2a21 - Revision history

OCA at 09:10, 14 February 2024

2024-02-14T09:10:49Z

←Older revision		Revision as of 09:10, 14 February 2024
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	<StructureSection load='2a21' size='340' side='right'caption='[[2a21]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2a21' size='340' side='right'caption='[[2a21]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2a21]] 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=2A21 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2A21 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2a21]] 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=2A21 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2A21 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=PEP:PHOSPHOENOLPYRUVATE'>PEP</scene>~~, ~~<scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.8Å</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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PEP:PHOSPHOENOLPYRUVATE'>PEP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=2a21 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a21 OCA], [https://pdbe.org/2a21 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2a21 RCSB], [https://www.ebi.ac.uk/pdbsum/2a21 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2a21 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=2a21 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a21 OCA], [https://pdbe.org/2a21 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2a21 RCSB], [https://www.ebi.ac.uk/pdbsum/2a21 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2a21 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]]
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	</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=2a21 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=2a21 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Aquifex aeolicus 3-deoxy-d-manno-octulosonate 8-phosphate synthase (KDO8PS) is active with a variety of different divalent metal ions bound in the active site. The Cd(2+), Zn(2+), and Cu(2+) substituted enzymes display similar values of k(cat) and similar dependence of K(m)(PEP) and K(m)(A5P) on both substrate and product concentrations. However, the flux-control coefficients for some of the catalytically relevant reaction steps are different in the presence of Zn(2+) or Cu(2+), suggesting that the type of metal bound in the active site affects the behavior of the enzyme in vivo. The type of metal also affects the rate of product release in the crystal environment. For example, the crystal structure of the Cu(2+) enzyme incubated with phosphoenolpyruvate (PEP) and arabinose 5-phosphate (A5P) shows the formed product, 3-deoxy-d-manno-octulosonate 8-phosphate (KDO8P), still bound in the active site in its linear conformation. This observation completes our structural studies of the condensation reaction, which altogether have provided high-resolution structures for the reactants, the intermediate, and the product bound forms of KDO8PS. The crystal structures of the Cd(2+), Zn(2+), and Cu(2+) substituted enzymes show four residues (Cys-11, His-185, Glu-222, and Asp-233) and a water molecule as possible metal ligands. Combined quantum mechanics/molecular mechanics (QM/MM) geometry optimizations reveal that the metal centers have a delocalized electronic structure, and that their true geometry is square pyramidal for Cd(2+) and Zn(2+) and distorted octahedral or distorted tetrahedral for Cu(2+). These geometries are different from those obtained by QM optimization in the gas phase (tetrahedral for Cd(2+) and Zn(2+), distorted tetrahedral for Cu(2+)) and may represent conformations of the metal center that minimize the reorganization energy between the substrate-bound and product-bound states. The QM/MM calculations also show that when only PEP is bound to the enzyme the electronic structure of the metal center is optimized to prevent a wasteful reaction of PEP with water.
-
-	Electronic structure of the metal center in the Cd(2+), Zn(2+), and Cu(2+) substituted forms of KDO8P synthase: implications for catalysis.,Kona F, Tao P, Martin P, Xu X, Gatti DL Biochemistry. 2009 Apr 28;48(16):3610-30. PMID:19228070<ref>PMID:19228070</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2a21" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Kdo-8-phosphate synthase\|Kdo-8-phosphate synthase]]		*[[Kdo-8-phosphate synthase\|Kdo-8-phosphate synthase]]
-	== References ==
-	<references/>
	__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: Lu, J]]	+	[[Category: Lu J]]
-	[[Category: Martin, P]]	+	[[Category: Martin P]]
-	[[Category: Xu, X]]	+	[[Category: Xu X]]
-	~~[[Category: Transferase~~]]	+

OCA at 08:24, 27 January 2021

2021-01-27T08:24:17Z

←Older revision		Revision as of 08:24, 27 January 2021
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	==Aquifex aeolicus KDO8PS in complex with PEP, PO4, and Zn2+==		==Aquifex aeolicus KDO8PS in complex with PEP, PO4, and Zn2+==
-	<StructureSection load='2a21' size='340' side='right' caption='[[2a21]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='2a21' size='340' side='right'caption='[[2a21]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2a21]] 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=2A21 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2A21 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2a21]] 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=2A21 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2A21 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PEP:PHOSPHOENOLPYRUVATE'>PEP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PEP:PHOSPHOENOLPYRUVATE'>PEP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=2a21 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a21 OCA], [~~http~~://pdbe.org/2a21 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2a21 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2a21 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2a21 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=2a21 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a21 OCA], [https://pdbe.org/2a21 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2a21 RCSB], [https://www.ebi.ac.uk/pdbsum/2a21 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2a21 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/a2/2a21_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/a2/2a21_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 28:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 2a21" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2a21" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Kdo-8-phosphate synthase\|Kdo-8-phosphate synthase]]
	== References ==		== References ==
	<references/>		<references/>
Line 34:		Line 37:
	[[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 10:08, 12 October 2017

2017-10-12T10:08:43Z

←Older revision		Revision as of 10:08, 12 October 2017
Line 1:		Line 1:
		+
	==Aquifex aeolicus KDO8PS in complex with PEP, PO4, and Zn2+==		==Aquifex aeolicus KDO8PS in complex with PEP, PO4, and Zn2+==
	<StructureSection load='2a21' size='340' side='right' caption='[[2a21]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2a21' size='340' side='right' caption='[[2a21]], [[Resolution\|resolution]] 1.80Å' scene=''>
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	<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=2a21 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a21 OCA], [http://pdbe.org/2a21 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2a21 RCSB], [http://www.ebi.ac.uk/pdbsum/2a21 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=2a21 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a21 OCA], [http://pdbe.org/2a21 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2a21 RCSB], [http://www.ebi.ac.uk/pdbsum/2a21 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2a21 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 16:		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=2a21 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 27:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 2a21" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2a21" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Kdo-8-phosphate synthase\|Kdo-8-phosphate synthase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 17:16, 11 September 2015

2015-09-11T17:16:26Z

←Older revision		Revision as of 17:16, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2a21' size='340' side='right' caption='[[2a21]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2a21' size='340' side='right' caption='[[2a21]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2a21]] 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=2A21 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2A21 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2a21]] 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=2A21 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2A21 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PEP:PHOSPHOENOLPYRUVATE'>PEP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PEP:PHOSPHOENOLPYRUVATE'>PEP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=2a21 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a21 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2a21 RCSB], [http://www.ebi.ac.uk/pdbsum/2a21 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=2a21 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a21 OCA], [http://pdbe.org/2a21 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2a21 RCSB], [http://www.ebi.ac.uk/pdbsum/2a21 PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	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 2a21" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 33:		Line 34:
	__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 09:54, 8 January 2015

2015-01-08T09:54:05Z

←Older revision		Revision as of 09:54, 8 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2a21]] 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=2A21 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2A21 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2a21]] 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=2A21 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2A21 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PEP:PHOSPHOENOLPYRUVATE'>PEP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PEP:PHOSPHOENOLPYRUVATE'>PEP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=2a21 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a21 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2a21 RCSB], [http://www.ebi.ac.uk/pdbsum/2a21 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=2a21 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a21 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2a21 RCSB], [http://www.ebi.ac.uk/pdbsum/2a21 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 35:		Line 35:
	[[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: Lu, J.]]	+	[[Category: Lu, J]]
-	[[Category: Martin, P.]]	+	[[Category: Martin, P]]
-	[[Category: Xu, X.]]	+	[[Category: Xu, X]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 02:44, 29 September 2014

2014-09-29T02:44:40Z

←Older revision		Revision as of 02:44, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2a21.~~png~~\|~~left~~\|200px]]	+	==Aquifex aeolicus KDO8PS in complex with PEP, PO4, and Zn2+==
		+	<StructureSection load='2a21' size='340' side='right' caption='[[2a21]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2a21]] 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=2A21 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2A21 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PEP:PHOSPHOENOLPYRUVATE'>PEP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<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=2a21 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a21 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2a21 RCSB], [http://www.ebi.ac.uk/pdbsum/2a21 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/a2/2a21_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 ==
		+	Aquifex aeolicus 3-deoxy-d-manno-octulosonate 8-phosphate synthase (KDO8PS) is active with a variety of different divalent metal ions bound in the active site. The Cd(2+), Zn(2+), and Cu(2+) substituted enzymes display similar values of k(cat) and similar dependence of K(m)(PEP) and K(m)(A5P) on both substrate and product concentrations. However, the flux-control coefficients for some of the catalytically relevant reaction steps are different in the presence of Zn(2+) or Cu(2+), suggesting that the type of metal bound in the active site affects the behavior of the enzyme in vivo. The type of metal also affects the rate of product release in the crystal environment. For example, the crystal structure of the Cu(2+) enzyme incubated with phosphoenolpyruvate (PEP) and arabinose 5-phosphate (A5P) shows the formed product, 3-deoxy-d-manno-octulosonate 8-phosphate (KDO8P), still bound in the active site in its linear conformation. This observation completes our structural studies of the condensation reaction, which altogether have provided high-resolution structures for the reactants, the intermediate, and the product bound forms of KDO8PS. The crystal structures of the Cd(2+), Zn(2+), and Cu(2+) substituted enzymes show four residues (Cys-11, His-185, Glu-222, and Asp-233) and a water molecule as possible metal ligands. Combined quantum mechanics/molecular mechanics (QM/MM) geometry optimizations reveal that the metal centers have a delocalized electronic structure, and that their true geometry is square pyramidal for Cd(2+) and Zn(2+) and distorted octahedral or distorted tetrahedral for Cu(2+). These geometries are different from those obtained by QM optimization in the gas phase (tetrahedral for Cd(2+) and Zn(2+), distorted tetrahedral for Cu(2+)) and may represent conformations of the metal center that minimize the reorganization energy between the substrate-bound and product-bound states. The QM/MM calculations also show that when only PEP is bound to the enzyme the electronic structure of the metal center is optimized to prevent a wasteful reaction of PEP with water.

-	~~{{STRUCTURE_2a21\| PDB=2a21 \| SCENE= }}~~	+	Electronic structure of the metal center in the Cd(2+), Zn(2+), and Cu(2+) substituted forms of KDO8P synthase: implications for catalysis.,Kona F, Tao P, Martin P, Xu X, Gatti DL Biochemistry. 2009 Apr 28;48(16):3610-30. PMID:19228070<ref>PMID:19228070</ref>

-	~~===Aquifex aeolicus KDO8PS in complex with PEP~~, ~~PO4, and Zn2+===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19228070}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2a21]] 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=2A21 OCA].~~	+

	==See Also==		==See Also==
-	*[[~~Aldolase~~\|~~Aldolase~~]]	+	*[[Kdo-8-phosphate synthase\|Kdo-8-phosphate synthase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:019228070<~~/~~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 20:33, 20 October 2012

2012-10-20T20:33:38Z

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

	==About this Structure==		==About this Structure==
-	[[2a21]] 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=2A21 OCA].	+	[[2a21]] 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=2A21 OCA].

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

OCA: Protected "2a21" [edit=sysop:move=sysop]

2012-07-27T10:54:14Z

Protected "2a21" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:54, 27 July 2012

OCA at 10:54, 27 July 2012

2012-07-27T10:54:12Z

←Older revision		Revision as of 10:54, 27 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2a21.png\|left\|200px]]		[[Image:2a21.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2a21", 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_2a21\| PDB=2a21 \| SCENE= }}		{{STRUCTURE_2a21\| PDB=2a21 \| SCENE= }}

	===Aquifex aeolicus KDO8PS in complex with PEP, PO4, and Zn2+===		===Aquifex aeolicus KDO8PS in complex with PEP, PO4, and Zn2+===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19228070}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19228070 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_19228070}}		{{ABSTRACT_PUBMED_19228070}}

	==About this Structure==		==About this Structure==
-	~~2A21~~ 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=2A21 OCA].	+	[[2a21]] 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=2A21 OCA].
		+
		+	==See Also==
		+	*[[Aldolase\|Aldolase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19228070~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019228070</ref><references group="xtra"/>
	[[Category: 3-deoxy-8-phosphooctulonate synthase]]		[[Category: 3-deoxy-8-phosphooctulonate synthase]]
	[[Category: Aquifex aeolicus]]		[[Category: Aquifex aeolicus]]
Line 32:		Line 23:
	[[Category: Xu, X.]]		[[Category: Xu, X.]]
	[[Category: Transferase]]		[[Category: Transferase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 13 08:48:55 2009''

OCA at 05:48, 13 May 2009

2009-05-13T05:48:56Z

←Older revision		Revision as of 05:48, 13 May 2009
Line 12:		Line 12:
	===Aquifex aeolicus KDO8PS in complex with PEP, PO4, and Zn2+===		===Aquifex aeolicus KDO8PS in complex with PEP, PO4, and Zn2+===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_19228070}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 19228070 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_19228070}}

	==About this Structure==		==About this Structure==
	2A21 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=2A21 OCA].		2A21 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=2A21 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:19228070</ref><references group="xtra"/>
	[[Category: 3-deoxy-8-phosphooctulonate synthase]]		[[Category: 3-deoxy-8-phosphooctulonate synthase]]
	[[Category: Aquifex aeolicus]]		[[Category: Aquifex aeolicus]]
Line 24:		Line 33:
	[[Category: Transferase]]		[[Category: Transferase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Feb 18 04~~:32:36 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 13 08:48:55 2009''