1lwy - Revision history

OCA at 08:28, 10 April 2024

2024-04-10T08:28:51Z

←Older revision		Revision as of 08:28, 10 April 2024
Line 3:		Line 3:
	<StructureSection load='1lwy' size='340' side='right'caption='[[1lwy]], [[Resolution\|resolution]] 2.01Å' scene=''>		<StructureSection load='1lwy' size='340' side='right'caption='[[1lwy]], [[Resolution\|resolution]] 2.01Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1lwy]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. 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 [~~http~~://proteopedia.org/fgij/fg.htm?mol=1LWY FirstGlance]. <br>	+	<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>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene></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]] 2.01Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max~~-~~height: 3em;'>[[1hu0\|1hu0]]~~, [[~~1lwv~~\|~~1lwv~~]]~~, [[1lww\|1lww]], [[1ebm\|1ebm]], [[1fn7\|1fn7]]</div>~~</td></tr>	+	<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>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~ogg1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=5~~&id=9606 HUMAN])~~</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=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>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1lwy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lwy OCA], [~~http~~://pdbe.org/1lwy PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1lwy RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1lwy PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1lwy ProSAT]</span></td></tr>	+
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/OGG1_HUMAN OGG1_HUMAN]] Defects in OGG1 may be a cause of renal cell carcinoma (RCC) [MIM:[~~http~~://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.	+	[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 ==		== Function ==
-	[~~[http~~://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.	+	[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 ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 23:		Line 22:
	</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].		</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>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	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.
-
-	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:12592398<ref>PMID:12592398</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1lwy" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[DNA glycosylase 3D structures\|DNA glycosylase 3D structures]]		*[[DNA glycosylase 3D structures\|DNA glycosylase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[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: Hydrolase-dna complex]]~~	+
-	~~[[Category: Product-assisted catalysis]]~~	+
-	~~[[Category: Protein/dna]]~~	+
-	~~[[Category: Reaction intermediate~~]]	+

OCA at 08:03, 25 November 2020

2020-11-25T08:03:18Z

←Older revision		Revision as of 08:03, 25 November 2020
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	==hOgg1 Borohydride-Trapped Intermediate without 8-oxoguanine==		==hOgg1 Borohydride-Trapped Intermediate without 8-oxoguanine==
-	<StructureSection load='1lwy' size='340' side='right' caption='[[1lwy]], [[Resolution\|resolution]] 2.01Å' scene=''>	+	<StructureSection load='1lwy' size='340' side='right'caption='[[1lwy]], [[Resolution\|resolution]] 2.01Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1lwy]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. 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 [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1LWY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1lwy]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. 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 [http://proteopedia.org/fgij/fg.htm?mol=1LWY FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1hu0\|1hu0]], [[1lwv\|1lwv]], [[1lww\|1lww]], [[1ebm\|1ebm]], [[1fn7\|1fn7]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1hu0\|1hu0]], [[1lwv\|1lwv]], [[1lww\|1lww]], [[1ebm\|1ebm]], [[1fn7\|1fn7]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ogg1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ogg1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><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://pdbe.org/1lwy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lwy RCSB], [http://www.ebi.ac.uk/pdbsum/1lwy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1lwy ProSAT]</span></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=1lwy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lwy OCA], [http://pdbe.org/1lwy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lwy RCSB], [http://www.ebi.ac.uk/pdbsum/1lwy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1lwy ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 17:		Line 17:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lw/1lwy_consurf.spt"</scriptWhenChecked>	+	<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>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 34:		Line 34:

	==See Also==		==See Also==
-	*[[DNA glycosylase\|DNA glycosylase]]	+	*[[DNA glycosylase 3D structures\|DNA glycosylase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 40:		Line 40:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Bruner, S D]]		[[Category: Bruner, S D]]
	[[Category: Fromme, J C]]		[[Category: Fromme, J C]]

OCA at 10:58, 18 October 2017

2017-10-18T10:58:02Z

←Older revision		Revision as of 10:58, 18 October 2017
Line 1:		Line 1:
		+
	==hOgg1 Borohydride-Trapped Intermediate without 8-oxoguanine==		==hOgg1 Borohydride-Trapped Intermediate without 8-oxoguanine==
	<StructureSection load='1lwy' size='340' side='right' caption='[[1lwy]], [[Resolution\|resolution]] 2.01Å' scene=''>		<StructureSection load='1lwy' size='340' side='right' caption='[[1lwy]], [[Resolution\|resolution]] 2.01Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1hu0\|1hu0]], [[1lwv\|1lwv]], [[1lww\|1lww]], [[1ebm\|1ebm]], [[1fn7\|1fn7]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1hu0\|1hu0]], [[1lwv\|1lwv]], [[1lww\|1lww]], [[1ebm\|1ebm]], [[1fn7\|1fn7]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ogg1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ogg1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><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://pdbe.org/1lwy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lwy RCSB], [http://www.ebi.ac.uk/pdbsum/1lwy PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><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://pdbe.org/1lwy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lwy RCSB], [http://www.ebi.ac.uk/pdbsum/1lwy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1lwy ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 20:		Line 21:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</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/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</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>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 22:44, 11 September 2015

2015-09-11T22:44:26Z

←Older revision		Revision as of 22:44, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1lwy' size='340' side='right' caption='[[1lwy]], [[Resolution\|resolution]] 2.01Å' scene=''>		<StructureSection load='1lwy' size='340' side='right' caption='[[1lwy]], [[Resolution\|resolution]] 2.01Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1lwy]] is a 3 chain structure with 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]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LWY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1lwy]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LWY FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1hu0\|1hu0]], [[1lwv\|1lwv]], [[1lww\|1lww]], [[1ebm\|1ebm]], [[1fn7\|1fn7]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1hu0\|1hu0]], [[1lwv\|1lwv]], [[1lww\|1lww]], [[1ebm\|1ebm]], [[1fn7\|1fn7]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ogg1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ogg1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><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.rcsb.org/pdb/explore.do?structureId=1lwy RCSB], [http://www.ebi.ac.uk/pdbsum/1lwy PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><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://pdbe.org/1lwy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lwy RCSB], [http://www.ebi.ac.uk/pdbsum/1lwy PDBsum]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 30:		Line 30:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1lwy" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 37:		Line 38:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Bruner, S D]]		[[Category: Bruner, S D]]
	[[Category: Fromme, J C]]		[[Category: Fromme, J C]]

OCA at 16:17, 5 January 2015

2015-01-05T16:17:11Z

←Older revision		Revision as of 16:17, 5 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1lwy]] is a 3 chain structure with 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]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LWY FirstGlance]. <br>		<table><tr><td colspan='2'>[[1lwy]] is a 3 chain structure with 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]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LWY FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene></td></tr>	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1hu0\|1hu0]], [[1lwv\|1lwv]], [[1lww\|1lww]], [[1ebm\|1ebm]], [[1fn7\|1fn7]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1hu0\|1hu0]], [[1lwv\|1lwv]], [[1lww\|1lww]], [[1ebm\|1ebm]], [[1fn7\|1fn7]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ogg1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ogg1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><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.rcsb.org/pdb/explore.do?structureId=1lwy RCSB], [http://www.ebi.ac.uk/pdbsum/1lwy PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><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.rcsb.org/pdb/explore.do?structureId=1lwy RCSB], [http://www.ebi.ac.uk/pdbsum/1lwy PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Disease ==		== Disease ==
	[[http://www.uniprot.org/uniprot/OGG1_HUMAN OGG1_HUMAN]] Defects in OGG1 may be a cause of renal cell carcinoma (RCC) [MIM:[http://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.		[[http://www.uniprot.org/uniprot/OGG1_HUMAN OGG1_HUMAN]] Defects in OGG1 may be a cause of renal cell carcinoma (RCC) [MIM:[http://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.
Line 38:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Bruner, S D.]]	+	[[Category: Bruner, S D]]
-	[[Category: Fromme, J C.]]	+	[[Category: Fromme, J C]]
-	[[Category: Karplus, M.]]	+	[[Category: Karplus, M]]
-	[[Category: Verdine, G L.]]	+	[[Category: Verdine, G L]]
-	[[Category: Yang, W.]]	+	[[Category: Yang, W]]
	[[Category: Borohydride]]		[[Category: Borohydride]]
	[[Category: Covalent trapping]]		[[Category: Covalent trapping]]

OCA at 09:41, 3 October 2014

2014-10-03T09:41:29Z

←Older revision		Revision as of 09:41, 3 October 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_1lwy\| PDB=1lwy \| SCENE= }}~~	+	==hOgg1 Borohydride-Trapped Intermediate without 8-oxoguanine==
-	===hOgg1 Borohydride-Trapped Intermediate without 8-oxoguanine===	+	<StructureSection load='1lwy' size='340' side='right' caption='[[1lwy]], [[Resolution\|resolution]] 2.01Å' scene=''>
-	~~{{ABSTRACT_PUBMED_12592398}}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[1lwy]] is a 3 chain structure with 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]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LWY FirstGlance]. <br>
-	==Disease==	+	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1hu0\|1hu0]], [[1lwv\|1lwv]], [[1lww\|1lww]], [[1ebm\|1ebm]], [[1fn7\|1fn7]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ogg1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><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.rcsb.org/pdb/explore.do?structureId=1lwy RCSB], [http://www.ebi.ac.uk/pdbsum/1lwy PDBsum]</span></td></tr>
		+	<table>
		+	== Disease ==
	[[http://www.uniprot.org/uniprot/OGG1_HUMAN OGG1_HUMAN]] Defects in OGG1 may be a cause of renal cell carcinoma (RCC) [MIM:[http://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.		[[http://www.uniprot.org/uniprot/OGG1_HUMAN OGG1_HUMAN]] Defects in OGG1 may be a cause of renal cell carcinoma (RCC) [MIM:[http://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 ==
-	==Function==	+
	[[http://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.		[[http://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/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	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==~~	+	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:12592398<ref>PMID:12592398</ref>
-	~~[[1lwy]] is a~~ 3 ~~chain structure with 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].~~	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

	==See Also==		==See Also==
-	*[[DNA ~~glycosylate~~\|DNA ~~glycosylate~~]]	+	*[[DNA glycosylase\|DNA glycosylase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:012592398</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Bruner, S D.]]		[[Category: Bruner, S D.]]

OCA at 01:58, 25 March 2013

2013-03-25T01:58:53Z

←Older revision		Revision as of 01:58, 25 March 2013
Line 1:		Line 1:
-	[[Image:1lwy.png\|left\|200px]]
-
	{{STRUCTURE_1lwy\| PDB=1lwy \| SCENE= }}		{{STRUCTURE_1lwy\| PDB=1lwy \| SCENE= }}
-
	===hOgg1 Borohydride-Trapped Intermediate without 8-oxoguanine===		===hOgg1 Borohydride-Trapped Intermediate without 8-oxoguanine===
		+	{{ABSTRACT_PUBMED_12592398}}

-	~~{{ABSTRACT_PUBMED_12592398}}~~	+	==Disease==
		+	[[http://www.uniprot.org/uniprot/OGG1_HUMAN OGG1_HUMAN]] Defects in OGG1 may be a cause of renal cell carcinoma (RCC) [MIM:[http://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==
		+	[[http://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.

	==About this Structure==		==About this Structure==
Line 14:		Line 16:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:012592398</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012592398</ref><references group="xtra"/><references/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Bruner, S D.]]		[[Category: Bruner, S D.]]

OCA at 21:05, 20 October 2012

2012-10-20T21:05:56Z

←Older revision		Revision as of 21:05, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1lwy]] is a 3 chain structure ~~of [[DNA glycosylate]]~~ with 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].	+	[[1lwy]] is a 3 chain structure with 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].

	==See Also==		==See Also==

OCA: Protected "1lwy" [edit=sysop:move=sysop]

2012-07-27T12:35:11Z

Protected "1lwy" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:35, 27 July 2012

OCA at 12:35, 27 July 2012

2012-07-27T12:35:09Z

←Older revision		Revision as of 12:35, 27 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1lwy.png\|left\|200px]]		[[Image:1lwy.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1lwy", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_1lwy\| PDB=1lwy \| SCENE= }}		{{STRUCTURE_1lwy\| PDB=1lwy \| SCENE= }}

	===hOgg1 Borohydride-Trapped Intermediate without 8-oxoguanine===		===hOgg1 Borohydride-Trapped Intermediate without 8-oxoguanine===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_12592398}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 12592398 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_12592398}}		{{ABSTRACT_PUBMED_12592398}}

	==About this Structure==		==About this Structure==
-	~~1LWY~~ is a 3 ~~chains~~ structure of ~~sequences~~ 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].	+	[[1lwy]] is a 3 chain structure of [[DNA glycosylate]] with 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].
		+
		+	==See Also==
		+	*[[DNA glycosylate\|DNA glycosylate]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~12592398~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012592398</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Bruner, S D.]]		[[Category: Bruner, S D.]]
Line 34:		Line 25:
	[[Category: Dna glycosylase]]		[[Category: Dna glycosylase]]
	[[Category: Dna repair]]		[[Category: Dna repair]]
		+	[[Category: Hydrolase-dna complex]]
	[[Category: Product-assisted catalysis]]		[[Category: Product-assisted catalysis]]
	[[Category: Protein/dna]]		[[Category: Protein/dna]]
	[[Category: Reaction intermediate]]		[[Category: Reaction intermediate]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 06:11:54 2009''