2hk9 - Revision history

OCA at 09:58, 30 August 2023

OCA — Wed, 30 Aug 2023 09:58:36 GMT

←Older revision		Revision as of 09:58, 30 August 2023
Line 3:		Line 3:
	<StructureSection load='2hk9' size='340' side='right'caption='[[2hk9]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='2hk9' size='340' side='right'caption='[[2hk9]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2hk9]] is a 4 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=2HK9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HK9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2hk9]] is a 4 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=2HK9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HK9 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATR:2-MONOPHOSPHOADENOSINE-5-DIPHOSPHATE'>ATR</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=SKM:(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC+ACID'>SKM</scene~~></td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.2Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2ev9\|2ev9]], [[1wxd\|1wxd]], [[2hk7\|2hk7]], [[2hk8\|2hk8]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATR:2-MONOPHOSPHOADENOSINE-5-DIPHOSPHATE'>ATR</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=SKM:(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC+ACID'>SKM</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aroE ([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/Shikimate_dehydrogenase Shikimate dehydrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.25 1.1.1.25] </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=2hk9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hk9 OCA], [https://pdbe.org/2hk9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hk9 RCSB], [https://www.ebi.ac.uk/pdbsum/2hk9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hk9 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=2hk9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hk9 OCA], [https://pdbe.org/2hk9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hk9 RCSB], [https://www.ebi.ac.uk/pdbsum/2hk9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hk9 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/AROE_AQUAE AROE_AQUAE]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	==See Also==		==See Also==
-	*[[Shikimate dehydrogenase\|Shikimate dehydrogenase]]	+	*[[Shikimate dehydrogenase 3D structures\|Shikimate dehydrogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Aquifex aeolicus ~~huber and stetter 2001~~]]	+	[[Category: Aquifex aeolicus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Shikimate dehydrogenase]]~~	+	[[Category: Andrykovitch M]]
-	[[Category: Andrykovitch, M]]	+	[[Category: Gan JH]]
-	[[Category: Gan~~, J H~~]]	+	[[Category: Gu YJ]]
-	[[Category: Gu~~, Y J~~]]	+	[[Category: Ji X]]
-	[[Category: Ji, X]]	+	[[Category: Li Y]]
-	[[Category: Li, Y]]	+	[[Category: Liu HH]]
-	[[Category: Liu~~, H H~~]]	+	[[Category: Prabakaran P]]
-	[[Category: Prabakaran, P]]	+	[[Category: Yan H]]
-	[[Category: Yan, H]]	+
-	~~[[Category: Drug design]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Shikimate pathway~~]]	+

OCA at 07:17, 24 March 2021

OCA — Wed, 24 Mar 2021 07:17:14 GMT

←Older revision		Revision as of 07:17, 24 March 2021
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	==Crystal structure of shikimate dehydrogenase from aquifex aeolicus in complex with shikimate and NADP+ at 2.2 angstrom resolution==		==Crystal structure of shikimate dehydrogenase from aquifex aeolicus in complex with shikimate and NADP+ at 2.2 angstrom resolution==
-	<StructureSection load='2hk9' size='340' side='right' caption='[[2hk9]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='2hk9' size='340' side='right'caption='[[2hk9]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2hk9]] is a 4 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=2HK9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2HK9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2hk9]] is a 4 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=2HK9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HK9 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATR:2-MONOPHOSPHOADENOSINE-5-DIPHOSPHATE'>ATR</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=SKM:(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC+ACID'>SKM</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATR:2-MONOPHOSPHOADENOSINE-5-DIPHOSPHATE'>ATR</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=SKM:(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC+ACID'>SKM</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ev9\|2ev9]], [[1wxd\|1wxd]], [[2hk7\|2hk7]], [[2hk8\|2hk8]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2ev9\|2ev9]], [[1wxd\|1wxd]], [[2hk7\|2hk7]], [[2hk8\|2hk8]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aroE ([~~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">aroE ([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/Shikimate_dehydrogenase Shikimate dehydrogenase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.25 1.1.1.25] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Shikimate_dehydrogenase Shikimate dehydrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.25 1.1.1.25] </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=2hk9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hk9 OCA], [~~http~~://pdbe.org/2hk9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2hk9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2hk9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2hk9 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=2hk9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hk9 OCA], [https://pdbe.org/2hk9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hk9 RCSB], [https://www.ebi.ac.uk/pdbsum/2hk9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hk9 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 14:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hk/2hk9_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hk/2hk9_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 29:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 2hk9" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2hk9" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Shikimate dehydrogenase\|Shikimate dehydrogenase]]
	== References ==		== References ==
	<references/>		<references/>
Line 34:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Aquifex aeolicus huber and stetter 2001]]		[[Category: Aquifex aeolicus huber and stetter 2001]]
		+	[[Category: Large Structures]]
	[[Category: Shikimate dehydrogenase]]		[[Category: Shikimate dehydrogenase]]
	[[Category: Andrykovitch, M]]		[[Category: Andrykovitch, M]]

OCA at 08:13, 18 October 2017

OCA — Wed, 18 Oct 2017 08:13:35 GMT

←Older revision		Revision as of 08:13, 18 October 2017
Line 1:		Line 1:
		+
	==Crystal structure of shikimate dehydrogenase from aquifex aeolicus in complex with shikimate and NADP+ at 2.2 angstrom resolution==		==Crystal structure of shikimate dehydrogenase from aquifex aeolicus in complex with shikimate and NADP+ at 2.2 angstrom resolution==
	<StructureSection load='2hk9' size='340' side='right' caption='[[2hk9]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='2hk9' size='340' side='right' caption='[[2hk9]], [[Resolution\|resolution]] 2.20Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aroE ([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">aroE ([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/Shikimate_dehydrogenase Shikimate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.25 1.1.1.25] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Shikimate_dehydrogenase Shikimate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.25 1.1.1.25] </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=2hk9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hk9 OCA], [http://pdbe.org/2hk9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2hk9 RCSB], [http://www.ebi.ac.uk/pdbsum/2hk9 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=2hk9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hk9 OCA], [http://pdbe.org/2hk9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2hk9 RCSB], [http://www.ebi.ac.uk/pdbsum/2hk9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2hk9 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 17:		Line 18:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2hk9 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 28:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 2hk9" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2hk9" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Shikimate dehydrogenase\|Shikimate dehydrogenase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 14:13, 11 September 2015

OCA — Fri, 11 Sep 2015 14:13:24 GMT

←Older revision		Revision as of 14:13, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2hk9' size='340' side='right' caption='[[2hk9]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='2hk9' size='340' side='right' caption='[[2hk9]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2hk9]] is a 4 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=2HK9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HK9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2hk9]] is a 4 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=2HK9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HK9 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATR:2-MONOPHOSPHOADENOSINE-5-DIPHOSPHATE'>ATR</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=SKM:(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC+ACID'>SKM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATR:2-MONOPHOSPHOADENOSINE-5-DIPHOSPHATE'>ATR</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=SKM:(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC+ACID'>SKM</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ev9\|2ev9]], [[1wxd\|1wxd]], [[2hk7\|2hk7]], [[2hk8\|2hk8]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ev9\|2ev9]], [[1wxd\|1wxd]], [[2hk7\|2hk7]], [[2hk8\|2hk8]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aroE ([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">aroE ([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/Shikimate_dehydrogenase Shikimate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.25 1.1.1.25] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Shikimate_dehydrogenase Shikimate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.25 1.1.1.25] </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=2hk9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hk9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2hk9 RCSB], [http://www.ebi.ac.uk/pdbsum/2hk9 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=2hk9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hk9 OCA], [http://pdbe.org/2hk9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2hk9 RCSB], [http://www.ebi.ac.uk/pdbsum/2hk9 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 2hk9" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Aquifex aeolicus]]	+	[[Category: Aquifex aeolicus huber and stetter 2001]]
	[[Category: Shikimate dehydrogenase]]		[[Category: Shikimate dehydrogenase]]
	[[Category: Andrykovitch, M]]		[[Category: Andrykovitch, M]]

OCA at 08:45, 16 January 2015

OCA — Fri, 16 Jan 2015 08:45:50 GMT

←Older revision		Revision as of 08:45, 16 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2hk9]] is a 4 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=2HK9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HK9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2hk9]] is a 4 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=2HK9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HK9 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATR:2-MONOPHOSPHOADENOSINE-5-DIPHOSPHATE'>ATR</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=SKM:(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC+ACID'>SKM</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATR:2-MONOPHOSPHOADENOSINE-5-DIPHOSPHATE'>ATR</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=SKM:(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC+ACID'>SKM</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ev9\|2ev9]], [[1wxd\|1wxd]], [[2hk7\|2hk7]], [[2hk8\|2hk8]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ev9\|2ev9]], [[1wxd\|1wxd]], [[2hk7\|2hk7]], [[2hk8\|2hk8]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aroE ([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">aroE ([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/Shikimate_dehydrogenase Shikimate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.25 1.1.1.25] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Shikimate_dehydrogenase Shikimate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.25 1.1.1.25] </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=2hk9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hk9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2hk9 RCSB], [http://www.ebi.ac.uk/pdbsum/2hk9 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=2hk9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hk9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2hk9 RCSB], [http://www.ebi.ac.uk/pdbsum/2hk9 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: Aquifex aeolicus]]		[[Category: Aquifex aeolicus]]
	[[Category: Shikimate dehydrogenase]]		[[Category: Shikimate dehydrogenase]]
-	[[Category: Andrykovitch, M.]]	+	[[Category: Andrykovitch, M]]
-	[[Category: Gan, J H.]]	+	[[Category: Gan, J H]]
-	[[Category: Gu, Y J.]]	+	[[Category: Gu, Y J]]
-	[[Category: Ji, X.]]	+	[[Category: Ji, X]]
-	[[Category: Li, Y.]]	+	[[Category: Li, Y]]
-	[[Category: Liu, H H.]]	+	[[Category: Liu, H H]]
-	[[Category: Prabakaran, P.]]	+	[[Category: Prabakaran, P]]
-	[[Category: Yan, H.]]	+	[[Category: Yan, H]]
	[[Category: Drug design]]		[[Category: Drug design]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
-	[[Category: Shikimate dehydrogenase]]
	[[Category: Shikimate pathway]]		[[Category: Shikimate pathway]]

OCA at 08:22, 30 September 2014

OCA — Tue, 30 Sep 2014 08:22:24 GMT

←Older revision		Revision as of 08:22, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2hk9.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of shikimate dehydrogenase from aquifex aeolicus in complex with shikimate and NADP+ at 2.2 angstrom resolution==
		+	<StructureSection load='2hk9' size='340' side='right' caption='[[2hk9]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2hk9]] is a 4 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=2HK9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HK9 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATR:2-MONOPHOSPHOADENOSINE-5-DIPHOSPHATE'>ATR</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=SKM:(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC+ACID'>SKM</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ev9\|2ev9]], [[1wxd\|1wxd]], [[2hk7\|2hk7]], [[2hk8\|2hk8]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aroE ([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/Shikimate_dehydrogenase Shikimate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.25 1.1.1.25] </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=2hk9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hk9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2hk9 RCSB], [http://www.ebi.ac.uk/pdbsum/2hk9 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/hk/2hk9_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The shikimate biosynthetic pathway is essential to microorganisms, plants, and parasites but absent from mammals. Therefore, shikimate dehydrogenase (SD) and other enzymes in the pathway are attractive targets for developing nontoxic antimicrobial agents, herbicides, and antiparasite drugs. SD catalyzes the fourth reaction in the pathway, the nicotinamide adenine dinucleotide phosphate- (NADP-) dependent reduction of 3-dehydroshikimic acid to shikimic acid (SA), as well as its reverse, by the transfer of a hydride. Previous structural studies reveal that the enzyme exists in two major conformations, an open and a closed form. For the reaction to occur, it is believed that the catalytic complex assumes the closed conformation. Nonetheless, the only structure containing both SA and NADP+ exhibits an open conformation (PDB entry 2EV9). Here, we present two crystal structures of Aquifex aeolicus SD, including a ternary complex with both SA and NADP+, which assumes the closed conformation and therefore contains a catalytically competent active site. On the basis of preexisting and novel structural and biochemical data, a catalytic mechanism is proposed.

-	~~{{STRUCTURE_2hk9\| PDB=2hk9 \| SCENE= }}~~	+	Structural and biochemical analyses of shikimate dehydrogenase AroE from Aquifex aeolicus: implications for the catalytic mechanism.,Gan J, Wu Y, Prabakaran P, Gu Y, Li Y, Andrykovitch M, Liu H, Gong Y, Yan H, Ji X Biochemistry. 2007 Aug 21;46(33):9513-22. Epub 2007 Jul 25. PMID:17649975<ref>PMID:17649975</ref>

-	~~===Crystal structure~~ of ~~shikimate dehydrogenase from aquifex aeolicus in complex with shikimate and NADP+ at 2~~.~~2 angstrom resolution===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_17649975}}~~	+	==See Also==
-		+	*[[Shikimate dehydrogenase\|Shikimate dehydrogenase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~2hk9~~]] is a 4 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=2HK9 OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:017649975<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Aquifex aeolicus]]		[[Category: Aquifex aeolicus]]
	[[Category: Shikimate dehydrogenase]]		[[Category: Shikimate dehydrogenase]]

OCA: Protected "2hk9" [edit=sysop:move=sysop]

OCA — Mon, 07 Jan 2013 13:24:08 GMT

Protected "2hk9" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:24, 7 January 2013

OCA at 13:24, 7 January 2013

OCA — Mon, 07 Jan 2013 13:24:06 GMT

←Older revision		Revision as of 13:24, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2hk9.png\|left\|200px]]		[[Image:2hk9.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2hk9", 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_2hk9\| PDB=2hk9 \| SCENE= }}		{{STRUCTURE_2hk9\| PDB=2hk9 \| SCENE= }}

	===Crystal structure of shikimate dehydrogenase from aquifex aeolicus in complex with shikimate and NADP+ at 2.2 angstrom resolution===		===Crystal structure of shikimate dehydrogenase from aquifex aeolicus in complex with shikimate and NADP+ at 2.2 angstrom resolution===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17649975}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17649975 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17649975}}		{{ABSTRACT_PUBMED_17649975}}

	==About this Structure==		==About this Structure==
-	~~2HK9~~ is a 4 ~~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=2HK9 OCA].	+	[[2hk9]] is a 4 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=2HK9 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17649975~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017649975</ref><references group="xtra"/>
	[[Category: Aquifex aeolicus]]		[[Category: Aquifex aeolicus]]
	[[Category: Shikimate dehydrogenase]]		[[Category: Shikimate dehydrogenase]]
Line 38:		Line 26:
	[[Category: Shikimate dehydrogenase]]		[[Category: Shikimate dehydrogenase]]
	[[Category: Shikimate pathway]]		[[Category: Shikimate pathway]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 00:19:34 2009''

OCA at 22:19, 17 February 2009

OCA — Tue, 17 Feb 2009 22:19:35 GMT

←Older revision		Revision as of 22:19, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2HK9 is a ~~[[Single protein]]~~ structure of ~~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=2HK9 OCA].	+	2HK9 is a 4 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=2HK9 OCA].

	==Reference==		==Reference==
-	Structural and biochemical analyses of shikimate dehydrogenase AroE from Aquifex aeolicus: implications for the catalytic mechanism., Gan J, Wu Y, Prabakaran P, Gu Y, Li Y, Andrykovitch M, Liu H, Gong Y, Yan H, Ji X, Biochemistry. 2007 Aug 21;46(33):9513-22. Epub 2007 Jul 25. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17649975 17649975]~~	+	<ref group="xtra">PMID:17649975</ref><references group="xtra"/>
	[[Category: Aquifex aeolicus]]		[[Category: Aquifex aeolicus]]
	[[Category: Shikimate dehydrogenase]]		[[Category: Shikimate dehydrogenase]]
-	[[Category: Single protein]]
	[[Category: Andrykovitch, M.]]		[[Category: Andrykovitch, M.]]
	[[Category: Gan, J H.]]		[[Category: Gan, J H.]]
Line 40:		Line 39:
	[[Category: Shikimate pathway]]		[[Category: Shikimate pathway]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Jul 29 07~~:40:~~43 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 00:19:34 2009''

OCA at 04:40, 29 July 2008

OCA — Tue, 29 Jul 2008 04:40:49 GMT

←Older revision		Revision as of 04:40, 29 July 2008
Line 1:		Line 1:
-	[[Image:2hk9.~~jpg~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:2hk9.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_2hk9\| PDB=2hk9 \| SCENE= }}		{{STRUCTURE_2hk9\| PDB=2hk9 \| SCENE= }}

-	~~'''~~Crystal structure of shikimate dehydrogenase from aquifex aeolicus in complex with shikimate and NADP+ at 2.2 angstrom resolution~~'''~~	+	===Crystal structure of shikimate dehydrogenase from aquifex aeolicus in complex with shikimate and NADP+ at 2.2 angstrom resolution===


-	~~==Overview==~~	+	<!--
-	The ~~shikimate biosynthetic pathway is essential to microorganisms~~, ~~plants~~, ~~and parasites but absent from mammals. Therefore, shikimate dehydrogenase (SD) and other enzymes in~~ the ~~pathway are attractive targets for developing nontoxic antimicrobial agents, herbicides, and antiparasite drugs. SD catalyzes~~ the ~~fourth reaction in the pathway, the nicotinamide adenine dinucleotide phosphate-~~ (~~NADP-) dependent reduction of 3-dehydroshikimic acid to shikimic acid (SA),~~ as ~~well as its reverse, by the transfer of a hydride~~. ~~Previous structural studies reveal that the enzyme exists in two major conformations, an open and a closed form~~. ~~For the reaction to occur~~, it is ~~believed that~~ the catalytic complex assumes the closed conformation. Nonetheless, the only structure containing both SA and NADP+ exhibits an open conformation (PDB entry 2EV9). Here, we present two crystal structures of Aquifex aeolicus SD, including a ternary complex with both SA and NADP+, which assumes the closed conformation and therefore contains a catalytically competent active site. On the basis of preexisting and novel structural and biochemical data, a catalytic mechanism is proposed.	+	The line below this paragraph, {{ABSTRACT_PUBMED_17649975}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 17649975 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_17649975}}

	==About this Structure==		==About this Structure==
Line 35:		Line 39:
	[[Category: Shikimate dehydrogenase]]		[[Category: Shikimate dehydrogenase]]
	[[Category: Shikimate pathway]]		[[Category: Shikimate pathway]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May 4 06~~:23:17 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 07:40:43 2008''