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| | ==mouse MBD4 glycosylase domain in complex with a G:5hmU (5-hydroxymethyluracil) mismatch== | | ==mouse MBD4 glycosylase domain in complex with a G:5hmU (5-hydroxymethyluracil) mismatch== |
| - | <StructureSection load='4ew0' size='340' side='right' caption='[[4ew0]], [[Resolution|resolution]] 2.39Å' scene=''> | + | <StructureSection load='4ew0' size='340' side='right'caption='[[4ew0]], [[Resolution|resolution]] 2.39Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4ew0]] 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=4EW0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4EW0 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4ew0]] 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=4EW0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4EW0 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.39Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5HU:5-HYDROXYMETHYLURIDINE-2-DEOXY-5-MONOPHOSPHATE'>5HU</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5HU:5-HYDROXYMETHYLURIDINE-2-DEOXY-5-MONOPHOSPHATE'>5HU</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1ngn|1ngn]], [[4evv|4evv]], [[4ew4|4ew4]]</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=4ew0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ew0 OCA], [https://pdbe.org/4ew0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ew0 RCSB], [https://www.ebi.ac.uk/pdbsum/4ew0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ew0 ProSAT]</span></td></tr> |
| - | <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=4ew0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ew0 OCA], [http://pdbe.org/4ew0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ew0 RCSB], [http://www.ebi.ac.uk/pdbsum/4ew0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ew0 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[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. | + | [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;">
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| - | == Publication Abstract from PubMed ==
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| - | The mammalian DNA glycosylase-methyl-CpG binding domain protein 4 (MBD4)-is involved in active DNA demethylation via the base excision repair pathway. MBD4 contains an N-terminal MBD and a C-terminal DNA glycosylase domain. MBD4 can excise the mismatched base paired with a guanine (G:X), where X is uracil, thymine or 5-hydroxymethyluracil (5hmU). These are, respectively, the deamination products of cytosine, 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). Here, we present three structures of the MBD4 C-terminal glycosylase domain (wild-type and its catalytic mutant D534N), in complex with DNA containing a G:T or G:5hmU mismatch. MBD4 flips the target nucleotide from the double-stranded DNA. The catalytic mutant D534N captures the intact target nucleotide in the active site binding pocket. MBD4 specifically recognizes the Watson-Crick polar edge of thymine or 5hmU via the O(2), N(3) and O(4) atoms, thus restricting its activity to thymine/uracil-based modifications while excluding cytosine and its derivatives. The wild-type enzyme cleaves the N-glycosidic bond, leaving the ribose ring in the flipped state, while the cleaved base is released. Unexpectedly, the C(1)' of the sugar has yet to be hydrolyzed and appears to form a stable intermediate with one of the side chain carboxyl oxygen atoms of D534, via either electrostatic or covalent interaction, suggesting a different catalytic mechanism from those of other DNA glycosylases.
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| - | Excision of thymine and 5-hydroxymethyluracil by the MBD4 DNA glycosylase domain: structural basis and implications for active DNA demethylation.,Hashimoto H, Zhang X, Cheng X Nucleic Acids Res. 2012 Jun 27. PMID:22740654<ref>PMID:22740654</ref>
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
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| - | <div class="pdbe-citations 4ew0" style="background-color:#fffaf0;"></div>
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| | ==See Also== | | ==See Also== |
| - | *[[Methyl CpG binding protein|Methyl CpG binding protein]] | + | *[[Methyl CpG binding protein 3D structures|Methyl CpG binding protein 3D structures]] |
| - | == References ==
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| - | <references/>
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Lk3 transgenic mice]] | + | [[Category: Large Structures]] |
| - | [[Category: Cheng, X]] | + | [[Category: Mus musculus]] |
| - | [[Category: Hashimoto, H]] | + | [[Category: Cheng X]] |
| - | [[Category: Zhang, X]]
| + | [[Category: Hashimoto H]] |
| - | [[Category: 5-hydroxymethyluracil]] | + | [[Category: Zhang X]] |
| - | [[Category: 5-methylcytosine]] | + | |
| - | [[Category: Active dna demethylation]]
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| - | [[Category: Deamination]]
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| - | [[Category: Dna glycosylase]]
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| - | [[Category: Helix-hairpin-helix]]
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| - | [[Category: Hydrolase-dna complex]]
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