1m3h: Difference between revisions

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-[[Image:1m3h.gif|left|200px]]
-<!--
+==Crystal Structure of Hogg1 D268E Mutant with Product Oligonucleotide==
-The line below this paragraph, containing "STRUCTURE_1m3h", creates the "Structure Box" on the page.
+<StructureSection load='1m3h' size='340' side='right'caption='[[1m3h]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1m3h]] is a 4 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=1M3H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M3H FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.05&#8491;</td></tr>
--->
+<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=DDX:2,3-DEHYDRO-2,3-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>DDX</scene></td></tr>
-{{STRUCTURE_1m3h|  PDB=1m3h  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1m3h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m3h OCA], [https://pdbe.org/1m3h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m3h RCSB], [https://www.ebi.ac.uk/pdbsum/1m3h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m3h ProSAT]</span></td></tr>
+</table>
+== 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/m3/1m3h_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=1m3h ConSurf].
+<div style="clear:both"></div>
-'''Crystal Structure of Hogg1 D268E Mutant with Product Oligonucleotide'''
+==See Also==
+*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
+__TOC__
-==Overview==
+</StructureSection>
-DNA glycosylase/lyases initiate the repair of damaged nucleobases in the genome by catalyzing excision of aberrant nucleobases and nicking of the lesion-containing DNA strand. Nearly all of these proteins have the unusual property of remaining tightly bound in vitro to the end products of the reaction cascade. We have taken advantage of this property to crystallize and structurally characterize the end product resulting from complete DNA processing by a catalytically active mutant form of human 8-oxoguanine DNA glycosylase (D268E hOgg1). The resulting structure is consistent with the currently accepted catalytic mechanism for the protein. Unexpectedly, however, soaking of a nucleobase analog into the crystals results in religation of the DNA backbone in situ.
-==About this Structure==
-M3H 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=1M3H OCA].
-==Reference==
-Structures of end products resulting from lesion processing by a DNA glycosylase/lyase., Chung SJ, Verdine GL, Chem Biol. 2004 Dec;11(12):1643-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15610848 15610848]
 [[Category: Homo sapiens]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Chung, S J.]]
+[[Category: Chung SJ]]
-[[Category: Verdine, G L.]]
+[[Category: Verdine GL]]
-[[Category: Dna glycosylase]]
-[[Category: Dna repair]]
-[[Category: End product]]
-[[Category: Enzyme]]
-[[Category: Mutant]]
-[[Category: Protein-dna complex]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 00:35:17 2008''