2nob - Revision history

OCA at 00:09, 28 December 2023

2023-12-28T00:09:13Z

←Older revision		Revision as of 00:09, 28 December 2023
Line 3:		Line 3:
	<StructureSection load='2nob' size='340' side='right'caption='[[2nob]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2nob' size='340' side='right'caption='[[2nob]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2nob]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NOB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NOB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2nob]] 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=2NOB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NOB FirstGlance]. <br>
-	</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>~~</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]] 2.1Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;~~'>~~[[1ko9\|1ko9]], [[1ebm\|1ebm]], [[1yqk\|1yqk]], [[1fn7\|1fn7]], [[1n3c\|1n3c]], [[2noe\|2noe]], [[2nof\|2nof]], [[2noh\|2noh]], [[2noi\|2noi]], [[2nol\|2nol]], [[2noz\|2noz]]~~</~~div~~>~~</td></tr>~~	+
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">OGG1, MMH, MUTM, OGH1 ([https://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=2nob FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nob OCA], [https://pdbe.org/2nob PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2nob RCSB], [https://www.ebi.ac.uk/pdbsum/2nob PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2nob ProSAT]</span></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=2nob FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nob OCA], [https://pdbe.org/2nob PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2nob RCSB], [https://www.ebi.ac.uk/pdbsum/2nob PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2nob ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== 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.	+	[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 ==
-	[[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.	+	[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]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Banerjee, A]]	+	[[Category: Banerjee A]]
-	[[Category: Radom~~, C T~~]]	+	[[Category: Radom CT]]
-	[[Category: Verdine~~, G L]]~~	+	[[Category: Verdine GL]]
-	~~[[Category: 8-oxoguanine]]~~	+
-	~~[[Category: Dna repair]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Lyase-dna complex]]~~	+
-	~~[[Category: N-glycosylase/dna lyase~~]]	+

OCA at 15:47, 8 June 2021

2021-06-08T15:47:02Z

←Older revision		Revision as of 15:47, 8 June 2021
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	==Structure of catalytically inactive H270A human 8-oxoguanine glycosylase crosslinked to 8-oxoguanine DNA==		==Structure of catalytically inactive H270A human 8-oxoguanine glycosylase crosslinked to 8-oxoguanine DNA==
-	<StructureSection load='2nob' size='340' side='right' caption='[[2nob]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='2nob' size='340' side='right'caption='[[2nob]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2nob]] 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=2NOB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2NOB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2nob]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NOB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NOB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>	+	</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></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ko9\|1ko9]], [[1ebm\|1ebm]], [[1yqk\|1yqk]], [[1fn7\|1fn7]], [[1n3c\|1n3c]], [[2noe\|2noe]], [[2nof\|2nof]], [[2noh\|2noh]], [[2noi\|2noi]], [[2nol\|2nol]], [[2noz\|2noz]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ko9\|1ko9]], [[1ebm\|1ebm]], [[1yqk\|1yqk]], [[1fn7\|1fn7]], [[1n3c\|1n3c]], [[2noe\|2noe]], [[2nof\|2nof]], [[2noh\|2noh]], [[2noi\|2noi]], [[2nol\|2nol]], [[2noz\|2noz]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">OGG1, MMH, MUTM, OGH1 ([~~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, MMH, MUTM, OGH1 ([https://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=2nob FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nob OCA], [~~http~~://pdbe.org/2nob PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2nob RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2nob PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2nob ProSAT]</span></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=2nob FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nob OCA], [https://pdbe.org/2nob PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2nob RCSB], [https://www.ebi.ac.uk/pdbsum/2nob PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2nob 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]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/no/2nob_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/no/2nob_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 35:		Line 35:

	==See Also==		==See Also==
-	*[[DNA glycosylase\|DNA glycosylase]]	+	*[[DNA glycosylase 3D structures\|DNA glycosylase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Banerjee, A]]		[[Category: Banerjee, A]]
	[[Category: Radom, C T]]		[[Category: Radom, C T]]

OCA at 08:37, 18 October 2017

2017-10-18T08:37:33Z

←Older revision		Revision as of 08:37, 18 October 2017
Line 1:		Line 1:
		+
	==Structure of catalytically inactive H270A human 8-oxoguanine glycosylase crosslinked to 8-oxoguanine DNA==		==Structure of catalytically inactive H270A human 8-oxoguanine glycosylase crosslinked to 8-oxoguanine DNA==
	<StructureSection load='2nob' size='340' side='right' caption='[[2nob]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2nob' size='340' side='right' caption='[[2nob]], [[Resolution\|resolution]] 2.10Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ko9\|1ko9]], [[1ebm\|1ebm]], [[1yqk\|1yqk]], [[1fn7\|1fn7]], [[1n3c\|1n3c]], [[2noe\|2noe]], [[2nof\|2nof]], [[2noh\|2noh]], [[2noi\|2noi]], [[2nol\|2nol]], [[2noz\|2noz]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ko9\|1ko9]], [[1ebm\|1ebm]], [[1yqk\|1yqk]], [[1fn7\|1fn7]], [[1n3c\|1n3c]], [[2noe\|2noe]], [[2nof\|2nof]], [[2noh\|2noh]], [[2noi\|2noi]], [[2nol\|2nol]], [[2noz\|2noz]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">OGG1, MMH, MUTM, OGH1 ([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, MMH, MUTM, OGH1 ([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=2nob FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nob OCA], [http://pdbe.org/2nob PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2nob RCSB], [http://www.ebi.ac.uk/pdbsum/2nob 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=2nob FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nob OCA], [http://pdbe.org/2nob PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2nob RCSB], [http://www.ebi.ac.uk/pdbsum/2nob PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2nob ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 21:		Line 22:
	<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=2nob ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 12:26, 11 September 2015

2015-09-11T12:26:05Z

←Older revision		Revision as of 12:26, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2nob' size='340' side='right' caption='[[2nob]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2nob' size='340' side='right' caption='[[2nob]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2nob]] 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=2NOB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2NOB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2nob]] 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=2NOB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2NOB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ko9\|1ko9]], [[1ebm\|1ebm]], [[1yqk\|1yqk]], [[1fn7\|1fn7]], [[1n3c\|1n3c]], [[2noe\|2noe]], [[2nof\|2nof]], [[2noh\|2noh]], [[2noi\|2noi]], [[2nol\|2nol]], [[2noz\|2noz]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ko9\|1ko9]], [[1ebm\|1ebm]], [[1yqk\|1yqk]], [[1fn7\|1fn7]], [[1n3c\|1n3c]], [[2noe\|2noe]], [[2nof\|2nof]], [[2noh\|2noh]], [[2noi\|2noi]], [[2nol\|2nol]], [[2noz\|2noz]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">OGG1, MMH, MUTM, OGH1 ([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, MMH, MUTM, OGH1 ([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=2nob FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nob OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2nob RCSB], [http://www.ebi.ac.uk/pdbsum/2nob 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=2nob FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nob OCA], [http://pdbe.org/2nob PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2nob RCSB], [http://www.ebi.ac.uk/pdbsum/2nob PDBsum]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
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	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 2nob" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 38:		Line 39:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Banerjee, A]]		[[Category: Banerjee, A]]
	[[Category: Radom, C T]]		[[Category: Radom, C T]]

OCA at 17:00, 19 January 2015

2015-01-19T17:00:00Z

←Older revision		Revision as of 17:00, 19 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2nob]] 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=2NOB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2NOB FirstGlance]. <br>		<table><tr><td colspan='2'>[[2nob]] 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=2NOB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2NOB FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ko9\|1ko9]], [[1ebm\|1ebm]], [[1yqk\|1yqk]], [[1fn7\|1fn7]], [[1n3c\|1n3c]], [[2noe\|2noe]], [[2nof\|2nof]], [[2noh\|2noh]], [[2noi\|2noi]], [[2nol\|2nol]], [[2noz\|2noz]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ko9\|1ko9]], [[1ebm\|1ebm]], [[1yqk\|1yqk]], [[1fn7\|1fn7]], [[1n3c\|1n3c]], [[2noe\|2noe]], [[2nof\|2nof]], [[2noh\|2noh]], [[2noi\|2noi]], [[2nol\|2nol]], [[2noz\|2noz]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">OGG1, MMH, MUTM, OGH1 ([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, MMH, MUTM, OGH1 ([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=2nob FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nob OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2nob RCSB], [http://www.ebi.ac.uk/pdbsum/2nob 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=2nob FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nob OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2nob RCSB], [http://www.ebi.ac.uk/pdbsum/2nob 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 39:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Banerjee, A.]]	+	[[Category: Banerjee, A]]
-	[[Category: Radom, C T.]]	+	[[Category: Radom, C T]]
-	[[Category: Verdine, G L.]]	+	[[Category: Verdine, G L]]
	[[Category: 8-oxoguanine]]		[[Category: 8-oxoguanine]]
	[[Category: Dna repair]]		[[Category: Dna repair]]

OCA at 09:32, 3 October 2014

2014-10-03T09:32:03Z

←Older revision		Revision as of 09:32, 3 October 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_2nob\| PDB=2nob \| SCENE= }}~~	+	==Structure of catalytically inactive H270A human 8-oxoguanine glycosylase crosslinked to 8-oxoguanine DNA==
-	===Structure of catalytically inactive H270A human 8-oxoguanine glycosylase crosslinked to 8-oxoguanine DNA===	+	<StructureSection load='2nob' size='340' side='right' caption='[[2nob]], [[Resolution\|resolution]] 2.10Å' scene=''>
-	~~{{ABSTRACT_PUBMED_17114185}}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[2nob]] 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=2NOB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2NOB FirstGlance]. <br>
-	==Disease==	+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ko9\|1ko9]], [[1ebm\|1ebm]], [[1yqk\|1yqk]], [[1fn7\|1fn7]], [[1n3c\|1n3c]], [[2noe\|2noe]], [[2nof\|2nof]], [[2noh\|2noh]], [[2noi\|2noi]], [[2nol\|2nol]], [[2noz\|2noz]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">OGG1, MMH, MUTM, OGH1 ([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=2nob FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nob OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2nob RCSB], [http://www.ebi.ac.uk/pdbsum/2nob 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/no/2nob_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 ==
		+	The human 8-oxoguanine DNA glycosylase (hOGG1) protein is responsible for initiating base excision DNA repair of the endogenous mutagen 8-oxoguanine. Like nearly all DNA glycosylases, hOGG1 extrudes its substrate from the DNA helix and inserts it into an extrahelical enzyme active site pocket lined with residues that participate in lesion recognition and catalysis. Structural analysis has been performed on mutant versions of hOGG1 having changes in catalytic residues but not on variants having altered 7,8-dihydro-8-oxoguanine (oxoG) contact residues. Here we report high resolution structural analysis of such recognition variants. We found that Ala substitution at residues that contact the phosphate 5' to the lesion (H270A mutation) and its Watson-Crick face (Q315A mutation) simply removed key functionality from the contact interface but otherwise had no effect on structure. Ala substitution at the only residue making an oxoG-specific contact (G42A mutation) introduced torsional stress into the DNA contact surface of hOGG1, but this was overcome by local interactions within the folded protein, indicating that this oxoG recognition motif is "hardwired." Introduction of a side chain intended to sterically obstruct the active site pocket (Q315F mutation) led to two different structures, one of which (Q315F(149)) has the oxoG lesion in an exosite flanking the active site and the other of which (Q315F(292)) has the oxoG inserted nearly completely into the lesion recognition pocket. The latter structure offers a view of the latest stage in the base extrusion pathway yet observed, and its lack of catalytic activity demonstrates that the transition state for displacement of the lesion base is geometrically demanding.

-	~~==About this Structure==~~	+	Structural characterization of human 8-oxoguanine DNA glycosylase variants bearing active site mutations.,Radom CT, Banerjee A, Verdine GL J Biol Chem. 2007 Mar 23;282(12):9182-94. Epub 2006 Nov 16. PMID:17114185<ref>PMID:17114185</ref>
-	~~[[2nob]] 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=2NOB 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:017114185</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Banerjee, A.]]		[[Category: Banerjee, A.]]

OCA at 16:39, 24 March 2013

2013-03-24T16:39:47Z

←Older revision		Revision as of 16:39, 24 March 2013
Line 1:		Line 1:
-	[[Image:2nob.png\|left\|200px]]
-
	{{STRUCTURE_2nob\| PDB=2nob \| SCENE= }}		{{STRUCTURE_2nob\| PDB=2nob \| SCENE= }}
-
	===Structure of catalytically inactive H270A human 8-oxoguanine glycosylase crosslinked to 8-oxoguanine DNA===		===Structure of catalytically inactive H270A human 8-oxoguanine glycosylase crosslinked to 8-oxoguanine DNA===
		+	{{ABSTRACT_PUBMED_17114185}}

-	~~{{ABSTRACT_PUBMED_17114185}}~~	+	==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:017114185</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017114185</ref><references group="xtra"/><references/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Banerjee, A.]]		[[Category: Banerjee, A.]]

OCA at 18:52, 20 October 2012

2012-10-20T18:52:42Z

←Older revision		Revision as of 18:52, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2nob]] 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=2NOB OCA].	+	[[2nob]] 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=2NOB OCA].

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

OCA: Protected "2nob" [edit=sysop:move=sysop]

2012-07-27T05:33:39Z

Protected "2nob" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:33, 27 July 2012

OCA at 05:33, 27 July 2012

2012-07-27T05:33:38Z

←Older revision		Revision as of 05:33, 27 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2nob.png\|left\|200px]]		[[Image:2nob.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2nob", 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_2nob\| PDB=2nob \| SCENE= }}		{{STRUCTURE_2nob\| PDB=2nob \| SCENE= }}

	===Structure of catalytically inactive H270A human 8-oxoguanine glycosylase crosslinked to 8-oxoguanine DNA===		===Structure of catalytically inactive H270A human 8-oxoguanine glycosylase crosslinked to 8-oxoguanine DNA===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17114185}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17114185 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17114185}}		{{ABSTRACT_PUBMED_17114185}}

	==About this Structure==		==About this Structure==
-	~~2NOB~~ 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=2NOB OCA].	+	[[2nob]] 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=2NOB OCA].
		+
		+	==See Also==
		+	*[[DNA glycosylate\|DNA glycosylate]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17114185~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017114185</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Banerjee, A.]]		[[Category: Banerjee, A.]]
Line 30:		Line 21:
	[[Category: 8-oxoguanine]]		[[Category: 8-oxoguanine]]
	[[Category: Dna repair]]		[[Category: Dna repair]]
		+	[[Category: Hydrolase]]
		+	[[Category: Lyase-dna complex]]
	[[Category: N-glycosylase/dna lyase]]		[[Category: N-glycosylase/dna lyase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 21:41:54 2009''