2nxg - Revision history

OCA at 10:25, 30 August 2023

OCA — Wed, 30 Aug 2023 10:25:20 GMT

←Older revision		Revision as of 10:25, 30 August 2023
Line 3:		Line 3:
	<StructureSection load='2nxg' size='340' side='right'caption='[[2nxg]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='2nxg' size='340' side='right'caption='[[2nxg]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2nxg]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"aquifex_aeolicus"_huber_and_stetter_2001 "aquifex~~ aeolicus~~" huber and stetter 2001~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NXG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NXG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2nxg]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NXG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NXG FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1NT:(2R,4R,5R,6R,7R)-2,4,5,6,7-PENTAHYDROXY-2,8-BIS(PHOSPHONOOXY)OCTANOIC+ACID'>1NT</scene>, <scene name='pdbligand=A5P:ARABINOSE-5-PHOSPHATE'>A5P</scene>, <scene name='pdbligand=PEP:PHOSPHOENOLPYRUVATE'>PEP</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]] 1.95Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2nxh\|2nxh]], [[2nxi\|2nxi]], [[2nxk\|2nxk]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1NT:(2R,4R,5R,6R,7R)-2,4,5,6,7-PENTAHYDROXY-2,8-BIS(PHOSPHONOOXY)OCTANOIC+ACID'>1NT</scene>, <scene name='pdbligand=A5P:ARABINOSE-5-PHOSPHATE'>A5P</scene>, <scene name='pdbligand=PEP:PHOSPHOENOLPYRUVATE'>PEP</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">kdsA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 "Aquifex aeolicus" Huber and Stetter 2001])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/3-deoxy-8-phosphooctulonate_synthase 3-deoxy-8-phosphooctulonate synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.55 2.5.1.55] </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=2nxg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nxg OCA], [https://pdbe.org/2nxg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2nxg RCSB], [https://www.ebi.ac.uk/pdbsum/2nxg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2nxg 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=2nxg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nxg OCA], [https://pdbe.org/2nxg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2nxg RCSB], [https://www.ebi.ac.uk/pdbsum/2nxg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2nxg ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/KDSA_AQUAE KDSA_AQUAE]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Aquifex aeolicus ~~huber and stetter 2001]]~~	+	[[Category: Aquifex aeolicus]]
-	~~[[Category: 3-deoxy-8-phosphooctulonate synthase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Gatti~~, D L~~]]	+	[[Category: Gatti DL]]
-	[[Category: Kona, F]]	+	[[Category: Kona F]]
-	[[Category: Kuzmic, P]]	+	[[Category: Kuzmic P]]
-	[[Category: Martin, P]]	+	[[Category: Martin P]]
-	[[Category: Xu, X]]	+	[[Category: Xu X]]
-	~~[[Category: A5p]]~~	+
-	~~[[Category: Kdo]]~~	+
-	~~[[Category: Kdo8p]]~~	+
-	~~[[Category: Pep]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 15:53, 8 June 2021

OCA — Tue, 08 Jun 2021 15:53:28 GMT

←Older revision		Revision as of 15:53, 8 June 2021
Line 1:		Line 1:

	==Structural and mechanistic changes along an engineered path from metallo to non-metallo KDO8P synthase.==		==Structural and mechanistic changes along an engineered path from metallo to non-metallo KDO8P synthase.==
-	<StructureSection load='2nxg' size='340' side='right' caption='[[2nxg]], [[Resolution\|resolution]] 1.95Å' scene=''>	+	<StructureSection load='2nxg' size='340' side='right'caption='[[2nxg]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2nxg]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"aquifex_aeolicus"_huber_and_stetter_2001 "aquifex aeolicus" huber and stetter 2001]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NXG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2NXG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2nxg]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"aquifex_aeolicus"_huber_and_stetter_2001 "aquifex aeolicus" huber and stetter 2001]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NXG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NXG FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1NT:(2R,4R,5R,6R,7R)-2,4,5,6,7-PENTAHYDROXY-2,8-BIS(PHOSPHONOOXY)OCTANOIC+ACID'>1NT</scene>, <scene name='pdbligand=A5P:ARABINOSE-5-PHOSPHATE'>A5P</scene>, <scene name='pdbligand=PEP:PHOSPHOENOLPYRUVATE'>PEP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1NT:(2R,4R,5R,6R,7R)-2,4,5,6,7-PENTAHYDROXY-2,8-BIS(PHOSPHONOOXY)OCTANOIC+ACID'>1NT</scene>, <scene name='pdbligand=A5P:ARABINOSE-5-PHOSPHATE'>A5P</scene>, <scene name='pdbligand=PEP:PHOSPHOENOLPYRUVATE'>PEP</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2nxh\|2nxh]], [[2nxi\|2nxi]], [[2nxk\|2nxk]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2nxh\|2nxh]], [[2nxi\|2nxi]], [[2nxk\|2nxk]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">kdsA ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 "Aquifex aeolicus" Huber and Stetter 2001])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">kdsA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 "Aquifex aeolicus" Huber and Stetter 2001])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/3-deoxy-8-phosphooctulonate_synthase 3-deoxy-8-phosphooctulonate synthase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.55 2.5.1.55] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/3-deoxy-8-phosphooctulonate_synthase 3-deoxy-8-phosphooctulonate synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.55 2.5.1.55] </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=2nxg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nxg OCA], [~~http~~://pdbe.org/2nxg PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2nxg RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2nxg PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2nxg 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=2nxg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nxg OCA], [https://pdbe.org/2nxg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2nxg RCSB], [https://www.ebi.ac.uk/pdbsum/2nxg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2nxg ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 38:		Line 38:
	[[Category: Aquifex aeolicus huber and stetter 2001]]		[[Category: Aquifex aeolicus huber and stetter 2001]]
	[[Category: 3-deoxy-8-phosphooctulonate synthase]]		[[Category: 3-deoxy-8-phosphooctulonate synthase]]
		+	[[Category: Large Structures]]
	[[Category: Gatti, D L]]		[[Category: Gatti, D L]]
	[[Category: Kona, F]]		[[Category: Kona, F]]

OCA at 17:07, 15 August 2018

OCA — Wed, 15 Aug 2018 17:07:34 GMT

←Older revision		Revision as of 17:07, 15 August 2018
Line 1:		Line 1:
		+
	==Structural and mechanistic changes along an engineered path from metallo to non-metallo KDO8P synthase.==		==Structural and mechanistic changes along an engineered path from metallo to non-metallo KDO8P synthase.==
	<StructureSection load='2nxg' size='340' side='right' caption='[[2nxg]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='2nxg' size='340' side='right' caption='[[2nxg]], [[Resolution\|resolution]] 1.95Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">kdsA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 "Aquifex aeolicus" Huber and Stetter 2001])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">kdsA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 "Aquifex aeolicus" Huber and Stetter 2001])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-deoxy-8-phosphooctulonate_synthase 3-deoxy-8-phosphooctulonate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.55 2.5.1.55] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-deoxy-8-phosphooctulonate_synthase 3-deoxy-8-phosphooctulonate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.55 2.5.1.55] </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=2nxg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nxg OCA], [http://pdbe.org/2nxg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2nxg RCSB], [http://www.ebi.ac.uk/pdbsum/2nxg 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=2nxg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nxg OCA], [http://pdbe.org/2nxg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2nxg RCSB], [http://www.ebi.ac.uk/pdbsum/2nxg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2nxg ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nx/2nxg_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nx/2nxg_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 23:42, 9 February 2016

OCA — Tue, 09 Feb 2016 23:42:18 GMT

←Older revision		Revision as of 23:42, 9 February 2016
Line 17:		Line 17:
	<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=2nxg ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 03:13, 11 September 2015

OCA — Fri, 11 Sep 2015 03:13:37 GMT

←Older revision		Revision as of 03:13, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2nxg' size='340' side='right' caption='[[2nxg]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='2nxg' size='340' side='right' caption='[[2nxg]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2nxg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Aquifex_aeolicus Aquifex~~ aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NXG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2NXG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2nxg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"aquifex_aeolicus"_huber_and_stetter_2001 "aquifex aeolicus" huber and stetter 2001]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NXG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2NXG FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1NT:(2R,4R,5R,6R,7R)-2,4,5,6,7-PENTAHYDROXY-2,8-BIS(PHOSPHONOOXY)OCTANOIC+ACID'>1NT</scene>, <scene name='pdbligand=A5P:ARABINOSE-5-PHOSPHATE'>A5P</scene>, <scene name='pdbligand=PEP:PHOSPHOENOLPYRUVATE'>PEP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1NT:(2R,4R,5R,6R,7R)-2,4,5,6,7-PENTAHYDROXY-2,8-BIS(PHOSPHONOOXY)OCTANOIC+ACID'>1NT</scene>, <scene name='pdbligand=A5P:ARABINOSE-5-PHOSPHATE'>A5P</scene>, <scene name='pdbligand=PEP:PHOSPHOENOLPYRUVATE'>PEP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2nxh\|2nxh]], [[2nxi\|2nxi]], [[2nxk\|2nxk]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2nxh\|2nxh]], [[2nxi\|2nxi]], [[2nxk\|2nxk]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">kdsA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 Aquifex aeolicus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">kdsA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 "Aquifex aeolicus" Huber and Stetter 2001])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-deoxy-8-phosphooctulonate_synthase 3-deoxy-8-phosphooctulonate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.55 2.5.1.55] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-deoxy-8-phosphooctulonate_synthase 3-deoxy-8-phosphooctulonate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.55 2.5.1.55] </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=2nxg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nxg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2nxg RCSB], [http://www.ebi.ac.uk/pdbsum/2nxg 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=2nxg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nxg OCA], [http://pdbe.org/2nxg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2nxg RCSB], [http://www.ebi.ac.uk/pdbsum/2nxg PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 27:		Line 27:
	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 2nxg" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Aquifex aeolicus huber and stetter 2001]]
	[[Category: 3-deoxy-8-phosphooctulonate synthase]]		[[Category: 3-deoxy-8-phosphooctulonate synthase]]
-	[[Category: Aquifex aeolicus]]
	[[Category: Gatti, D L]]		[[Category: Gatti, D L]]
	[[Category: Kona, F]]		[[Category: Kona, F]]

OCA at 16:38, 19 January 2015

OCA — Mon, 19 Jan 2015 16:38:56 GMT

←Older revision		Revision as of 16:38, 19 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2nxg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NXG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2NXG FirstGlance]. <br>		<table><tr><td colspan='2'>[[2nxg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NXG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2NXG FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1NT:(2R,4R,5R,6R,7R)-2,4,5,6,7-PENTAHYDROXY-2,8-BIS(PHOSPHONOOXY)OCTANOIC+ACID'>1NT</scene>, <scene name='pdbligand=A5P:ARABINOSE-5-PHOSPHATE'>A5P</scene>, <scene name='pdbligand=PEP:PHOSPHOENOLPYRUVATE'>PEP</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1NT:(2R,4R,5R,6R,7R)-2,4,5,6,7-PENTAHYDROXY-2,8-BIS(PHOSPHONOOXY)OCTANOIC+ACID'>1NT</scene>, <scene name='pdbligand=A5P:ARABINOSE-5-PHOSPHATE'>A5P</scene>, <scene name='pdbligand=PEP:PHOSPHOENOLPYRUVATE'>PEP</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2nxh\|2nxh]], [[2nxi\|2nxi]], [[2nxk\|2nxk]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2nxh\|2nxh]], [[2nxi\|2nxi]], [[2nxk\|2nxk]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">kdsA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 Aquifex aeolicus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">kdsA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 Aquifex aeolicus])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-deoxy-8-phosphooctulonate_synthase 3-deoxy-8-phosphooctulonate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.55 2.5.1.55] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-deoxy-8-phosphooctulonate_synthase 3-deoxy-8-phosphooctulonate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.55 2.5.1.55] </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=2nxg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nxg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2nxg RCSB], [http://www.ebi.ac.uk/pdbsum/2nxg 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=2nxg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nxg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2nxg RCSB], [http://www.ebi.ac.uk/pdbsum/2nxg 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 36:		Line 36:
	[[Category: 3-deoxy-8-phosphooctulonate synthase]]		[[Category: 3-deoxy-8-phosphooctulonate synthase]]
	[[Category: Aquifex aeolicus]]		[[Category: Aquifex aeolicus]]
-	[[Category: Gatti, D L.]]	+	[[Category: Gatti, D L]]
-	[[Category: Kona, F.]]	+	[[Category: Kona, F]]
-	[[Category: Kuzmic, P.]]	+	[[Category: Kuzmic, P]]
-	[[Category: Martin, P.]]	+	[[Category: Martin, P]]
-	[[Category: Xu, X.]]	+	[[Category: Xu, X]]
	[[Category: A5p]]		[[Category: A5p]]
	[[Category: Kdo]]		[[Category: Kdo]]
-	[[Category: Kdo8p]]
	[[Category: Kdo8p]]		[[Category: Kdo8p]]
	[[Category: Pep]]		[[Category: Pep]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 05:41, 29 September 2014

OCA — Mon, 29 Sep 2014 05:41:28 GMT

←Older revision		Revision as of 05:41, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2nxg.~~png~~\|~~left~~\|200px]]	+	==Structural and mechanistic changes along an engineered path from metallo to non-metallo KDO8P synthase.==
		+	<StructureSection load='2nxg' size='340' side='right' caption='[[2nxg]], [[Resolution\|resolution]] 1.95Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2nxg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NXG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2NXG FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1NT:(2R,4R,5R,6R,7R)-2,4,5,6,7-PENTAHYDROXY-2,8-BIS(PHOSPHONOOXY)OCTANOIC+ACID'>1NT</scene>, <scene name='pdbligand=A5P:ARABINOSE-5-PHOSPHATE'>A5P</scene>, <scene name='pdbligand=PEP:PHOSPHOENOLPYRUVATE'>PEP</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2nxh\|2nxh]], [[2nxi\|2nxi]], [[2nxk\|2nxk]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">kdsA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 Aquifex aeolicus])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-deoxy-8-phosphooctulonate_synthase 3-deoxy-8-phosphooctulonate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.55 2.5.1.55] </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=2nxg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nxg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2nxg RCSB], [http://www.ebi.ac.uk/pdbsum/2nxg 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/nx/2nxg_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 ==
		+	There are two classes of KDO8P synthases characterized respectively by the presence or absence of a metal in the active site. The nonmetallo KDO8PS from Escherichia coli and the metallo KDO8PS from Aquifex aeolicus are the best characterized members of each class. All amino acid residues that make important contacts with the substrates are conserved in both enzymes with the exception of Pro-10, Cys-11, Ser-235, and Gln-237 of the A. aeolicus enzyme, which correspond respectively to Met-25, Asn-26, Pro-252, and Ala-254 in the E. coli enzyme. Interconversion between the two forms of KDO8P synthases can be achieved by substituting the metal-coordinating cysteine of metallo synthases with the corresponding asparagine of nonmetallo synthases, and vice versa. In this report we describe the structural changes elicited by the C11N mutation and by three combinations of mutations (P10M/C11N, C11N/S235P/Q237A, and P10M/C11N/S235P/Q237A) situated along possible evolutionary paths connecting the A. aeolicus and the E. coli enzyme. All four mutants are not capable of binding metal and lack the structural asymmetry among subunits with regard to substrate binding and conformation of the L7 loop, which is typical of A. aeolicus wild-type KDO8PS but is absent in the E. coli enzyme. Despite the lack of the active site metal, the mutant enzymes display levels of activity ranging from 46% to 24% of the wild type. With the sole exception of the quadruple mutant, metal loss does not affect the thermal stability of KDO8PS. The free energy of unfolding in water is also either unchanged or even increased in the mutant enzymes, suggesting that the primary role of the active site metal in A. aeolicus KDO8PS is not to increase the enzyme stability. In all four mutants A5P binding displaces a water molecule located on the si side of PEP. In particular, in the double and triple mutant, A5P binds with the aldehyde carbonyl in hydrogen bond distance of Asn-11, while in the wild type this functional group points away from Cys-11. This alternative conformation of A5P is likely to have functional significance as it resembles the conformation of the acyclic reaction intermediate, which is observed here for the first time in some of the active sites of the triple mutant. The direct visualization of this intermediate by X-ray crystallography confirms earlier mechanistic models of KDO8P synthesis. In particular, the configuration of the C2 chiral center of the intermediate supports a model of the reaction in nonmetallo KDO8PS, in which water attacks an oxocarbenium ion or PEP from the si side of C2. Several explanations are offered to reconcile this observation with the fact that no water molecule is observed at this position in the mutant enzymes in the presence of both PEP and A5P. Significant differences were observed between the wild-type and the mutant enzymes in the Km values for PEP and A5P and in the Kd values for inorganic phosphate and R5P. These differences may reflect an evolutionary adaptation of metallo and nonmetallo KDO8PS's to the cellular concentrations of these metabolites in their respective hosts.

-	~~{{STRUCTURE_2nxg\| PDB=2nxg \| SCENE= }}~~	+	Structural and mechanistic changes along an engineered path from metallo to nonmetallo 3-deoxy-D-manno-octulosonate 8-phosphate synthases.,Kona F, Xu X, Martin P, Kuzmic P, Gatti DL Biochemistry. 2007 Apr 17;46(15):4532-44. Epub 2007 Mar 24. PMID:17381075<ref>PMID:17381075</ref>

-	~~===Structural and mechanistic changes along an engineered path from metallo to non-metallo KDO8P synthase.===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17381075}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2nxg]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Aquifex_aeolicus Aquifex aeolicus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2NXG OCA].~~	+

	==See Also==		==See Also==
-	*[[~~Aldolase~~\|~~Aldolase~~]]	+	*[[Kdo-8-phosphate synthase\|Kdo-8-phosphate synthase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:017381075<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: 3-deoxy-8-phosphooctulonate synthase]]		[[Category: 3-deoxy-8-phosphooctulonate synthase]]
	[[Category: Aquifex aeolicus]]		[[Category: Aquifex aeolicus]]

OCA at 15:33, 20 October 2012

OCA — Sat, 20 Oct 2012 15:33:05 GMT

←Older revision		Revision as of 15:33, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2nxg]] is a 2 chain structure ~~of [[Aldolase]]~~ with sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NXG OCA].	+	[[2nxg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NXG OCA].

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

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

OCA — Thu, 26 Jul 2012 18:43:44 GMT

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

←Older revision

Revision as of 18:43, 26 July 2012

OCA at 18:43, 26 July 2012

OCA — Thu, 26 Jul 2012 18:43:42 GMT

←Older revision		Revision as of 18:43, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2nxg.png\|left\|200px]]		[[Image:2nxg.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2nxg", 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_2nxg\| PDB=2nxg \| SCENE= }}		{{STRUCTURE_2nxg\| PDB=2nxg \| SCENE= }}

	===Structural and mechanistic changes along an engineered path from metallo to non-metallo KDO8P synthase.===		===Structural and mechanistic changes along an engineered path from metallo to non-metallo KDO8P synthase.===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17381075}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17381075 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17381075}}		{{ABSTRACT_PUBMED_17381075}}

	==About this Structure==		==About this Structure==
-	~~2NXG~~ is a 2 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NXG OCA].	+	[[2nxg]] is a 2 chain structure of [[Aldolase]] with sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NXG OCA].
		+
		+	==See Also==
		+	*[[Aldolase\|Aldolase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17381075~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017381075</ref><references group="xtra"/>
	[[Category: 3-deoxy-8-phosphooctulonate synthase]]		[[Category: 3-deoxy-8-phosphooctulonate synthase]]
	[[Category: Aquifex aeolicus]]		[[Category: Aquifex aeolicus]]
Line 36:		Line 27:
	[[Category: Kdo8p]]		[[Category: Kdo8p]]
	[[Category: Pep]]		[[Category: Pep]]
-		+	[[Category: Transferase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 13:41:07 2009''~~	+