1kqj - Revision history

OCA at 09:02, 16 August 2023

OCA — Wed, 16 Aug 2023 09:02:41 GMT

←Older revision		Revision as of 09:02, 16 August 2023
Line 3:		Line 3:
	<StructureSection load='1kqj' size='340' side='right'caption='[[1kqj]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='1kqj' size='340' side='right'caption='[[1kqj]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kqj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KQJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KQJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kqj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KQJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KQJ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>~~, ~~<scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.7Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow: auto; max-height~~: ~~3em;~~'>~~[[1muy\|1muy]], [[1mud\|1mud]], [[1mun\|1mun]]~~</~~div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">MutY ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])~~</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=1kqj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kqj OCA], [https://pdbe.org/1kqj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kqj RCSB], [https://www.ebi.ac.uk/pdbsum/1kqj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kqj 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=1kqj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kqj OCA], [https://pdbe.org/1kqj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kqj RCSB], [https://www.ebi.ac.uk/pdbsum/1kqj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kqj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/MUTY_ECOLI MUTY_ECOLI]] Adenine glycosylase active on G-A mispairs. MutY also corrects error-prone DNA synthesis past GO lesions which are due to the oxidatively damaged form of guanine: 7,8-dihydro-8-oxoguanine (8-oxo-dGTP).	+	[https://www.uniprot.org/uniprot/MUTY_ECOLI MUTY_ECOLI] Adenine glycosylase active on G-A mispairs. MutY also corrects error-prone DNA synthesis past GO lesions which are due to the oxidatively damaged form of guanine: 7,8-dihydro-8-oxoguanine (8-oxo-dGTP).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 37:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chmiel~~, N H~~]]	+	[[Category: Chmiel NH]]
-	[[Category: David~~, S S~~]]	+	[[Category: David SS]]
-	[[Category: Golinelli~~, M P~~]]	+	[[Category: Golinelli MP]]
-	[[Category: Joshua-Tor, L]]	+	[[Category: Joshua-Tor L]]
-	[[Category: Messick~~, T E]]~~	+	[[Category: Messick TE]]
-	~~[[Category: All alpha-helix]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Two lobe~~]]	+

OCA at 14:43, 27 October 2021

OCA — Wed, 27 Oct 2021 14:43:32 GMT

←Older revision		Revision as of 14:43, 27 October 2021
Line 3:		Line 3:
	<StructureSection load='1kqj' size='340' side='right'caption='[[1kqj]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='1kqj' size='340' side='right'caption='[[1kqj]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kqj]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KQJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1KQJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kqj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KQJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KQJ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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;'>[[1muy\|1muy]], [[1mud\|1mud]], [[1mun\|1mun]]</div></td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1muy\|1muy]], [[1mud\|1mud]], [[1mun\|1mun]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MutY ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MutY ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=1kqj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kqj OCA], [~~http~~://pdbe.org/1kqj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1kqj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1kqj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1kqj 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=1kqj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kqj OCA], [https://pdbe.org/1kqj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kqj RCSB], [https://www.ebi.ac.uk/pdbsum/1kqj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kqj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/MUTY_ECOLI MUTY_ECOLI]] Adenine glycosylase active on G-A mispairs. MutY also corrects error-prone DNA synthesis past GO lesions which are due to the oxidatively damaged form of guanine: 7,8-dihydro-8-oxoguanine (8-oxo-dGTP).	+	[[https://www.uniprot.org/uniprot/MUTY_ECOLI MUTY_ECOLI]] Adenine glycosylase active on G-A mispairs. MutY also corrects error-prone DNA synthesis past GO lesions which are due to the oxidatively damaged form of guanine: 7,8-dihydro-8-oxoguanine (8-oxo-dGTP).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 07:48, 25 November 2020

OCA — Wed, 25 Nov 2020 07:48:47 GMT

←Older revision		Revision as of 07:48, 25 November 2020
Line 1:		Line 1:

	==Crystal Structure of a Mutant of MutY Catalytic Domain==		==Crystal Structure of a Mutant of MutY Catalytic Domain==
-	<StructureSection load='1kqj' size='340' side='right' caption='[[1kqj]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='1kqj' size='340' side='right'caption='[[1kqj]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kqj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KQJ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1KQJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kqj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KQJ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1KQJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1muy\|1muy]], [[1mud\|1mud]], [[1mun\|1mun]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1muy\|1muy]], [[1mud\|1mud]], [[1mun\|1mun]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MutY ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MutY ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=1kqj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kqj OCA], [http://pdbe.org/1kqj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kqj RCSB], [http://www.ebi.ac.uk/pdbsum/1kqj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1kqj 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=1kqj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kqj OCA], [http://pdbe.org/1kqj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kqj RCSB], [http://www.ebi.ac.uk/pdbsum/1kqj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1kqj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 1kqj" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1kqj" 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: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Chmiel, N H]]		[[Category: Chmiel, N H]]
	[[Category: David, S S]]		[[Category: David, S S]]

OCA at 21:13, 24 January 2018

OCA — Wed, 24 Jan 2018 21:13:02 GMT

←Older revision		Revision as of 21:13, 24 January 2018
Line 1:		Line 1:
		+
	==Crystal Structure of a Mutant of MutY Catalytic Domain==		==Crystal Structure of a Mutant of MutY Catalytic Domain==
	<StructureSection load='1kqj' size='340' side='right' caption='[[1kqj]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='1kqj' size='340' side='right' caption='[[1kqj]], [[Resolution\|resolution]] 1.70Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1muy\|1muy]], [[1mud\|1mud]], [[1mun\|1mun]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1muy\|1muy]], [[1mud\|1mud]], [[1mun\|1mun]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MutY ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MutY ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=1kqj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kqj OCA], [http://pdbe.org/1kqj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kqj RCSB], [http://www.ebi.ac.uk/pdbsum/1kqj 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=1kqj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kqj OCA], [http://pdbe.org/1kqj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kqj RCSB], [http://www.ebi.ac.uk/pdbsum/1kqj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1kqj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kq/1kqj_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kq/1kqj_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 29:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1kqj" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1kqj" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[DNA glycosylase\|DNA glycosylase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 21:12, 8 February 2016

OCA — Mon, 08 Feb 2016 21:12:00 GMT

←Older revision		Revision as of 21:12, 8 February 2016
Line 18:		Line 18:
	<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=1kqj ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 31:		Line 31:

	==See Also==		==See Also==
-	*[[Adenine glycosylase\|Adenine glycosylase]]
	*[[DNA glycosylase\|DNA glycosylase]]		*[[DNA glycosylase\|DNA glycosylase]]
	== References ==		== References ==

OCA at 15:26, 10 September 2015

OCA — Thu, 10 Sep 2015 15:26:10 GMT

←Older revision		Revision as of 15:26, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1kqj' size='340' side='right' caption='[[1kqj]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='1kqj' size='340' side='right' caption='[[1kqj]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kqj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KQJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KQJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kqj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KQJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KQJ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1muy\|1muy]], [[1mud\|1mud]], [[1mun\|1mun]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1muy\|1muy]], [[1mud\|1mud]], [[1mun\|1mun]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MutY ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 ~~Escherichia~~ coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MutY ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=1kqj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kqj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kqj RCSB], [http://www.ebi.ac.uk/pdbsum/1kqj 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=1kqj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kqj OCA], [http://pdbe.org/1kqj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kqj RCSB], [http://www.ebi.ac.uk/pdbsum/1kqj PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	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 1kqj" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: Chmiel, N H]]		[[Category: Chmiel, N H]]
	[[Category: David, S S]]		[[Category: David, S S]]

OCA at 02:11, 25 December 2014

OCA — Thu, 25 Dec 2014 02:11:04 GMT

←Older revision		Revision as of 02:11, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1kqj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KQJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KQJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1kqj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KQJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KQJ FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1muy\|1muy]], [[1mud\|1mud]], [[1mun\|1mun]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1muy\|1muy]], [[1mud\|1mud]], [[1mun\|1mun]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MutY ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MutY ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</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=1kqj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kqj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kqj RCSB], [http://www.ebi.ac.uk/pdbsum/1kqj 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=1kqj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kqj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kqj RCSB], [http://www.ebi.ac.uk/pdbsum/1kqj PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/MUTY_ECOLI MUTY_ECOLI]] Adenine glycosylase active on G-A mispairs. MutY also corrects error-prone DNA synthesis past GO lesions which are due to the oxidatively damaged form of guanine: 7,8-dihydro-8-oxoguanine (8-oxo-dGTP).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Chmiel, N H.]]	+	[[Category: Chmiel, N H]]
-	[[Category: David, S S.]]	+	[[Category: David, S S]]
-	[[Category: Golinelli, M P.]]	+	[[Category: Golinelli, M P]]
-	[[Category: Joshua-Tor, L.]]	+	[[Category: Joshua-Tor, L]]
-	[[Category: Messick, T E.]]	+	[[Category: Messick, T E]]
	[[Category: All alpha-helix]]		[[Category: All alpha-helix]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Two lobe]]		[[Category: Two lobe]]

OCA at 11:29, 3 October 2014

OCA — Fri, 03 Oct 2014 11:29:54 GMT

←Older revision		Revision as of 11:29, 3 October 2014
Line 1:		Line 1:
-	[[~~Image:~~1kqj.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of a Mutant of MutY Catalytic Domain==
		+	<StructureSection load='1kqj' size='340' side='right' caption='[[1kqj]], [[Resolution\|resolution]] 1.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1kqj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KQJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KQJ FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1muy\|1muy]], [[1mud\|1mud]], [[1mun\|1mun]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MutY ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</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=1kqj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kqj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kqj RCSB], [http://www.ebi.ac.uk/pdbsum/1kqj PDBsum]</span></td></tr>
		+	<table>
		+	== 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/kq/1kqj_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 Escherichia coli DNA repair enzyme MutY plays an important role in the recognition and repair of 7,8-dihydro-8-oxo-2'-deoxyguanosine-2'-deoxyadenosine (OG*A) mismatches in DNA. MutY prevents DNA mutations caused by the misincorporation of A opposite OG by catalyzing the deglycosylation of the aberrant adenine. MutY is representative of a unique subfamily of DNA repair enzymes that also contain a [4Fe-4S]2+ cluster, which has been implicated in substrate recognition. Previously, we have used site-directed mutagenesis to individually replace the cysteine ligands to the [4Fe-4S]2+ cluster of E. coli MutY with serine, histidine, or alanine. These experiments suggested that histidine coordination to the iron-sulfur cluster may be accommodated in MutY at position 199. Purification and enzymatic analysis of C199H and C199S forms indicated that these forms behave nearly identical to the WT enzyme. Furthermore, introduction of the C199H mutation in a truncated form of MutY (C199HT) allowed for crystallization and structural characterization of the modified [4Fe-4S] cluster coordination. The C199HT structure showed that histidine coordinated to the iron cluster although comparison to the structure of the WT truncated enzyme indicated that the occupancy of iron at the modified position had been reduced to 60%. Electron paramagnetic resonance (EPR) spectroscopy on samples of C199HT indicates that a significant percentage (15-30%) of iron clusters were of the [3Fe-4S]1+ form. Oxidation of the C199HT enzyme with ferricyanide increases the amount of the 3Fe cluster by approximately 2-fold. Detailed kinetic analysis on samples containing a mixture of [3Fe-4S]1+ and [4Fe-4S]2+ forms indicated that the reactivity of the [3Fe-4S]1+ C199HT enzyme does not differ significantly from that of the WT truncated enzyme. The relative resistance of the [4Fe-4S]2+ cluster toward oxidation, as well as the retention of activity of the [3Fe-4S]1+ form, may be an important aspect of the role of MutY in repair of DNA damage resulting from oxidative stress.

-	~~{{STRUCTURE_1kqj\| PDB=1kqj \| SCENE= }}~~	+	Noncysteinyl coordination to the [4Fe-4S]2+ cluster of the DNA repair adenine glycosylase MutY introduced via site-directed mutagenesis. Structural characterization of an unusual histidinyl-coordinated cluster.,Messick TE, Chmiel NH, Golinelli MP, Langer MR, Joshua-Tor L, David SS Biochemistry. 2002 Mar 26;41(12):3931-42. PMID:11900536<ref>PMID:11900536</ref>

-	~~===Crystal Structure of~~ a ~~Mutant~~ of ~~MutY Catalytic Domain===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_11900536}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1kqj]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Escherichia_coli Escherichia coli]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1KQJ OCA].~~	+

	==See Also==		==See Also==
-	*[[DNA ~~glycosylate~~\|DNA ~~glycosylate~~]]	+	*[[Adenine glycosylase\|Adenine glycosylase]]
-		+	*[[DNA glycosylase\|DNA glycosylase]]
-	==~~Reference~~==	+	== References ==
-	<~~ref group="xtra">PMID:011900536<~~/~~ref~~><~~references group="xtra"~~/>	+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Chmiel, N H.]]		[[Category: Chmiel, N H.]]

OCA at 11:29, 20 October 2012

OCA — Sat, 20 Oct 2012 11:29:32 GMT

←Older revision		Revision as of 11:29, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1kqj]] is a 1 chain structure ~~of [[DNA glycosylate]]~~ with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KQJ OCA].	+	[[1kqj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KQJ OCA].

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

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

OCA — Thu, 26 Jul 2012 05:34:18 GMT

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

←Older revision

Revision as of 05:34, 26 July 2012