2qvy - Revision history

OCA at 11:42, 30 August 2023

OCA — Wed, 30 Aug 2023 11:42:07 GMT

←Older revision		Revision as of 11:42, 30 August 2023
Line 3:		Line 3:
	<StructureSection load='2qvy' size='340' side='right'caption='[[2qvy]], [[Resolution\|resolution]] 2.76Å' scene=''>		<StructureSection load='2qvy' size='340' side='right'caption='[[2qvy]], [[Resolution\|resolution]] 2.76Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2qvy]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Alcaligenes_sp.~~_al3007~~ Alcaligenes sp. ~~al3007~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QVY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QVY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2qvy]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Alcaligenes_sp._AL3007 Alcaligenes sp. AL3007]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QVY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QVY FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=34Z:3~~,~~4-DICHLOROBENZOATE'>34Z</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]] 2.76Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style='overflow: auto; max-height: 3em;'>[[1t5d\|1t5d]], [[1pg4\|1pg4]], [[2qvx\|2qvx]], [[2qvz\|2qvz]], [[2qw0\|2qw0]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=34Z:3,4-DICHLOROBENZOATE'>34Z</scene></td></tr>
-	~~<tr~~ id~~='activity'><td class~~="~~sblockLbl~~"><~~b>Activity:</b></td><td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[https~~:~~//en.wikipedia.org/wiki/~~4-~~chlorobenzoate--CoA_ligase 4-chlorobenzoate--CoA ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.33 6.2.1.33]~~ </~~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=2qvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qvy OCA], [https://pdbe.org/2qvy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qvy RCSB], [https://www.ebi.ac.uk/pdbsum/2qvy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qvy 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=2qvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qvy OCA], [https://pdbe.org/2qvy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qvy RCSB], [https://www.ebi.ac.uk/pdbsum/2qvy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qvy ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q8GN86_9BURK Q8GN86_9BURK]
	== 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: 4-chlorobenzoate--CoA ligase]]~~	+	[[Category: Alcaligenes sp. AL3007]]
-	[[Category: Alcaligenes sp. ~~al3007~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cao, J]]	+	[[Category: Cao J]]
-	[[Category: Dunaway-Mariano, D]]	+	[[Category: Dunaway-Mariano D]]
-	[[Category: Gulick~~, A M~~]]	+	[[Category: Gulick AM]]
-	[[Category: Reger~~, A S~~]]	+	[[Category: Reger AS]]
-	[[Category: Wu, R]]	+	[[Category: Wu R]]
-	~~[[Category: Acyl-coa ligase]]~~	+
-	~~[[Category: Adenylate-forming enzyme]]~~	+
-	~~[[Category: Ligase~~]]	+

OCA at 07:45, 16 March 2022

OCA — Wed, 16 Mar 2022 07:45:33 GMT

←Older revision		Revision as of 07:45, 16 March 2022
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	<StructureSection load='2qvy' size='340' side='right'caption='[[2qvy]], [[Resolution\|resolution]] 2.76Å' scene=''>		<StructureSection load='2qvy' size='340' side='right'caption='[[2qvy]], [[Resolution\|resolution]] 2.76Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2qvy]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Alcaligenes_sp._al3007 Alcaligenes sp. al3007]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QVY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2QVY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2qvy]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Alcaligenes_sp._al3007 Alcaligenes sp. al3007]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QVY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QVY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=34Z:3,4-DICHLOROBENZOATE'>34Z</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=34Z:3,4-DICHLOROBENZOATE'>34Z</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t5d\|1t5d]], [[1pg4\|1pg4]], [[2qvx\|2qvx]], [[2qvz\|2qvz]], [[2qw0\|2qw0]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1t5d\|1t5d]], [[1pg4\|1pg4]], [[2qvx\|2qvx]], [[2qvz\|2qvz]], [[2qw0\|2qw0]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/4-chlorobenzoate--CoA_ligase 4-chlorobenzoate--CoA ligase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.33 6.2.1.33] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/4-chlorobenzoate--CoA_ligase 4-chlorobenzoate--CoA ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.33 6.2.1.33] </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=2qvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qvy OCA], [~~http~~://pdbe.org/2qvy PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2qvy RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2qvy PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2qvy 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=2qvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qvy OCA], [https://pdbe.org/2qvy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qvy RCSB], [https://www.ebi.ac.uk/pdbsum/2qvy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qvy ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 07:08, 10 June 2020

OCA — Wed, 10 Jun 2020 07:08:30 GMT

OCA at 10:59, 5 September 2018

OCA — Wed, 05 Sep 2018 10:59:27 GMT

←Older revision		Revision as of 10:59, 5 September 2018
Line 1:		Line 1:
		+
	==4-Chlorobenzoyl-CoA Ligase/Synthetase, I303G mutation, bound to 3,4-Dichlorobenzoate==		==4-Chlorobenzoyl-CoA Ligase/Synthetase, I303G mutation, bound to 3,4-Dichlorobenzoate==
	<StructureSection load='2qvy' size='340' side='right' caption='[[2qvy]], [[Resolution\|resolution]] 2.76Å' scene=''>		<StructureSection load='2qvy' size='340' side='right' caption='[[2qvy]], [[Resolution\|resolution]] 2.76Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t5d\|1t5d]], [[1pg4\|1pg4]], [[2qvx\|2qvx]], [[2qvz\|2qvz]], [[2qw0\|2qw0]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t5d\|1t5d]], [[1pg4\|1pg4]], [[2qvx\|2qvx]], [[2qvz\|2qvz]], [[2qw0\|2qw0]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-chlorobenzoate--CoA_ligase 4-chlorobenzoate--CoA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.33 6.2.1.33] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-chlorobenzoate--CoA_ligase 4-chlorobenzoate--CoA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.33 6.2.1.33] </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=2qvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qvy OCA], [http://pdbe.org/2qvy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2qvy RCSB], [http://www.ebi.ac.uk/pdbsum/2qvy 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=2qvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qvy OCA], [http://pdbe.org/2qvy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2qvy RCSB], [http://www.ebi.ac.uk/pdbsum/2qvy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2qvy ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qv/2qvy_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qv/2qvy_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>

OCA at 14:38, 7 February 2016

OCA — Sun, 07 Feb 2016 14:38:34 GMT

←Older revision		Revision as of 14:38, 7 February 2016
Line 16:		Line 16:
	<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=2qvy ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 02:27, 10 September 2015

OCA — Thu, 10 Sep 2015 02:27:12 GMT

←Older revision		Revision as of 02:27, 10 September 2015
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	<StructureSection load='2qvy' size='340' side='right' caption='[[2qvy]], [[Resolution\|resolution]] 2.76Å' scene=''>		<StructureSection load='2qvy' size='340' side='right' caption='[[2qvy]], [[Resolution\|resolution]] 2.76Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2qvy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Alcaligenes_sp. Alcaligenes sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QVY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QVY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2qvy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Alcaligenes_sp._al3007 Alcaligenes sp. al3007]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QVY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QVY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=34Z:3,4-DICHLOROBENZOATE'>34Z</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=34Z:3,4-DICHLOROBENZOATE'>34Z</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t5d\|1t5d]], [[1pg4\|1pg4]], [[2qvx\|2qvx]], [[2qvz\|2qvz]], [[2qw0\|2qw0]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t5d\|1t5d]], [[1pg4\|1pg4]], [[2qvx\|2qvx]], [[2qvz\|2qvz]], [[2qw0\|2qw0]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-chlorobenzoate--CoA_ligase 4-chlorobenzoate--CoA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.33 6.2.1.33] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-chlorobenzoate--CoA_ligase 4-chlorobenzoate--CoA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.33 6.2.1.33] </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=2qvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qvy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qvy RCSB], [http://www.ebi.ac.uk/pdbsum/2qvy 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=2qvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qvy OCA], [http://pdbe.org/2qvy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2qvy RCSB], [http://www.ebi.ac.uk/pdbsum/2qvy PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 26:		Line 26:
	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 2qvy" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 31:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: 4-chlorobenzoate--CoA ligase]]		[[Category: 4-chlorobenzoate--CoA ligase]]
-	[[Category: Alcaligenes sp]]	+	[[Category: Alcaligenes sp. al3007]]
	[[Category: Cao, J]]		[[Category: Cao, J]]
	[[Category: Dunaway-Mariano, D]]		[[Category: Dunaway-Mariano, D]]

OCA at 16:31, 19 January 2015

OCA — Mon, 19 Jan 2015 16:31:35 GMT

←Older revision		Revision as of 16:31, 19 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2qvy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Alcaligenes_sp. Alcaligenes sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QVY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QVY FirstGlance]. <br>		<table><tr><td colspan='2'>[[2qvy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Alcaligenes_sp. Alcaligenes sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QVY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QVY FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=34Z:3,4-DICHLOROBENZOATE'>34Z</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=34Z:3,4-DICHLOROBENZOATE'>34Z</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t5d\|1t5d]], [[1pg4\|1pg4]], [[2qvx\|2qvx]], [[2qvz\|2qvz]], [[2qw0\|2qw0]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t5d\|1t5d]], [[1pg4\|1pg4]], [[2qvx\|2qvx]], [[2qvz\|2qvz]], [[2qw0\|2qw0]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-chlorobenzoate--CoA_ligase 4-chlorobenzoate--CoA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.33 6.2.1.33] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-chlorobenzoate--CoA_ligase 4-chlorobenzoate--CoA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.33 6.2.1.33] </span></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=2qvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qvy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qvy RCSB], [http://www.ebi.ac.uk/pdbsum/2qvy 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=2qvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qvy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qvy RCSB], [http://www.ebi.ac.uk/pdbsum/2qvy PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: 4-chlorobenzoate--CoA ligase]]		[[Category: 4-chlorobenzoate--CoA ligase]]
-	[[Category: Alcaligenes sp.]]	+	[[Category: Alcaligenes sp]]
-	[[Category: Cao, J.]]	+	[[Category: Cao, J]]
-	[[Category: Dunaway-Mariano, D.]]	+	[[Category: Dunaway-Mariano, D]]
-	[[Category: Gulick, A M.]]	+	[[Category: Gulick, A M]]
-	[[Category: Reger, A S.]]	+	[[Category: Reger, A S]]
-	[[Category: Wu, R.]]	+	[[Category: Wu, R]]
	[[Category: Acyl-coa ligase]]		[[Category: Acyl-coa ligase]]
	[[Category: Adenylate-forming enzyme]]		[[Category: Adenylate-forming enzyme]]
	[[Category: Ligase]]		[[Category: Ligase]]

OCA at 19:18, 30 September 2014

OCA — Tue, 30 Sep 2014 19:18:37 GMT

←Older revision		Revision as of 19:18, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2qvy.~~png~~\|~~left~~\|200px]]	+	==4-Chlorobenzoyl-CoA Ligase/Synthetase, I303G mutation, bound to 3,4-Dichlorobenzoate==
		+	<StructureSection load='2qvy' size='340' side='right' caption='[[2qvy]], [[Resolution\|resolution]] 2.76Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2qvy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Alcaligenes_sp. Alcaligenes sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QVY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QVY FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=34Z:3,4-DICHLOROBENZOATE'>34Z</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t5d\|1t5d]], [[1pg4\|1pg4]], [[2qvx\|2qvx]], [[2qvz\|2qvz]], [[2qw0\|2qw0]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-chlorobenzoate--CoA_ligase 4-chlorobenzoate--CoA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.33 6.2.1.33] </span></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=2qvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qvy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qvy RCSB], [http://www.ebi.ac.uk/pdbsum/2qvy 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/qv/2qvy_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 ==
		+	Environmental aromatic acids are transformed to chemical energy in bacteria that possess the requisite secondary pathways. Some of these pathways rely on the activation of the aromatic acid by coenzyme A (CoA) thioesterification catalyzed by an aromatic acid: CoA ligase. Adaptation of such pathways to the bioremediation of man-made pollutants such as polychlorinated biphenyl (PCB) and dichlorodiphenyltrichloroethane (DDT) requires that the chlorinated benzoic acid byproduct that is formed be able to be eliminated by further degradation. To take advantage of natural benzoic acid degrading pathways requiring initial ring activation by thioesterification, the pathway aromatic acid:CoA ligase must be an effective catalyst with the chlorinated benzoic acid. This study, which focuses on the 4-chlorobenzoate:CoA ligase (CBL) of the 4-monochlorobiphenyl degrading bacterium Alcaligenes sp. strain ALP83, was carried out to determine if the 4-chlorobenzoate binding site of this enzyme can be transformed by rational design to recognize the chlorobenzoic acids formed in the course of breakdown of other environmental PCB congeners. The fundamental question addressed in this study is whether it is possible to add or subtract space from the substrate-binding pocket of this ligase (to complement the topology of the unnatural aromatic substrate) without causing disruption of the ligase catalytic machinery. Herein, we report the results of a substrate specificity analysis that, when interpreted within the context of the X-ray crystal structures, set the stage for the rational design of the ligase for thioesterification of two PCB-derived chlorobenzoic acids. The ligase was first optimized to catalyze CoA thioesterification of 3,4-dichlorobenzoic acid, a poor substrate, by truncating Ile303, a large hydrophobic residue that packs against the ring meta-C(H) group. The structural basis for the approximately 100-fold enhancement in the rate of 3,4-dichlorobenzoate thioesterification catalyzed by the I303A and I303G CBL mutants was validated by determination of the crystal structure of the 3,4-dichlorobenzoate-bound enzymes. Determinations of the structures of I303 mutant complexes of 3-chlorobenzoate, a very poor substrate, revealed nonproductive binding as a result of the inability of the substrate ring C(4)H group to fill the pocket that binds the C(4)Cl group of the native substrate. The C(4)Cl pocket of the CBL I303A mutant was then reduced in size by strategic amino acid replacement. A 54-fold improvement in catalytic efficiency was observed for the CBL F184W/I303A/V209T triple mutant. The results of this investigation are interpreted as evidence that the plasticity of the ligase catalytic scaffold is sufficient to allow expansion of substrate range by rational design. The combination of structural and kinetic analyses of the constructed mutants proved to be an effective approach to engineering the ligase for novel substrates.

-	~~{{STRUCTURE_2qvy\| PDB=2qvy \| SCENE= }}~~	+	Rational redesign of the 4-chlorobenzoate binding site of 4-chlorobenzoate: coenzyme a ligase for expanded substrate range(,)(,).,Wu R, Reger AS, Cao J, Gulick AM, Dunaway-Mariano D Biochemistry. 2007 Dec 18;46(50):14487-99. Epub 2007 Nov 21. PMID:18027984<ref>PMID:18027984</ref>

-	~~===4-Chlorobenzoyl-CoA Ligase~~/~~Synthetase~~, ~~I303G mutation, bound to 3,4-Dichlorobenzoate===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18027984}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2qvy]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Alcaligenes_sp~~. ~~Alcaligenes sp.]. Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2QVY OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:018027984<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: 4-chlorobenzoate--CoA ligase]]		[[Category: 4-chlorobenzoate--CoA ligase]]
	[[Category: Alcaligenes sp.]]		[[Category: Alcaligenes sp.]]

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

OCA — Mon, 07 Jan 2013 22:01:27 GMT

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

←Older revision

Revision as of 22:01, 7 January 2013

OCA at 22:01, 7 January 2013

OCA — Mon, 07 Jan 2013 22:01:25 GMT

←Older revision		Revision as of 22:01, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2qvy.png\|left\|200px]]		[[Image:2qvy.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2qvy", 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_2qvy\| PDB=2qvy \| SCENE= }}		{{STRUCTURE_2qvy\| PDB=2qvy \| SCENE= }}

	===4-Chlorobenzoyl-CoA Ligase/Synthetase, I303G mutation, bound to 3,4-Dichlorobenzoate===		===4-Chlorobenzoyl-CoA Ligase/Synthetase, I303G mutation, bound to 3,4-Dichlorobenzoate===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18027984}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18027984 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18027984}}		{{ABSTRACT_PUBMED_18027984}}

	==About this Structure==		==About this Structure==
-	~~2QVY~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Alcaligenes_sp. Alcaligenes sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QVY OCA].	+	[[2qvy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Alcaligenes_sp. Alcaligenes sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QVY OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18027984~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018027984</ref><references group="xtra"/>
	[[Category: 4-chlorobenzoate--CoA ligase]]		[[Category: 4-chlorobenzoate--CoA ligase]]
	[[Category: Alcaligenes sp.]]		[[Category: Alcaligenes sp.]]
Line 33:		Line 21:
	[[Category: Acyl-coa ligase]]		[[Category: Acyl-coa ligase]]
	[[Category: Adenylate-forming enzyme]]		[[Category: Adenylate-forming enzyme]]
-		+	[[Category: Ligase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Mon Feb 16 14:31:05 2009''~~	+

←Older revision		Revision as of 07:08, 10 June 2020
Line 1:		Line 1:

	==4-Chlorobenzoyl-CoA Ligase/Synthetase, I303G mutation, bound to 3,4-Dichlorobenzoate==		==4-Chlorobenzoyl-CoA Ligase/Synthetase, I303G mutation, bound to 3,4-Dichlorobenzoate==
-	<StructureSection load='2qvy' size='340' side='right' caption='[[2qvy]], [[Resolution\|resolution]] 2.76Å' scene=''>	+	<StructureSection load='2qvy' size='340' side='right'caption='[[2qvy]], [[Resolution\|resolution]] 2.76Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2qvy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Alcaligenes_sp._al3007 Alcaligenes sp. al3007]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QVY OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2QVY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2qvy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Alcaligenes_sp._al3007 Alcaligenes sp. al3007]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QVY OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2QVY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=34Z:3,4-DICHLOROBENZOATE'>34Z</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=34Z:3,4-DICHLOROBENZOATE'>34Z</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t5d\|1t5d]], [[1pg4\|1pg4]], [[2qvx\|2qvx]], [[2qvz\|2qvz]], [[2qw0\|2qw0]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1t5d\|1t5d]], [[1pg4\|1pg4]], [[2qvx\|2qvx]], [[2qvz\|2qvz]], [[2qw0\|2qw0]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-chlorobenzoate--CoA_ligase 4-chlorobenzoate--CoA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.33 6.2.1.33] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-chlorobenzoate--CoA_ligase 4-chlorobenzoate--CoA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.33 6.2.1.33] </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=2qvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qvy OCA], [http://pdbe.org/2qvy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2qvy RCSB], [http://www.ebi.ac.uk/pdbsum/2qvy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2qvy 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=2qvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qvy OCA], [http://pdbe.org/2qvy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2qvy RCSB], [http://www.ebi.ac.uk/pdbsum/2qvy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2qvy ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 34:		Line 34:
	[[Category: 4-chlorobenzoate--CoA ligase]]		[[Category: 4-chlorobenzoate--CoA ligase]]
	[[Category: Alcaligenes sp. al3007]]		[[Category: Alcaligenes sp. al3007]]
		+	[[Category: Large Structures]]
	[[Category: Cao, J]]		[[Category: Cao, J]]
	[[Category: Dunaway-Mariano, D]]		[[Category: Dunaway-Mariano, D]]