ref>PMID:12665582</ref> <ref>PMID:12697822</ref> <ref>PMID:14610093</ref> <ref>PMID:15327775</ref> <ref>PMID:14555760</ref>
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1ig4 ConSurf].
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1ig4 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
 
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== Publication Abstract from PubMed ==
 
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In vertebrates, the biological consequences of DNA methylation are often mediated by protein factors containing conserved methyl-CpG binding domains (MBDs). Mutations in the MBD protein MeCP2 cause the neurodevelopmental disease Rett syndrome. We report here the solution structure of the MBD of the human methylation-dependent transcriptional regulator MBD1 bound to methylated DNA. DNA binding causes a loop in MBD1 to fold into a major and novel DNA binding interface. Recognition of the methyl groups and CG sequence at the methylation site is due to five highly conserved residues that form a hydrophobic patch. The structure indicates how MBD may access nucleosomal DNA without encountering steric interference from core histones, and provides a basis to interpret mutations linked to Rett syndrome in MeCP2.
 
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Solution structure of the methyl-CpG binding domain of human MBD1 in complex with methylated DNA.,Ohki I, Shimotake N, Fujita N, Jee J, Ikegami T, Nakao M, Shirakawa M Cell. 2001 May 18;105(4):487-97. PMID:11371345<ref>PMID:11371345</ref>
 
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 
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</div>
 
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<div class="pdbe-citations 1ig4" style="background-color:#fffaf0;"></div>
 
==See Also==
==See Also==
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Human]]
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[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Fujita, N]]
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[[Category: Fujita N]]
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[[Category: Ikegami, T]]
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[[Category: Ikegami T]]
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[[Category: Jee, J G]]
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[[Category: Jee J-G]]
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[[Category: Nakao, M]]
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[[Category: Nakao M]]
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[[Category: Ohki, I]]
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[[Category: Ohki I]]
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[[Category: Shimotake, N]]
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[[Category: Shimotake N]]
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[[Category: Shirakawa, M]]
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[[Category: Shirakawa M]]
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[[Category: Alpha-beta]]
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[[Category: Double helix]]
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[[Category: Protein-dna complex]]
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[[Category: Recognition via beta-sheet]]
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[[Category: Transcription-dna complex]]
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Revision as of 07:46, 3 April 2024

Solution Structure of the Methyl-CpG-Binding Domain of Human MBD1 in Complex with Methylated DNA

PDB ID 1ig4

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