3don - Revision history

OCA at 08:24, 20 March 2024

2024-03-20T08:24:14Z

←Older revision		Revision as of 08:24, 20 March 2024
Line 3:		Line 3:
	<StructureSection load='3don' size='340' side='right'caption='[[3don]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3don' size='340' side='right'caption='[[3don]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3don]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Staeq Staeq~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DON OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DON FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3don]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_epidermidis_RP62A Staphylococcus epidermidis RP62A]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DON OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DON FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 2.1Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[3doo\|3doo]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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=~~176279 STAEQ])</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=3don FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3don OCA], [https://pdbe.org/3don PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3don RCSB], [https://www.ebi.ac.uk/pdbsum/3don PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3don 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=3don FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3don OCA], [https://pdbe.org/3don PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3don RCSB], [https://www.ebi.ac.uk/pdbsum/3don PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3don ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/AROE_STAEQ AROE_STAEQ]
	== 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=3don 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=3don ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Shikimate dehydrogenase (SDH) catalyzes the NADPH-dependent reduction of 3-dehydroshikimate to shikimate in the shikimate pathway. In this study, we determined the kinetic properties and crystal structures of Staphylococcus epidermidis SDH (SeSDH) both in its ligand-free form and in complex with shikimate. SeSDH has a k(cat) of 22.8 s(-1) and a K(m) of 73 mum towards shikimate, and a K(m) of 100 microM towards NADP. The overall folding of SeSDH comprises the N-terminal alpha/beta domain for substrate binding and the C-terminal Rossmann fold for NADP binding. The active site is within a large groove between the two domains. Residue Tyr211, normally regarded as important for substrate binding, does not interact with shikimate in the binary SeSDH-shikimate complex structure. However, the Y211F mutation leads to a significant decrease in k(cat) and a minor increase in the K(m) for shikimate. The results indicate that the main function of Tyr211 may be to stabilize the catalytic intermediate during catalysis. The NADP-binding domain of SeSDH is less conserved. The usually long helix specifically recognizing the adenine ribose phosphate is substituted with a short 3(10) helix in the NADP-binding domain. Moreover, the interdomain angle of SeSDH is the widest among all known SDH structures, indicating an inactive 'open' state of the SeSDH structure. Thus, a 'closing' process might occur upon NADP binding to bring the cofactor close to the substrate for catalysis.
-
-	X-ray crystallographic and enzymatic analyses of shikimate dehydrogenase from Staphylococcus epidermidis.,Han C, Hu T, Wu D, Qu S, Zhou J, Ding J, Shen X, Qu D, Jiang H FEBS J. 2009 Feb;276(4):1125-39. PMID:19215302<ref>PMID:19215302</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3don" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
-	*[[Shikimate dehydrogenase\|Shikimate dehydrogenase]]	+	*[[Shikimate dehydrogenase 3D structures\|Shikimate dehydrogenase 3D structures]]
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Shikimate dehydrogenase]]~~	+	[[Category: Staphylococcus epidermidis RP62A]]
-	~~[[Category: Staeq~~]]	+	[[Category: Han C]]
-	[[Category: Han, C]]	+	[[Category: Hu T]]
-	[[Category: Hu, T]]	+	[[Category: Jiang H]]
-	[[Category: Jiang, H]]	+	[[Category: Qu D]]
-	[[Category: Qu, D]]	+	[[Category: Shen X]]
-	[[Category: Shen, X]]	+	[[Category: Wu D]]
-	[[Category: Wu, D]]	+	[[Category: Zhou J]]
-	[[Category: Zhou, J]]	+
-	~~[[Category: Alpha-beta structure]]~~	+
-	~~[[Category: Amino-acid biosynthesis]]~~	+
-	~~[[Category: Aromatic amino acid biosynthesis]]~~	+
-	~~[[Category: Nadp]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Rossmann fold~~]]	+

OCA at 08:04, 9 February 2022

2022-02-09T08:04:15Z

←Older revision		Revision as of 08:04, 9 February 2022
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	==Crystal structure of shikimate dehydrogenase from Staphylococcus epidermidis==		==Crystal structure of shikimate dehydrogenase from Staphylococcus epidermidis==
-	<StructureSection load='3don' size='340' side='right' caption='[[3don]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='3don' size='340' side='right'caption='[[3don]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3don]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Staeq Staeq]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DON OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3DON FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3don]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staeq Staeq]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DON OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DON FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3doo\|3doo]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3doo\|3doo]]</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=176279 STAEQ])</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=176279 STAEQ])</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=3don FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3don OCA], [~~http~~://pdbe.org/3don PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3don RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3don PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3don 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=3don FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3don OCA], [https://pdbe.org/3don PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3don RCSB], [https://www.ebi.ac.uk/pdbsum/3don PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3don ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 36:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Shikimate dehydrogenase]]		[[Category: Shikimate dehydrogenase]]
	[[Category: Staeq]]		[[Category: Staeq]]

OCA at 09:22, 14 November 2018

2018-11-14T09:22:18Z

←Older revision		Revision as of 09:22, 14 November 2018
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/do/3don_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/do/3don_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 07:20, 11 August 2016

2016-08-11T07:20:12Z

←Older revision		Revision as of 07:20, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of shikimate dehydrogenase from Staphylococcus epidermidis==		==Crystal structure of shikimate dehydrogenase from Staphylococcus epidermidis==
	<StructureSection load='3don' size='340' side='right' caption='[[3don]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3don' size='340' side='right' caption='[[3don]], [[Resolution\|resolution]] 2.10Å' scene=''>
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	<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=176279 STAEQ])</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=176279 STAEQ])</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=3don FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3don OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3don RCSB], [http://www.ebi.ac.uk/pdbsum/3don 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=3don FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3don OCA], [http://pdbe.org/3don PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3don RCSB], [http://www.ebi.ac.uk/pdbsum/3don PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3don 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=3don 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:
	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 3don" style="background-color:#fffaf0;"></div>

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

OCA at 08:58, 25 January 2015

2015-01-25T08:58:45Z

←Older revision		Revision as of 08:58, 25 January 2015
Line 2:		Line 2:
	<StructureSection load='3don' size='340' side='right' caption='[[3don]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3don' size='340' side='right' caption='[[3don]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3don]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DON OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DON FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3don]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Staeq Staeq]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DON OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DON FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3doo\|3doo]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3doo\|3doo]]</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=176279 STAEQ])</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=3don FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3don OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3don RCSB], [http://www.ebi.ac.uk/pdbsum/3don 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=3don FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3don OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3don RCSB], [http://www.ebi.ac.uk/pdbsum/3don PDBsum]</span></td></tr>
Line 34:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Shikimate dehydrogenase]]		[[Category: Shikimate dehydrogenase]]
		+	[[Category: Staeq]]
	[[Category: Han, C]]		[[Category: Han, C]]
	[[Category: Hu, T]]		[[Category: Hu, T]]

OCA at 07:22, 12 November 2014

2014-11-12T07:22:41Z

←Older revision		Revision as of 07:22, 12 November 2014
Line 2:		Line 2:
	<StructureSection load='3don' size='340' side='right' caption='[[3don]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3don' size='340' side='right' caption='[[3don]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3don]] is a 1 chain structure ~~with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_epidermidis Staphylococcus epidermidis]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DON OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DON FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3don]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DON OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DON FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3doo\|3doo]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3doo\|3doo]]</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=1282 Staphylococcus epidermidis])</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=3don FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3don OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3don RCSB], [http://www.ebi.ac.uk/pdbsum/3don 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=3don FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3don OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3don RCSB], [http://www.ebi.ac.uk/pdbsum/3don PDBsum]</span></td></tr>
Line 35:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Shikimate dehydrogenase]]		[[Category: Shikimate dehydrogenase]]
-	~~[[Category: Staphylococcus epidermidis]]~~	+	[[Category: Han, C]]
-	[[Category: Han, C.]]	+	[[Category: Hu, T]]
-	[[Category: Hu, T.]]	+	[[Category: Jiang, H]]
-	[[Category: Jiang, H.]]	+	[[Category: Qu, D]]
-	[[Category: Qu, D.]]	+	[[Category: Shen, X]]
-	[[Category: Shen, X.]]	+	[[Category: Wu, D]]
-	[[Category: Wu, D.]]	+	[[Category: Zhou, J]]
-	[[Category: Zhou, J.]]	+
	[[Category: Alpha-beta structure]]		[[Category: Alpha-beta structure]]
	[[Category: Amino-acid biosynthesis]]		[[Category: Amino-acid biosynthesis]]

OCA at 14:05, 3 November 2014

2014-11-03T14:05:27Z

←Older revision		Revision as of 14:05, 3 November 2014
Line 1:		Line 1:
-	[[~~Image:~~3don.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of shikimate dehydrogenase from Staphylococcus epidermidis==
		+	<StructureSection load='3don' size='340' side='right' caption='[[3don]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3don]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_epidermidis Staphylococcus epidermidis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DON OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DON FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3doo\|3doo]]</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=1282 Staphylococcus epidermidis])</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=3don FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3don OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3don RCSB], [http://www.ebi.ac.uk/pdbsum/3don 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/do/3don_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 ==
		+	Shikimate dehydrogenase (SDH) catalyzes the NADPH-dependent reduction of 3-dehydroshikimate to shikimate in the shikimate pathway. In this study, we determined the kinetic properties and crystal structures of Staphylococcus epidermidis SDH (SeSDH) both in its ligand-free form and in complex with shikimate. SeSDH has a k(cat) of 22.8 s(-1) and a K(m) of 73 mum towards shikimate, and a K(m) of 100 microM towards NADP. The overall folding of SeSDH comprises the N-terminal alpha/beta domain for substrate binding and the C-terminal Rossmann fold for NADP binding. The active site is within a large groove between the two domains. Residue Tyr211, normally regarded as important for substrate binding, does not interact with shikimate in the binary SeSDH-shikimate complex structure. However, the Y211F mutation leads to a significant decrease in k(cat) and a minor increase in the K(m) for shikimate. The results indicate that the main function of Tyr211 may be to stabilize the catalytic intermediate during catalysis. The NADP-binding domain of SeSDH is less conserved. The usually long helix specifically recognizing the adenine ribose phosphate is substituted with a short 3(10) helix in the NADP-binding domain. Moreover, the interdomain angle of SeSDH is the widest among all known SDH structures, indicating an inactive 'open' state of the SeSDH structure. Thus, a 'closing' process might occur upon NADP binding to bring the cofactor close to the substrate for catalysis.

-	~~{{STRUCTURE_3don\| PDB=3don \| SCENE= }}~~	+	X-ray crystallographic and enzymatic analyses of shikimate dehydrogenase from Staphylococcus epidermidis.,Han C, Hu T, Wu D, Qu S, Zhou J, Ding J, Shen X, Qu D, Jiang H FEBS J. 2009 Feb;276(4):1125-39. PMID:19215302<ref>PMID:19215302</ref>

-	~~===Crystal structure~~ of ~~shikimate dehydrogenase from Staphylococcus epidermidis===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_19215302}}~~	+	==See Also==
-		+	*[[Shikimate dehydrogenase\|Shikimate dehydrogenase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~3don~~]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_epidermidis Staphylococcus epidermidis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DON OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:019215302<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Shikimate dehydrogenase]]		[[Category: Shikimate dehydrogenase]]
	[[Category: Staphylococcus epidermidis]]		[[Category: Staphylococcus epidermidis]]
Line 26:		Line 48:
	[[Category: Nadp]]		[[Category: Nadp]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
-	[[Category: ~~Rossman~~ fold]]	+	[[Category: Rossmann fold]]

OCA: Protected "3don" [edit=sysop:move=sysop]

2013-01-07T17:51:14Z

Protected "3don" [edit=sysop:move=sysop]

←Older revision

Revision as of 17:51, 7 January 2013

OCA at 17:51, 7 January 2013

2013-01-07T17:51:07Z

←Older revision		Revision as of 17:51, 7 January 2013
Line 1:		Line 1:
-	~~{{Seed}}~~	+	[[Image:3don.png\|left\|200px]]
-	[[Image:3don.~~jpg~~\|left\|200px]]	+

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3don", 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_3don\| PDB=3don \| SCENE= }}		{{STRUCTURE_3don\| PDB=3don \| SCENE= }}

	===Crystal structure of shikimate dehydrogenase from Staphylococcus epidermidis===		===Crystal structure of shikimate dehydrogenase from Staphylococcus epidermidis===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19215302}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19215302 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_19215302}}		{{ABSTRACT_PUBMED_19215302}}

	==About this Structure==		==About this Structure==
-	~~3DON~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Staphylococcus_epidermidis Staphylococcus epidermidis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DON OCA].	+	[[3don]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_epidermidis Staphylococcus epidermidis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DON OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19215302~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019215302</ref><references group="xtra"/>
	[[Category: Shikimate dehydrogenase]]		[[Category: Shikimate dehydrogenase]]
	[[Category: Staphylococcus epidermidis]]		[[Category: Staphylococcus epidermidis]]
Line 39:		Line 27:
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Rossman fold]]		[[Category: Rossman fold]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 6 10:03:38 2009''

OCA at 07:03, 6 May 2009

2009-05-06T07:03:39Z

←Older revision		Revision as of 07:03, 6 May 2009
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3don.jpg\|left\|200px]]

-	The ~~entry 3don~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3don", 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_3don\| PDB=3don \| SCENE= }}

-	~~Authors: Han, C., Hu, T., Wu, D., Qu, S., Zhou, J., Ding, J., Shen, X., Qu, D., Jiang, H.~~	+	===Crystal structure of shikimate dehydrogenase from Staphylococcus epidermidis===

-	Description: Crystal structure of shikimate dehydrogenase from Staphylococcus epidermidis

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Jul 23 12~~:15:~~54 2008~~''	+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_19215302}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 19215302 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_19215302}}
		+
		+	==About this Structure==
		+	3DON is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Staphylococcus_epidermidis Staphylococcus epidermidis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DON OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:19215302</ref><references group="xtra"/>
		+	[[Category: Shikimate dehydrogenase]]
		+	[[Category: Staphylococcus epidermidis]]
		+	[[Category: Han, C.]]
		+	[[Category: Hu, T.]]
		+	[[Category: Jiang, H.]]
		+	[[Category: Qu, D.]]
		+	[[Category: Shen, X.]]
		+	[[Category: Wu, D.]]
		+	[[Category: Zhou, J.]]
		+	[[Category: Alpha-beta structure]]
		+	[[Category: Amino-acid biosynthesis]]
		+	[[Category: Aromatic amino acid biosynthesis]]
		+	[[Category: Nadp]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Rossman fold]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 6 10:03:38 2009''