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1lwy

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hOgg1 Borohydride-Trapped Intermediate without 8-oxoguanine

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Retrieved from "http://52.214.119.220/wiki/index.php/1lwy"

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-[[Image:1lwy.gif|left|200px]]
- {{Structure
+==hOgg1 Borohydride-Trapped Intermediate without 8-oxoguanine==
-|PDB= 1lwy |SIZE=350|CAPTION= <scene name='initialview01'>1lwy</scene>, resolution 2.01&Aring;
+<StructureSection load='1lwy' size='340' side='right'caption='[[1lwy]], [[Resolution|resolution]] 2.01&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <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=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene>
+<table><tr><td colspan='2'>[[1lwy]] 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=1LWY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LWY FirstGlance]. <br>
-|ACTIVITY=
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.01&#8491;</td></tr>
-|GENE= ogg1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene></td></tr>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1lwy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lwy OCA], [https://pdbe.org/1lwy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lwy RCSB], [https://www.ebi.ac.uk/pdbsum/1lwy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lwy ProSAT]</span></td></tr>
-|RELATEDENTRY=[[1hu0|1HU0]], [[1lwv|1LWV]], [[1lww|1LWW]], [[1ebm|1EBM]], [[1fn7|1FN7]]
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1lwy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lwy OCA], [http://www.ebi.ac.uk/pdbsum/1lwy PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1lwy RCSB]</span>
+== Disease ==
-}}
+[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.
+== Function ==
+[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.
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lw/1lwy_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=1lwy ConSurf].
+<div style="clear:both"></div>
-'''hOgg1 Borohydride-Trapped Intermediate without 8-oxoguanine'''
+==See Also==
+*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
+__TOC__
-==Overview==
+</StructureSection>
-Most spontaneous damage to bases in DNA is corrected through the action of the base-excision DNA repair pathway. Base excision repair is initiated by DNA glycosylases, lesion-specific enzymes that intercept aberrant bases in DNA and catalyze their excision. How such proteins accomplish the feat of catalyzing no fewer than five sequential reaction steps using a single active site has been unknown. To help answer this, we report the structure of a trapped catalytic intermediate in DNA repair by human 8-oxoguanine DNA glycosylase. This structure and supporting biochemical results reveal that the enzyme sequesters the excised lesion base and exploits it as a cofactor to participate in catalysis. To our knowledge, the present example represents the first documented case of product-assisted catalysis in an enzyme-catalyzed reaction.
-==About this Structure==
-LWY 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=1LWY OCA].
-==Reference==
-Product-assisted catalysis in base-excision DNA repair., Fromme JC, Bruner SD, Yang W, Karplus M, Verdine GL, Nat Struct Biol. 2003 Mar;10(3):204-11. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12592398 12592398]
 [[Category: Homo sapiens]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Bruner, S D.]]
+[[Category: Bruner SD]]
-[[Category: Fromme, J C.]]
+[[Category: Fromme JC]]
-[[Category: Karplus, M.]]
+[[Category: Karplus M]]
-[[Category: Verdine, G L.]]
+[[Category: Verdine GL]]
-[[Category: Yang, W.]]
+[[Category: Yang W]]
-[[Category: borohydride]]
-[[Category: covalent trapping]]
-[[Category: dna glycosylase]]
-[[Category: dna repair]]
-[[Category: product-assisted catalysis]]
-[[Category: protein/dna]]
-[[Category: reaction intermediate]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:08:27 2008''

1lwy

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hOgg1 Borohydride-Trapped Intermediate without 8-oxoguanine

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Disease

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Evolutionary Conservation

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