3knt

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{{Seed}}
 
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[[Image:3knt.jpg|left|200px]]
 
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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 line below this paragraph, containing "STRUCTURE_3knt", creates the "Structure Box" on the page.
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<StructureSection load='3knt' size='340' side='right'caption='[[3knt]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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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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or leave the SCENE parameter empty for the default display.
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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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{{STRUCTURE_3knt| PDB=3knt | SCENE= }}
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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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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 3knt" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_20083120}}, adds the Publication Abstract to the page
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*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 20083120 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_20083120}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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3KNT is a 12 chains structure with sequences 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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==Reference==
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<ref group="xtra">PMID:20083120</ref><references group="xtra"/>
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[[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: 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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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 3 09:33:37 2010''
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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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