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| - | | + | #REDIRECT [[6u7t]] This PDB entry is obsolete and replaced by 6u7t |
| - | ==MutY adenine glycosylase bound to a transition state analog (1N) paired with d(8-oxoG) in duplexed DNA to 2.2 A==
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| - | <StructureSection load='5dpk' size='340' side='right' caption='[[5dpk]], [[Resolution|resolution]] 2.20Å' scene=''>
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| - | == Structural highlights ==
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| - | <table><tr><td colspan='2'>[[5dpk]] is a 3 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3fsq 3fsq]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DPK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DPK 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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></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=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene>, <scene name='pdbligand=NR1:(3R,4R)-3-HYDROXY-4-[(PHOSPHONOOXY)METHYL]PYRROLIDINIUM'>NR1</scene></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=5dpk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dpk OCA], [http://pdbe.org/5dpk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dpk RCSB], [http://www.ebi.ac.uk/pdbsum/5dpk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dpk ProSAT]</span></td></tr>
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| - | </table>
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| - | <div style="background-color:#fffaf0;">
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| - | == Publication Abstract from PubMed ==
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| - | MutY adenine glycosylases prevent DNA mutations by excising adenine from promutagenic 8-oxo-7,8-dihydroguanine (OG):A mismatches. Here, we describe structural features of the MutY active site bound to an azaribose transition state analog which indicate a catalytic role for Tyr126 and approach of the water nucleophile on the same side as the departing adenine base. The idea that Tyr126 participates in catalysis, recently predicted by modeling calculations, is strongly supported by mutagenesis and by seeing close contact between the hydroxyl group of this residue and the azaribose moiety of the transition state analog. NMR analysis of MutY methanolysis products corroborates a mechanism for adenine removal with retention of stereochemistry. Based on these results, we propose a revised mechanism for MutY that involves two nucleophilic displacement steps akin to the mechanisms accepted for 'retaining' O-glycosidases. This new-for-MutY yet familiar mechanism may also be operative in related base excision repair glycosylases and provides a critical framework for analysis of human MutY (MUTYH) variants associated with inherited colorectal cancer.
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| - | Structure and stereochemistry of the base excision repair glycosylase MutY reveal a mechanism similar to retaining glycosidases.,Woods RD, O'Shea VL, Chu A, Cao S, Richards JL, Horvath MP, David SS Nucleic Acids Res. 2015 Dec 15. pii: gkv1469. PMID:26673696<ref>PMID:26673696</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 5dpk" style="background-color:#fffaf0;"></div>
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| - | == References ==
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| - | <references/>
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| - | __TOC__
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| - | </StructureSection>
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| - | [[Category: Cao, S]]
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| - | [[Category: David, S S]]
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| - | [[Category: Horvath, M P]]
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| - | [[Category: Shea, V L.O]]
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| - | [[Category: Dna repair]]
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| - | [[Category: Glycosylase]]
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| - | [[Category: Hydrolase-dna complex]]
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| - | [[Category: Protein-dna complex]]
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| - | [[Category: Transition state analog]]
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