3gpu - Revision history

OCA at 07:09, 6 September 2023

2023-09-06T07:09:46Z

← Older revision		Revision as of 07:09, 6 September 2023
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	<StructureSection load='3gpu' size='340' side='right'caption='[[3gpu]], [[Resolution\|resolution]] 1.62Å' scene=''>		<StructureSection load='3gpu' size='340' side='right'caption='[[3gpu]], [[Resolution\|resolution]] 1.62Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3gpu]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_12980 Atcc 12980~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GPU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GPU FirstGlance]. <br>		<table><tr><td colspan='2'>[[3gpu]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GPU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GPU FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.62Å</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=ZN:ZINC+ION'>ZN</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;'>[[3gpp\|3gpp]], [[3gpx\|3gpx]], [[3gpy\|3gpy]]~~, ~~[[3gq3\|3gq3]], [[3gq4\|3gq4]], [[3gq5\|3gq5]]~~<~~/div></td></tr>~~
	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b></td><td class="sblockDat">MutM ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ATCC 12980])</td></tr>~~
	~~<tr id='activity~~'>~~<td class="sblockLbl"><b>Activity:~~</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/DNA-(apurinic_or_apyrimidinic_site)_lyase DNA-(apurinic or apyrimidinic site) lyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.99.18 4.2.99.18] </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=3gpu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gpu OCA], [https://pdbe.org/3gpu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gpu RCSB], [https://www.ebi.ac.uk/pdbsum/3gpu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gpu 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=3gpu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gpu OCA], [https://pdbe.org/3gpu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gpu RCSB], [https://www.ebi.ac.uk/pdbsum/3gpu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gpu ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/P84131_GEOSE P84131_GEOSE]] Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates (By similarity).[HAMAP-Rule:MF_00103][SAAS:SAAS020629_004_120556]		[https://www.uniprot.org/uniprot/P84131_GEOSE P84131_GEOSE] Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates (By similarity).[HAMAP-Rule:MF_00103][SAAS:SAAS020629_004_120556]
	== 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: ~~Atcc 12980~~]]		[[Category: Geobacillus stearothermophilus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Banerjee, A]]		[[Category: Banerjee A]]
	[[Category: Qi, Y]]		[[Category: Qi Y]]
	[[Category: Verdine~~, G L]]~~		[[Category: Verdine GL]]
	~~[[Category: Base extrusion]]~~
	~~[[Category: Damage search]]~~
	~~[[Category: Disulfide crosslinking]]~~
	~~[[Category: Dna damage]]~~
	~~[[Category: Dna glycosylase]]~~
	~~[[Category: Dna repair]]~~
	~~[[Category: Dna-binding]]~~
	~~[[Category: Glycosidase]]~~
	~~[[Category: Hydrolase]]~~
	~~[[Category: Lyase]]~~
	~~[[Category: Lyase-dna complex]]~~
	~~[[Category: Metal-binding]]~~
	~~[[Category: Multifunctional enzyme]]~~
	~~[[Category: Zinc-finger~~]]

OCA at 20:08, 20 October 2021

2021-10-20T20:08:46Z

← Older revision		Revision as of 20:08, 20 October 2021
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	==MutM encountering an intrahelical 8-oxoguanine (oxoG) lesion in EC4-loop deletion complex==		==MutM encountering an intrahelical 8-oxoguanine (oxoG) lesion in EC4-loop deletion complex==
	<StructureSection load='3gpu' size='340' side='right' caption='[[3gpu]], [[Resolution\|resolution]] 1.62Å' scene=''>		<StructureSection load='3gpu' size='340' side='right'caption='[[3gpu]], [[Resolution\|resolution]] 1.62Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3gpu]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GPU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3GPU FirstGlance]. <br>		<table><tr><td colspan='2'>[[3gpu]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GPU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GPU FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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">[[3gpp\|3gpp]], [[3gpx\|3gpx]], [[3gpy\|3gpy]], [[3gq3\|3gq3]], [[3gq4\|3gq4]], [[3gq5\|3gq5]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3gpp\|3gpp]], [[3gpx\|3gpx]], [[3gpy\|3gpy]], [[3gq3\|3gq3]], [[3gq4\|3gq4]], [[3gq5\|3gq5]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MutM ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ATCC 12980])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MutM ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ATCC 12980])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/DNA-(apurinic_or_apyrimidinic_site)_lyase DNA-(apurinic or apyrimidinic site) lyase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.99.18 4.2.99.18] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/DNA-(apurinic_or_apyrimidinic_site)_lyase DNA-(apurinic or apyrimidinic site) lyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.99.18 4.2.99.18] </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=3gpu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gpu OCA], [~~http~~://pdbe.org/3gpu PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3gpu RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3gpu PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3gpu 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=3gpu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gpu OCA], [https://pdbe.org/3gpu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gpu RCSB], [https://www.ebi.ac.uk/pdbsum/3gpu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gpu ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/P84131_GEOSE P84131_GEOSE]] Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates (By similarity).[HAMAP-Rule:MF_00103][SAAS:SAAS020629_004_120556]		[[https://www.uniprot.org/uniprot/P84131_GEOSE P84131_GEOSE]] Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates (By similarity).[HAMAP-Rule:MF_00103][SAAS:SAAS020629_004_120556]
	== 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/gp/3gpu_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gp/3gpu_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>
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	</div>		</div>
	<div class="pdbe-citations 3gpu" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3gpu" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[DNA glycosylase 3D structures\|DNA glycosylase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Atcc 12980]]		[[Category: Atcc 12980]]
			[[Category: Large Structures]]
	[[Category: Banerjee, A]]		[[Category: Banerjee, A]]
	[[Category: Qi, Y]]		[[Category: Qi, Y]]

OCA at 07:10, 1 November 2017

2017-11-01T07:10:06Z

← Older revision		Revision as of 07:10, 1 November 2017
Line 1:		Line 1:

	==MutM encountering an intrahelical 8-oxoguanine (oxoG) lesion in EC4-loop deletion complex==		==MutM encountering an intrahelical 8-oxoguanine (oxoG) lesion in EC4-loop deletion complex==
	<StructureSection load='3gpu' size='340' side='right' caption='[[3gpu]], [[Resolution\|resolution]] 1.62Å' scene=''>		<StructureSection load='3gpu' size='340' side='right' caption='[[3gpu]], [[Resolution\|resolution]] 1.62Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MutM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ATCC 12980])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MutM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ATCC 12980])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-(apurinic_or_apyrimidinic_site)_lyase DNA-(apurinic or apyrimidinic site) lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.99.18 4.2.99.18] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-(apurinic_or_apyrimidinic_site)_lyase DNA-(apurinic or apyrimidinic site) lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.99.18 4.2.99.18] </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=3gpu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gpu OCA], [http://pdbe.org/3gpu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3gpu RCSB], [http://www.ebi.ac.uk/pdbsum/3gpu 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=3gpu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gpu OCA], [http://pdbe.org/3gpu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3gpu RCSB], [http://www.ebi.ac.uk/pdbsum/3gpu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3gpu ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 3gpu" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3gpu" style="background-color:#fffaf0;"></div>

	~~==See Also==~~
	*[[DNA glycosylase\|DNA glycosylase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 01:34, 9 February 2016

2016-02-09T01:34:30Z

← Older revision		Revision as of 01:34, 9 February 2016
Line 2:		Line 2:
	<StructureSection load='3gpu' size='340' side='right' caption='[[3gpu]], [[Resolution\|resolution]] 1.62Å' scene=''>		<StructureSection load='3gpu' size='340' side='right' caption='[[3gpu]], [[Resolution\|resolution]] 1.62Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3gpu]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Geobacillus_stearothermophilus Geobacillus stearothermophilus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GPU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GPU FirstGlance]. <br>		<table><tr><td colspan='2'>[[3gpu]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GPU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GPU FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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">[[3gpp\|3gpp]], [[3gpx\|3gpx]], [[3gpy\|3gpy]], [[3gq3\|3gq3]], [[3gq4\|3gq4]], [[3gq5\|3gq5]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gpp\|3gpp]], [[3gpx\|3gpx]], [[3gpy\|3gpy]], [[3gq3\|3gq3]], [[3gq4\|3gq4]], [[3gq5\|3gq5]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MutM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ~~Geobacillus stearothermophilus~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MutM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ATCC 12980])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-(apurinic_or_apyrimidinic_site)_lyase DNA-(apurinic or apyrimidinic site) lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.99.18 4.2.99.18] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-(apurinic_or_apyrimidinic_site)_lyase DNA-(apurinic or apyrimidinic site) lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.99.18 4.2.99.18] </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=3gpu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gpu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3gpu RCSB], [http://www.ebi.ac.uk/pdbsum/3gpu 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=3gpu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gpu OCA], [http://pdbe.org/3gpu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3gpu RCSB], [http://www.ebi.ac.uk/pdbsum/3gpu PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/~~P84131_BACST P84131_BACST~~]] Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates (By similarity).[HAMAP-Rule:MF_00103][SAAS:~~SAAS015886_004_120556~~]		[[http://www.uniprot.org/uniprot/P84131_GEOSE P84131_GEOSE]] Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates (By similarity).[HAMAP-Rule:MF_00103][SAAS:SAAS020629_004_120556]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 20:		Line 20:
	<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=3gpu ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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 3gpu" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 37:		Line 38:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Geobacillus stearothermophilus~~]]		[[Category: Atcc 12980]]
	[[Category: Banerjee, A]]		[[Category: Banerjee, A]]
	[[Category: Qi, Y]]		[[Category: Qi, Y]]

OCA at 14:48, 5 January 2015

2015-01-05T14:48:50Z

← Older revision		Revision as of 14:48, 5 January 2015
Line 1:		Line 1:
	[[Image:~~3gpu~~.~~png~~\|~~left~~\|~~200px~~]]		==MutM encountering an intrahelical 8-oxoguanine (oxoG) lesion in EC4-loop deletion complex==
			<StructureSection load='3gpu' size='340' side='right' caption='[[3gpu]], [[Resolution\|resolution]] 1.62Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[3gpu]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GPU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GPU FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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">[[3gpp\|3gpp]], [[3gpx\|3gpx]], [[3gpy\|3gpy]], [[3gq3\|3gq3]], [[3gq4\|3gq4]], [[3gq5\|3gq5]]</td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MutM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 Geobacillus stearothermophilus])</td></tr>
			<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-(apurinic_or_apyrimidinic_site)_lyase DNA-(apurinic or apyrimidinic site) lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.99.18 4.2.99.18] </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=3gpu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gpu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3gpu RCSB], [http://www.ebi.ac.uk/pdbsum/3gpu PDBsum]</span></td></tr>
			</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/P84131_BACST P84131_BACST]] Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates (By similarity).[HAMAP-Rule:MF_00103][SAAS:SAAS015886_004_120556]
			== 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/gp/3gpu_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 ==
			How living systems detect the presence of genotoxic damage embedded in a million-fold excess of undamaged DNA is an unresolved question in biology. Here we have captured and structurally elucidated a base-excision DNA repair enzyme, MutM, at the stage of initial encounter with a damaged nucleobase, 8-oxoguanine (oxoG), nested within a DNA duplex. Three structures of intrahelical oxoG-encounter complexes are compared with sequence-matched structures containing a normal G base in place of an oxoG lesion. Although the protein-DNA interfaces in the matched complexes differ by only two atoms-those that distinguish oxoG from G-their pronounced structural differences indicate that MutM can detect a lesion in DNA even at the earliest stages of encounter. All-atom computer simulations show the pathway by which encounter of the enzyme with the lesion causes extrusion from the DNA duplex, and they elucidate the critical free energy difference between oxoG and G along the extrusion pathway.

	~~{{STRUCTURE_3gpu\| PDB=3gpu \| SCENE= }}~~		Encounter and extrusion of an intrahelical lesion by a DNA repair enzyme.,Qi Y, Spong MC, Nam K, Banerjee A, Jiralerspong S, Karplus M, Verdine GL Nature. 2009 Dec 10;462(7274):762-6. PMID:20010681<ref>PMID:20010681</ref>

	~~===MutM encountering an intrahelical 8-oxoguanine (oxoG) lesion in EC4-loop deletion complex===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_20010681}}~~

	~~==About this Structure==~~
	~~[[3gpu]] is~~ a ~~3 chain structure with sequence from [http://en.wikipedia~~.~~org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann.ac.il/oca-bin~~/~~ocashort?id=3GPU OCA].~~

	==See Also==		==See Also==
	*[[DNA ~~glycosylate~~\|DNA ~~glycosylate~~]]		*[[DNA glycosylase\|DNA glycosylase]]
			== References ==
	==~~Reference~~==		<references/>
	<~~ref group="xtra">PMID:020010681<~~/~~ref~~><~~references group="xtra"~~/>		__TOC__
			</StructureSection>
	[[Category: Geobacillus stearothermophilus]]		[[Category: Geobacillus stearothermophilus]]
	[[Category: Banerjee, A.]]		[[Category: Banerjee, A]]
	[[Category: Qi, Y.]]		[[Category: Qi, Y]]
	[[Category: Verdine, G L.]]		[[Category: Verdine, G L]]
	[[Category: Base extrusion]]		[[Category: Base extrusion]]
	[[Category: Damage search]]		[[Category: Damage search]]

OCA at 12:11, 20 October 2012

2012-10-20T12:11:03Z

← Older revision		Revision as of 12:11, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
	[[3gpu]] is a 3 chain structure ~~of [[DNA glycosylate]]~~ with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GPU OCA].		[[3gpu]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GPU OCA].

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

OCA: Protected "3gpu" [edit=sysop:move=sysop]

2012-07-26T07:53:05Z

Protected "3gpu" [edit=sysop:move=sysop]

← Older revision	Revision as of 07:53, 26 July 2012
(No difference)

OCA at 07:53, 26 July 2012

2012-07-26T07:53:03Z

← Older revision		Revision as of 07:53, 26 July 2012
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	~~{{Seed}}~~
	[[Image:3gpu.png\|left\|200px]]		[[Image:3gpu.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_3gpu", 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_3gpu\| PDB=3gpu \| SCENE= }}		{{STRUCTURE_3gpu\| PDB=3gpu \| SCENE= }}

	===MutM encountering an intrahelical 8-oxoguanine (oxoG) lesion in EC4-loop deletion complex===		===MutM encountering an intrahelical 8-oxoguanine (oxoG) lesion in EC4-loop deletion complex===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_20010681}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 20010681 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_20010681}}		{{ABSTRACT_PUBMED_20010681}}

	==About this Structure==		==About this Structure==
	~~3GPU~~ is a 3 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GPU OCA].		[[3gpu]] is a 3 chain structure of [[DNA glycosylate]] with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GPU OCA].

			==See Also==
			*[[DNA glycosylate\|DNA glycosylate]]

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~20010681~~</ref><references group="xtra"/>		<ref group="xtra">PMID:020010681</ref><references group="xtra"/>
	[[Category: Geobacillus stearothermophilus]]		[[Category: Geobacillus stearothermophilus]]
	[[Category: Banerjee, A.]]		[[Category: Banerjee, A.]]
Line 38:		Line 29:
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Lyase/dna complex]]		[[Category: Lyase-dna complex]]
	[[Category: Metal-binding]]		[[Category: Metal-binding]]
	[[Category: Multifunctional enzyme]]		[[Category: Multifunctional enzyme]]
	~~[[Category: Zinc]]~~
	[[Category: Zinc-finger]]		[[Category: Zinc-finger]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 3 09:09:58 2010''~~

OCA at 07:09, 3 February 2010

2010-02-03T07:09:58Z

← Older revision		Revision as of 07:09, 3 February 2010
Line 1:		Line 1:
	{{Seed}}		{{Seed}}
	[[Image:3gpu.~~jpg~~\|left\|200px]]		[[Image:3gpu.png\|left\|200px]]

	<!--		<!--
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	===MutM encountering an intrahelical 8-oxoguanine (oxoG) lesion in EC4-loop deletion complex===		===MutM encountering an intrahelical 8-oxoguanine (oxoG) lesion in EC4-loop deletion complex===


			<!--
			The line below this paragraph, {{ABSTRACT_PUBMED_20010681}}, adds the Publication Abstract to the page
			(as it appears on PubMed at http://www.pubmed.gov), where 20010681 is the PubMed ID number.
			-->
			{{ABSTRACT_PUBMED_20010681}}

	==About this Structure==		==About this Structure==
	3GPU is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GPU OCA].		3GPU is a 3 chains structure with sequences from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GPU OCA].

			==Reference==
			<ref group="xtra">PMID:20010681</ref><references group="xtra"/>
	[[Category: Geobacillus stearothermophilus]]		[[Category: Geobacillus stearothermophilus]]
	[[Category: Banerjee, A.]]		[[Category: Banerjee, A.]]
Line 35:		Line 44:
	[[Category: Zinc-finger]]		[[Category: Zinc-finger]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Nov 11 22~~:24:~~31 2009~~''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 3 09:09:58 2010''

OCA at 20:24, 11 November 2009

2009-11-11T20:24:34Z

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
+{{Seed}}
-The entry 3gpu is ON HOLD  until Paper Publication
+<!--
-Authors: Banerjee, A., Qi, Y., Verdine, G.L.
+===MutM encountering an intrahelical 8-oxoguanine (oxoG) lesion in EC4-loop deletion complex===
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 15 09:55:59 2009''
+==About this Structure==