2v7b - Revision history

OCA at 15:08, 13 December 2023

2023-12-13T15:08:42Z

←Older revision		Revision as of 15:08, 13 December 2023
Line 3:		Line 3:
	<StructureSection load='2v7b' size='340' side='right'caption='[[2v7b]], [[Resolution\|resolution]] 1.84Å' scene=''>		<StructureSection load='2v7b' size='340' side='right'caption='[[2v7b]], [[Resolution\|resolution]] 1.84Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2v7b]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Burkholderia_cepacia_lb400 Burkholderia cepacia lb400~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V7B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V7B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2v7b]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Paraburkholderia_xenovorans_LB400 Paraburkholderia xenovorans LB400]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V7B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V7B FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</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]] 1.84Å</td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[https://en.wikipedia.org/wiki/Benzoate--CoA_ligase Benzoate--CoA ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.25 6.2.1.25]~~ </~~span~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene></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=2v7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v7b OCA], [https://pdbe.org/2v7b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2v7b RCSB], [https://www.ebi.ac.uk/pdbsum/2v7b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2v7b 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=2v7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v7b OCA], [https://pdbe.org/2v7b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2v7b RCSB], [https://www.ebi.ac.uk/pdbsum/2v7b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2v7b ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q13WK3_PARXL Q13WK3_PARXL]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Benzoate--CoA ligase]]
-	[[Category: Burkholderia cepacia lb400]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Bains, J~~]]	+	[[Category: Paraburkholderia xenovorans LB400]]
-	[[Category: ~~Boulanger, M~~ J]]	+	[[Category: Bains J]]
-	[[Category: ~~Benzoate coa ligase]]~~	+	[[Category: J Boulanger M]]
-	~~[[Category: Benzoate oxidation]]~~	+
-	~~[[Category: Ligase~~]]	+

OCA at 12:40, 23 March 2022

2022-03-23T12:40:30Z

←Older revision		Revision as of 12:40, 23 March 2022
Line 3:		Line 3:
	<StructureSection load='2v7b' size='340' side='right'caption='[[2v7b]], [[Resolution\|resolution]] 1.84Å' scene=''>		<StructureSection load='2v7b' size='340' side='right'caption='[[2v7b]], [[Resolution\|resolution]] 1.84Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2v7b]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Burkholderia_cepacia_lb400 Burkholderia cepacia lb400]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V7B OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2V7B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2v7b]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Burkholderia_cepacia_lb400 Burkholderia cepacia lb400]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V7B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V7B FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Benzoate--CoA_ligase Benzoate--CoA ligase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.25 6.2.1.25] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Benzoate--CoA_ligase Benzoate--CoA ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.25 6.2.1.25] </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=2v7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v7b OCA], [~~http~~://pdbe.org/2v7b PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2v7b RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2v7b PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2v7b 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=2v7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v7b OCA], [https://pdbe.org/2v7b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2v7b RCSB], [https://www.ebi.ac.uk/pdbsum/2v7b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2v7b ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 11:22, 17 June 2020

2020-06-17T11:22:03Z

←Older revision		Revision as of 11:22, 17 June 2020
Line 1:		Line 1:

	==Crystal structures of a benzoate CoA ligase from Burkholderia xenovorans LB400==		==Crystal structures of a benzoate CoA ligase from Burkholderia xenovorans LB400==
-	<StructureSection load='2v7b' size='340' side='right' caption='[[2v7b]], [[Resolution\|resolution]] 1.84Å' scene=''>	+	<StructureSection load='2v7b' size='340' side='right'caption='[[2v7b]], [[Resolution\|resolution]] 1.84Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2v7b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_cepacia_lb400 Burkholderia cepacia lb400]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V7B OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2V7B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2v7b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_cepacia_lb400 Burkholderia cepacia lb400]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V7B OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2V7B FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Benzoate--CoA_ligase Benzoate--CoA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.25 6.2.1.25] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Benzoate--CoA_ligase Benzoate--CoA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.25 6.2.1.25] </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=2v7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v7b OCA], [http://pdbe.org/2v7b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2v7b RCSB], [http://www.ebi.ac.uk/pdbsum/2v7b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2v7b 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=2v7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v7b OCA], [http://pdbe.org/2v7b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2v7b RCSB], [http://www.ebi.ac.uk/pdbsum/2v7b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2v7b ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 33:		Line 33:
	[[Category: Benzoate--CoA ligase]]		[[Category: Benzoate--CoA ligase]]
	[[Category: Burkholderia cepacia lb400]]		[[Category: Burkholderia cepacia lb400]]
		+	[[Category: Large Structures]]
	[[Category: Bains, J]]		[[Category: Bains, J]]
	[[Category: Boulanger, M J]]		[[Category: Boulanger, M J]]

OCA at 08:38, 12 September 2018

2018-09-12T08:38:59Z

←Older revision		Revision as of 08:38, 12 September 2018
Line 1:		Line 1:
-	==~~CRYSTAL STRUCTURES OF A BENZOATE COA LIGASE FROM BURKHOLDERIA XENOVORANS~~ LB400==	+
		+	==Crystal structures of a benzoate CoA ligase from Burkholderia xenovorans LB400==
	<StructureSection load='2v7b' size='340' side='right' caption='[[2v7b]], [[Resolution\|resolution]] 1.84Å' scene=''>		<StructureSection load='2v7b' size='340' side='right' caption='[[2v7b]], [[Resolution\|resolution]] 1.84Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2v7b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Burxl Burxl~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V7B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2V7B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2v7b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_cepacia_lb400 Burkholderia cepacia lb400]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V7B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2V7B FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Benzoate--CoA_ligase Benzoate--CoA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.25 6.2.1.25] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Benzoate--CoA_ligase Benzoate--CoA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.25 6.2.1.25] </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=2v7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v7b OCA], [http://pdbe.org/2v7b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2v7b RCSB], [http://www.ebi.ac.uk/pdbsum/2v7b 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=2v7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v7b OCA], [http://pdbe.org/2v7b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2v7b RCSB], [http://www.ebi.ac.uk/pdbsum/2v7b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2v7b ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 11:		Line 12:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/v7/2v7b_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/v7/2v7b_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 31:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Benzoate--CoA ligase]]		[[Category: Benzoate--CoA ligase]]
-	[[Category: ~~Burxl~~]]	+	[[Category: Burkholderia cepacia lb400]]
	[[Category: Bains, J]]		[[Category: Bains, J]]
	[[Category: Boulanger, M J]]		[[Category: Boulanger, M J]]

OCA at 07:58, 8 February 2016

2016-02-08T07:58:47Z

←Older revision		Revision as of 07:58, 8 February 2016
Line 2:		Line 2:
	<StructureSection load='2v7b' size='340' side='right' caption='[[2v7b]], [[Resolution\|resolution]] 1.84Å' scene=''>		<StructureSection load='2v7b' size='340' side='right' caption='[[2v7b]], [[Resolution\|resolution]] 1.84Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2v7b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Burkholderia_xenovorans Burkholderia xenovorans~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V7B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2V7B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2v7b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Burxl Burxl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V7B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2V7B FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Benzoate--CoA_ligase Benzoate--CoA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.25 6.2.1.25] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Benzoate--CoA_ligase Benzoate--CoA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.25 6.2.1.25] </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=2v7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v7b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2v7b RCSB], [http://www.ebi.ac.uk/pdbsum/2v7b 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=2v7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v7b OCA], [http://pdbe.org/2v7b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2v7b RCSB], [http://www.ebi.ac.uk/pdbsum/2v7b PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 15:		Line 15:
	<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=2v7b ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 25:		Line 25:
	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 2v7b" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 30:		Line 31:
	</StructureSection>		</StructureSection>
	[[Category: Benzoate--CoA ligase]]		[[Category: Benzoate--CoA ligase]]
-	[[Category: ~~Burkholderia xenovorans~~]]	+	[[Category: Burxl]]
	[[Category: Bains, J]]		[[Category: Bains, J]]
	[[Category: Boulanger, M J]]		[[Category: Boulanger, M J]]

OCA at 18:06, 19 January 2015

2015-01-19T18:06:01Z

←Older revision		Revision as of 18:06, 19 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2v7b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_xenovorans Burkholderia xenovorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V7B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2V7B FirstGlance]. <br>		<table><tr><td colspan='2'>[[2v7b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_xenovorans Burkholderia xenovorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V7B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2V7B FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Benzoate--CoA_ligase Benzoate--CoA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.25 6.2.1.25] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Benzoate--CoA_ligase Benzoate--CoA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.25 6.2.1.25] </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=2v7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v7b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2v7b RCSB], [http://www.ebi.ac.uk/pdbsum/2v7b 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=2v7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v7b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2v7b RCSB], [http://www.ebi.ac.uk/pdbsum/2v7b PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 31:
	[[Category: Benzoate--CoA ligase]]		[[Category: Benzoate--CoA ligase]]
	[[Category: Burkholderia xenovorans]]		[[Category: Burkholderia xenovorans]]
-	[[Category: Bains, J.]]	+	[[Category: Bains, J]]
-	[[Category: Boulanger, M J.]]	+	[[Category: Boulanger, M J]]
	[[Category: Benzoate coa ligase]]		[[Category: Benzoate coa ligase]]
	[[Category: Benzoate oxidation]]		[[Category: Benzoate oxidation]]
	[[Category: Ligase]]		[[Category: Ligase]]

OCA at 02:06, 1 October 2014

2014-10-01T02:06:01Z

←Older revision		Revision as of 02:06, 1 October 2014
Line 1:		Line 1:
-	[[~~Image~~:2v7b.~~png\|left~~\|200px]]	+	==CRYSTAL STRUCTURES OF A BENZOATE COA LIGASE FROM BURKHOLDERIA XENOVORANS LB400==
		+	<StructureSection load='2v7b' size='340' side='right' caption='[[2v7b]], [[Resolution\|resolution]] 1.84Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2v7b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_xenovorans Burkholderia xenovorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V7B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2V7B FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene><br>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Benzoate--CoA_ligase Benzoate--CoA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.25 6.2.1.25] </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=2v7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v7b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2v7b RCSB], [http://www.ebi.ac.uk/pdbsum/2v7b 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/v7/2v7b_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 ==
		+	Xenobiotic aromatic compounds represent one of the most significant classes of environmental pollutants. A novel benzoate oxidation (box) pathway has been identified recently in Burkholderia xenovorans LB400 (referred to simply as LB400) that is capable of assimilating benzoate and intimately tied to the degradation of polychlorinated biphenyls (PCBs). The box pathway in LB400 is present in two paralogous copies (boxM and boxC) and encodes eight enzymes with the first committed step catalyzed by benzoate CoA ligase (BCL). As a first step towards delineating the biochemical role of the box pathway in LB400, we have carried out functional studies of the paralogous BCL enzymes (BCLM and BCLC) with 20 different putative substrates. We have established a structural rationale for the observed substrate specificities on the basis of a 1.84 A crystal structure of BCLM in complex with benzoate. These data show that, while BCLM and BCLC display similar overall substrate specificities, BCLM is significantly more active towards benzoate and 2-aminobenzoate with tighter binding (Km) and a faster reaction rate (Vmax). Despite these clear functional differences, the residues that define the substrate-binding site in BCLM are completely conserved in BCLC, suggesting that second shell residues may play a significant role in substrate recognition and catalysis. Furthermore, comparison of the active site of BCLM with the recently solved structures of 4-chlorobenzoate CoA ligase and 2, 3-dihydroxybenzoate CoA ligase offers additional insight into the molecular features that mediate substrate binding in adenylate-forming enzymes. This study provides the first biochemical characterization of a Box enzyme from LB400 and the first structural characterization of a Box enzyme from any organism, and further substantiates the concept of distinct roles for the two paralogous box pathways in LB400.

-	~~{{STRUCTURE_2v7b\| PDB=2v7b \| SCENE= }}~~	+	Biochemical and structural characterization of the paralogous benzoate CoA ligases from Burkholderia xenovorans LB400: defining the entry point into the novel benzoate oxidation (box) pathway.,Bains J, Boulanger MJ J Mol Biol. 2007 Nov 2;373(4):965-77. Epub 2007 Aug 19. PMID:17884091<ref>PMID:17884091</ref>

-	~~===CRYSTAL STRUCTURES OF A BENZOATE COA LIGASE FROM BURKHOLDERIA XENOVORANS LB400===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17884091}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2v7b]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Burkholderia_xenovorans Burkholderia xenovorans]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2V7B OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:017884091<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Benzoate--CoA ligase]]		[[Category: Benzoate--CoA ligase]]
	[[Category: Burkholderia xenovorans]]		[[Category: Burkholderia xenovorans]]

OCA: Protected "2v7b" [edit=sysop:move=sysop]

2013-01-07T23:02:39Z

Protected "2v7b" [edit=sysop:move=sysop]

←Older revision

Revision as of 23:02, 7 January 2013

OCA at 23:02, 7 January 2013

2013-01-07T23:02:36Z

←Older revision		Revision as of 23:02, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2v7b.png\|left\|200px]]		[[Image:2v7b.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2v7b", 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_2v7b\| PDB=2v7b \| SCENE= }}		{{STRUCTURE_2v7b\| PDB=2v7b \| SCENE= }}

	===CRYSTAL STRUCTURES OF A BENZOATE COA LIGASE FROM BURKHOLDERIA XENOVORANS LB400===		===CRYSTAL STRUCTURES OF A BENZOATE COA LIGASE FROM BURKHOLDERIA XENOVORANS LB400===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17884091}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17884091 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17884091}}		{{ABSTRACT_PUBMED_17884091}}

	==About this Structure==		==About this Structure==
-	~~2V7B~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Burkholderia_xenovorans Burkholderia xenovorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V7B OCA].	+	[[2v7b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_xenovorans Burkholderia xenovorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V7B OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17884091~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017884091</ref><references group="xtra"/>
	[[Category: Benzoate--CoA ligase]]		[[Category: Benzoate--CoA ligase]]
	[[Category: Burkholderia xenovorans]]		[[Category: Burkholderia xenovorans]]
Line 31:		Line 19:
	[[Category: Benzoate oxidation]]		[[Category: Benzoate oxidation]]
	[[Category: Ligase]]		[[Category: Ligase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 20:23:15 2009''

OCA at 18:23, 16 February 2009

2009-02-16T18:23:17Z

←Older revision		Revision as of 18:23, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2V7B is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Burkholderia_xenovorans Burkholderia xenovorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V7B OCA].	+	2V7B is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Burkholderia_xenovorans Burkholderia xenovorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V7B OCA].

	==Reference==		==Reference==
-	Biochemical and structural characterization of the paralogous benzoate CoA ligases from Burkholderia xenovorans LB400: defining the entry point into the novel benzoate oxidation (box) pathway., Bains J, Boulanger MJ, J Mol Biol. 2007 Nov 2;373(4):965-77. Epub 2007 Aug 19. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17884091 17884091]~~	+	<ref group="xtra">PMID:17884091</ref><references group="xtra"/>
	[[Category: Benzoate--CoA ligase]]		[[Category: Benzoate--CoA ligase]]
	[[Category: Burkholderia xenovorans]]		[[Category: Burkholderia xenovorans]]
-	[[Category: Single protein]]
	[[Category: Bains, J.]]		[[Category: Bains, J.]]
	[[Category: Boulanger, M J.]]		[[Category: Boulanger, M J.]]
Line 33:		Line 32:
	[[Category: Ligase]]		[[Category: Ligase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon ~~Jul 28 00~~:33:~~57 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 20:23:15 2009''