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3vyb

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==Crystal structure of methyl CpG binding domain of MBD4 in complex with the 5mCG/hmCG sequence==
==Crystal structure of methyl CpG binding domain of MBD4 in complex with the 5mCG/hmCG sequence==
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<StructureSection load='3vyb' size='340' side='right' caption='[[3vyb]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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<StructureSection load='3vyb' size='340' side='right'caption='[[3vyb]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3vyb]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VYB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VYB FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3vyb]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VYB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VYB FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
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<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>, <scene name='pdbligand=5HC:2-DEOXY-5-(HYDROXYMETHYL)CYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>5HC</scene></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>, <scene name='pdbligand=5HC:2-DEOXY-5-(HYDROXYMETHYL)CYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>5HC</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3vxv|3vxv]], [[3vxx|3vxx]], [[3vyq|3vyq]]</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3vyb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vyb OCA], [https://pdbe.org/3vyb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vyb RCSB], [https://www.ebi.ac.uk/pdbsum/3vyb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vyb ProSAT]</span></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Mbd4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3vyb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vyb OCA], [http://pdbe.org/3vyb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3vyb RCSB], [http://www.ebi.ac.uk/pdbsum/3vyb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3vyb ProSAT]</span></td></tr>
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</table>
</table>
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/MBD4_MOUSE MBD4_MOUSE]] Mismatch-specific DNA N-glycosylase involved in DNA repair. Has thymine glycosylase activity and is specific for G:T mismatches within methylated and unmethylated CpG sites. Can also remove uracil or 5-fluorouracil in G:U mismatches. Has no lyase activity. Was first identified as methyl-CpG-binding protein.
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[https://www.uniprot.org/uniprot/MBD4_MOUSE MBD4_MOUSE] Mismatch-specific DNA N-glycosylase involved in DNA repair. Has thymine glycosylase activity and is specific for G:T mismatches within methylated and unmethylated CpG sites. Can also remove uracil or 5-fluorouracil in G:U mismatches. Has no lyase activity. Was first identified as methyl-CpG-binding protein.
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
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==See Also==
==See Also==
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*[[Methyl CpG binding protein|Methyl CpG binding protein]]
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*[[Methyl CpG binding protein 3D structures|Methyl CpG binding protein 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Lk3 transgenic mice]]
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[[Category: Large Structures]]
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[[Category: Arita, K]]
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[[Category: Mus musculus]]
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[[Category: Ariyoshi, M]]
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[[Category: Arita K]]
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[[Category: Kato, T]]
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[[Category: Ariyoshi M]]
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[[Category: Kinoshita, M]]
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[[Category: Kato T]]
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[[Category: Otani, J]]
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[[Category: Kinoshita M]]
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[[Category: Shirakawa, M]]
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[[Category: Otani J]]
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[[Category: Hydrolase-dna complex]]
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[[Category: Shirakawa M]]
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[[Category: Methyl cpg binding domain]]
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[[Category: Protein-dna complex]]
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[[Category: Versatile base recognition]]
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Current revision

Crystal structure of methyl CpG binding domain of MBD4 in complex with the 5mCG/hmCG sequence

PDB ID 3vyb

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