3knt

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[[Image:3knt.png|left|200px]]
 
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{{STRUCTURE_3knt| PDB=3knt | SCENE= }}
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==Crystal structure of Methanocaldococcus jannaschii 8-oxoguanine glycosylase/lyase in complex with 15mer DNA containing 8-oxoguanine==
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<StructureSection load='3knt' size='340' side='right'caption='[[3knt]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[3knt]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KNT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KNT FirstGlance]. <br>
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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]] 2.7&#8491;</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=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></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=3knt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3knt OCA], [https://pdbe.org/3knt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3knt RCSB], [https://www.ebi.ac.uk/pdbsum/3knt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3knt ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/OGG1_METJA OGG1_METJA] Responsible for removing an oxidatively damaged form of guanine (7,8-dihydro-8-oxoguanine = 7-oxoG) from DNA. Also nicks DNA at apurinic/apyrimidinic sites (AP sites). Has little specificity for the base opposite oxoG.[HAMAP-Rule:MF_00241]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kn/3knt_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=3knt ConSurf].
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<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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7,8-Dihydro-8-oxoguanine (8-oxoG) is a major oxidative lesion found in DNA. The 8-oxoguanine DNA glycosylases (Ogg) responsible for the removal of 8-oxoG are divided into three families Ogg1, Ogg2 and AGOG. The Ogg2 members are devoid of the recognition loop used by Ogg1 to discriminate between 8-oxoG and guanine and it was unclear until recently how Ogg2 enzymes recognize the oxidized base. We present here the first crystallographic structure of an Ogg2 member, Methanocaldococcus janischii Ogg, in complex with a DNA duplex containing the 8-oxoG lesion. This structure highlights the crucial role of the C-terminal lysine, strictly conserved in Ogg2, in the recognition of 8-oxoG. The structure also reveals that Ogg2 undergoes a conformational change upon DNA binding similar to that observed in Ogg1 glycosylases. Furthermore, this work provides a structural rationale for the lack of opposite base specificity in this family of enzymes.
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===Crystal structure of Methanocaldococcus jannaschii 8-oxoguanine glycosylase/lyase in complex with 15mer DNA containing 8-oxoguanine===
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The C-terminal lysine of Ogg2 DNA glycosylases is a major molecular determinant for guanine/8-oxoguanine distinction.,Faucher F, Wallace SS, Doublie S J Mol Biol. 2010 Mar 19;397(1):46-56. Epub 2010 Jan 18. PMID:20083120<ref>PMID:20083120</ref>
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{{ABSTRACT_PUBMED_20083120}}
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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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==About this Structure==
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<div class="pdbe-citations 3knt" style="background-color:#fffaf0;"></div>
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[[3knt]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KNT OCA].
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==See Also==
==See Also==
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*[[DNA glycosylate|DNA glycosylate]]
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*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
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== References ==
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==Reference==
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<references/>
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<ref group="xtra">PMID:020083120</ref><references group="xtra"/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Methanocaldococcus jannaschii]]
[[Category: Methanocaldococcus jannaschii]]
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[[Category: Doublie, S.]]
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[[Category: Doublie S]]
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[[Category: Faucher, F.]]
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[[Category: Faucher F]]
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[[Category: 8-oxog]]
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[[Category: 8-oxoguanine]]
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[[Category: Dna damage]]
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[[Category: Dna repair]]
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[[Category: Glycosidase]]
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[[Category: Glycosylase]]
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[[Category: Helix-hairpin-helix]]
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[[Category: Hydrolase]]
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[[Category: Lyase-dna complex]]
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[[Category: Multifunctional enzyme]]
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[[Category: Nuclease]]
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[[Category: Ogg]]
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[[Category: Protein-dna complex]]
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Current revision

Crystal structure of Methanocaldococcus jannaschii 8-oxoguanine glycosylase/lyase in complex with 15mer DNA containing 8-oxoguanine

PDB ID 3knt

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