OCA at 08:24, 11 October 2023

OCA — Wed, 11 Oct 2023 08:24:20 GMT

←Older revision		Revision as of 08:24, 11 October 2023
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-	====	+	==Human 8-oxoguanine glycosylase interrogating fully intrahelical undamaged DNA==
-	<StructureSection load='6w0r' size='340' side='right'caption='[[6w0r]]' scene=''>	+	<StructureSection load='6w0r' size='340' side='right'caption='[[6w0r]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6w0r]] 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=6W0R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6W0R FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6w0r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6w0r OCA], [~~http~~://pdbe.org/6w0r PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6w0r RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6w0r PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6w0r ProSAT]</span></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.35Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=S5Y:2-(2-ethoxyethoxy)ethanethiol'>S5Y</scene></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6w0r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6w0r OCA], [https://pdbe.org/6w0r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6w0r RCSB], [https://www.ebi.ac.uk/pdbsum/6w0r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6w0r ProSAT]</span></td></tr>
	</table>		</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.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Efficient search for DNA damage embedded in vast expanses of the DNA genome presents one of the greatest challenges to DNA repair enzymes. We report here crystal structures of human 8-oxoguanine (oxoG) DNA glycosylase, hOGG1, that interact with the DNA containing the damaged base oxoG and the normal base G while they are nested in the DNA helical stack. The structures reveal that hOGG1 engages the DNA using different protein-DNA contacts from those observed in the previously determined lesion recognition complex and other hOGG1-DNA complexes. By applying molecular dynamics simulations, we have determined the pathways taken by the lesion and normal bases when extruded from the DNA helix and their associated free energy profiles. These results reveal how the human oxoG DNA glycosylase hOGG1 locates the lesions inside the DNA helix and facilitates their extrusion for repair.
		+
		+	The trajectory of intrahelical lesion recognition and extrusion by the human 8-oxoguanine DNA glycosylase.,Shigdel UK, Ovchinnikov V, Lee SJ, Shih JA, Karplus M, Nam K, Verdine GL Nat Commun. 2020 Sep 7;11(1):4437. doi: 10.1038/s41467-020-18290-2. PMID:32895378<ref>PMID:32895378</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6w0r" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA glycosylase 3D structures\|DNA glycosylase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Shigdel U]]
		+	[[Category: Verdine G]]

OCA at 11:11, 23 September 2020

OCA — Wed, 23 Sep 2020 11:11:22 GMT

←Older revision		Revision as of 11:11, 23 September 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6w0r ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='6w0r' size='340' side='right'caption='[[6w0r]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6w0r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6w0r OCA], [http://pdbe.org/6w0r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6w0r RCSB], [http://www.ebi.ac.uk/pdbsum/6w0r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6w0r ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 18:16, 24 June 2020

OCA — Wed, 24 Jun 2020 18:16:02 GMT

←Older revision		Revision as of 18:16, 24 June 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6w0r is ON HOLD	+	The entry 6w0r is ON HOLD until Paper Publication

	Authors:		Authors:

OCA at 08:31, 17 June 2020

OCA — Wed, 17 Jun 2020 08:31:26 GMT

←Older revision		Revision as of 08:31, 17 June 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6w0r is ON HOLD ~~until Paper Publication~~	+	The entry 6w0r is ON HOLD

	Authors:		Authors:

OCA: Protected "6w0r" [edit=sysop:move=sysop]

OCA — Wed, 11 Mar 2020 06:07:57 GMT

Protected "6w0r" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:07, 11 March 2020

OCA: New page: '''Unreleased structure''' The entry 6w0r is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 11 Mar 2020 06:07:56 GMT

New page: '''Unreleased structure''' The entry 6w0r is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page