1yqk

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[[Image:1yqk.gif|left|200px]]
 
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{{Structure
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==Human 8-oxoguanine glycosylase crosslinked with guanine containing DNA==
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|PDB= 1yqk |SIZE=350|CAPTION= <scene name='initialview01'>1yqk</scene>, resolution 2.50&Aring;
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<StructureSection load='1yqk' size='340' side='right'caption='[[1yqk]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>
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<table><tr><td colspan='2'>[[1yqk]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YQK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YQK FirstGlance]. <br>
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|ACTIVITY=
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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]] 2.5&#8491;</td></tr>
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|GENE= OGG1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
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|DOMAIN=
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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=1yqk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yqk OCA], [https://pdbe.org/1yqk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yqk RCSB], [https://www.ebi.ac.uk/pdbsum/1yqk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yqk ProSAT]</span></td></tr>
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|RELATEDENTRY=[[1ebm|1EBM]], [[1ko9|1KO9]], [[1fn7|1FN7]], [[1yql|1YQL]], [[1yqm|1YQM]], [[1yqr|1YQR]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1yqk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yqk OCA], [http://www.ebi.ac.uk/pdbsum/1yqk PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1yqk RCSB]</span>
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== Disease ==
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}}
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[https://www.uniprot.org/uniprot/OGG1_HUMAN OGG1_HUMAN] Defects in OGG1 may be a cause of renal cell carcinoma (RCC) [MIM:[https://omim.org/entry/144700 144700]. It is a heterogeneous group of sporadic or hereditary carcinoma derived from cells of the proximal renal tubular epithelium. It is subclassified into clear cell renal carcinoma (non-papillary carcinoma), papillary renal cell carcinoma, chromophobe renal cell carcinoma, collecting duct carcinoma with medullary carcinoma of the kidney, and unclassified renal cell carcinoma.
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== Function ==
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[https://www.uniprot.org/uniprot/OGG1_HUMAN OGG1_HUMAN] DNA repair enzyme that incises DNA at 8-oxoG residues. Excises 7,8-dihydro-8-oxoguanine and 2,6-diamino-4-hydroxy-5-N-methylformamidopyrimidine (FAPY) from damaged DNA. Has a beta-lyase activity that nicks DNA 3' to the lesion.
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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/yq/1yqk_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=1yqk ConSurf].
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<div style="clear:both"></div>
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'''Human 8-oxoguanine glycosylase crosslinked with guanine containing DNA'''
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==See Also==
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*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
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__TOC__
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==Overview==
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</StructureSection>
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How DNA repair proteins distinguish between the rare sites of damage and the vast expanse of normal DNA is poorly understood. Recognizing the mutagenic lesion 8-oxoguanine (oxoG) represents an especially formidable challenge, because this oxidized nucleobase differs by only two atoms from its normal counterpart, guanine (G). Here we report the use of a covalent trapping strategy to capture a human oxoG repair protein, 8-oxoguanine DNA glycosylase I (hOGG1), in the act of interrogating normal DNA. The X-ray structure of the trapped complex features a target G nucleobase extruded from the DNA helix but denied insertion into the lesion recognition pocket of the enzyme. Free energy difference calculations show that both attractive and repulsive interactions have an important role in the preferential binding of oxoG compared with G to the active site. The structure reveals a remarkably effective gate-keeping strategy for lesion discrimination and suggests a mechanism for oxoG insertion into the hOGG1 active site.
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==Disease==
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Known disease associated with this structure: Renal cell carcinoma, clear cell, somatic OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=601982 601982]]
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==About this Structure==
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1YQK is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YQK OCA].
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==Reference==
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Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA., Banerjee A, Yang W, Karplus M, Verdine GL, Nature. 2005 Mar 31;434(7033):612-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15800616 15800616]
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[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Banerjee, A.]]
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[[Category: Banerjee A]]
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[[Category: Karplus, M.]]
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[[Category: Karplus M]]
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[[Category: Verdine, G L.]]
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[[Category: Verdine GL]]
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[[Category: Yang, W.]]
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[[Category: Yang W]]
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[[Category: disulfide crosslink]]
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[[Category: dna glycosylase]]
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[[Category: undamaged dna]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:18:06 2008''
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Current revision

Human 8-oxoguanine glycosylase crosslinked with guanine containing DNA

PDB ID 1yqk

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