3dbn - Revision history

OCA at 08:23, 20 March 2024

OCA — Wed, 20 Mar 2024 08:23:45 GMT

←Older revision		Revision as of 08:23, 20 March 2024
Line 3:		Line 3:
	<StructureSection load='3dbn' size='340' side='right'caption='[[3dbn]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='3dbn' size='340' side='right'caption='[[3dbn]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3dbn]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Strsy Strsy~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DBN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DBN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3dbn]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_suis_05ZYH33 Streptococcus suis 05ZYH33]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DBN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DBN FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CS2:D~~-~~MANNONIC+ACID'>CS2</scene>~~, ~~<scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 2.9Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>uxuA, SSU05_1157 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~391295 STRSY])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CS2:D-MANNONIC+ACID'>CS2</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/Mannonate_dehydratase Mannonate dehydratase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.8 4.2.1.8]~~ </~~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=3dbn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dbn OCA], [https://pdbe.org/3dbn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dbn RCSB], [https://www.ebi.ac.uk/pdbsum/3dbn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dbn 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=3dbn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dbn OCA], [https://pdbe.org/3dbn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dbn RCSB], [https://www.ebi.ac.uk/pdbsum/3dbn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dbn ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/UXUA_STRSY UXUA_STRSY]] Catalyzes the dehydration of D-mannonate (By similarity).	+	[https://www.uniprot.org/uniprot/UXUA_STRSY UXUA_STRSY] Catalyzes the dehydration of D-mannonate (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 21:		Line 20:
	</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=3dbn 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=3dbn ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Mannonate dehydratase (ManD) is found only in certain bacterial species, where it participates in the dissimilation of glucuronate. ManD catalyzes the dehydration of d-mannonate to yield 2-keto-3-deoxygluconate (2-KDG), the carbon and energy source for growth. Selective inactivation of ManD by drug targeting is of therapeutic interest in the treatment of human Streptococcus suis infections. Here, we report the overexpression, purification, functional characterization, and crystallographic structure of ManD from S. suis. Importantly, by Fourier transform mass spectrometry, we show that 2-KDG is formed when the chemically synthesized substrate (d-mannonate) is incubated with ManD. Inductively coupled plasma-mass spectrometry revealed the presence of Mn(2+) in the purified protein, and in the solution state catalytically active ManD exists as a homodimer of two 41-kDa subunits. The crystal structures of S. suis ManD in native form and in complex with its substrate and Mn(2+) ion have been solved at a resolution of 2.9 A. The core structure of S. suis ManD is a TIM barrel similar to that of other members of the xylose isomerase-like superfamily. Structural analyses and comparative amino acid sequence alignments provide evidence for the importance of His311 and Tyr325 in ManD activity. The results of site-directed mutagenesis confirmed the functional role(s) of these residues in the dehydration reaction and a plausible mechanism for the ManD-catalyzed reaction is proposed.
-
-	Crystal structures of Streptococcus suis mannonate dehydratase (ManD) and its complex with substrate: genetic and biochemical evidence for a catalytic mechanism.,Zhang Q, Gao F, Peng H, Cheng H, Liu Y, Tang J, Thompson J, Wei G, Zhang J, Du Y, Yan J, Gao GF J Bacteriol. 2009 Sep;191(18):5832-7. Epub 2009 Jul 17. PMID:19617363<ref>PMID:19617363</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3dbn" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Mannonate dehydratase]]~~	+	[[Category: Streptococcus suis 05ZYH33]]
-	~~[[Category: Strsy~~]]	+	[[Category: Gao F]]
-	[[Category: Gao, F]]	+	[[Category: Gao GF]]
-	[[Category: Gao~~, G F~~]]	+	[[Category: Peng H]]
-	[[Category: Peng, H]]	+	[[Category: Zhang Q]]
-	[[Category: Zhang, Q]]	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Tim barrel~~]]	+

OCA at 07:59, 2 February 2022

OCA — Wed, 02 Feb 2022 07:59:38 GMT

←Older revision		Revision as of 07:59, 2 February 2022
Line 1:		Line 1:

	==Crystal structure of the Streptoccocus suis serotype2 D-mannonate dehydratase in complex with its substrate==		==Crystal structure of the Streptoccocus suis serotype2 D-mannonate dehydratase in complex with its substrate==
-	<StructureSection load='3dbn' size='340' side='right' caption='[[3dbn]], [[Resolution\|resolution]] 2.90Å' scene=''>	+	<StructureSection load='3dbn' size='340' side='right'caption='[[3dbn]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3dbn]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Strsy Strsy]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DBN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3DBN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3dbn]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Strsy Strsy]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DBN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DBN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CS2:D-MANNONIC+ACID'>CS2</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CS2:D-MANNONIC+ACID'>CS2</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">uxuA, SSU05_1157 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=391295 STRSY])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">uxuA, SSU05_1157 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=391295 STRSY])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Mannonate_dehydratase Mannonate dehydratase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.8 4.2.1.8] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Mannonate_dehydratase Mannonate dehydratase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.8 4.2.1.8] </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=3dbn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dbn OCA], [~~http~~://pdbe.org/3dbn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3dbn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3dbn PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3dbn 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=3dbn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dbn OCA], [https://pdbe.org/3dbn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dbn RCSB], [https://www.ebi.ac.uk/pdbsum/3dbn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dbn ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/UXUA_STRSY UXUA_STRSY]] Catalyzes the dehydration of D-mannonate (By similarity).	+	[[https://www.uniprot.org/uniprot/UXUA_STRSY UXUA_STRSY]] Catalyzes the dehydration of D-mannonate (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Mannonate dehydratase]]		[[Category: Mannonate dehydratase]]
	[[Category: Strsy]]		[[Category: Strsy]]

OCA at 09:36, 14 November 2018

OCA — Wed, 14 Nov 2018 09:36:16 GMT

←Older revision		Revision as of 09:36, 14 November 2018
Line 1:		Line 1:
		+
	==Crystal structure of the Streptoccocus suis serotype2 D-mannonate dehydratase in complex with its substrate==		==Crystal structure of the Streptoccocus suis serotype2 D-mannonate dehydratase in complex with its substrate==
	<StructureSection load='3dbn' size='340' side='right' caption='[[3dbn]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='3dbn' size='340' side='right' caption='[[3dbn]], [[Resolution\|resolution]] 2.90Å' scene=''>
Line 6:		Line 7:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">uxuA, SSU05_1157 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=391295 STRSY])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">uxuA, SSU05_1157 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=391295 STRSY])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Mannonate_dehydratase Mannonate dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.8 4.2.1.8] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Mannonate_dehydratase Mannonate dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.8 4.2.1.8] </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=3dbn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dbn OCA], [http://pdbe.org/3dbn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dbn RCSB], [http://www.ebi.ac.uk/pdbsum/3dbn 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=3dbn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dbn OCA], [http://pdbe.org/3dbn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dbn RCSB], [http://www.ebi.ac.uk/pdbsum/3dbn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3dbn ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/db/3dbn_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/db/3dbn_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 09:38, 9 February 2016

OCA — Tue, 09 Feb 2016 09:38:36 GMT

←Older revision		Revision as of 09:38, 9 February 2016
Line 2:		Line 2:
	<StructureSection load='3dbn' size='340' side='right' caption='[[3dbn]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='3dbn' size='340' side='right' caption='[[3dbn]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3dbn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Streptococcus_suis Streptococcus suis~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DBN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DBN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3dbn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Strsy Strsy]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DBN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DBN FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CS2:D-MANNONIC+ACID'>CS2</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CS2:D-MANNONIC+ACID'>CS2</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">uxuA, SSU05_1157 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~1307 Streptococcus suis~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">uxuA, SSU05_1157 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=391295 STRSY])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Mannonate_dehydratase Mannonate dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.8 4.2.1.8] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Mannonate_dehydratase Mannonate dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.8 4.2.1.8] </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=3dbn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dbn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dbn RCSB], [http://www.ebi.ac.uk/pdbsum/3dbn 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=3dbn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dbn OCA], [http://pdbe.org/3dbn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dbn RCSB], [http://www.ebi.ac.uk/pdbsum/3dbn PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		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=3dbn ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 28:		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 3dbn" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 33:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Mannonate dehydratase]]		[[Category: Mannonate dehydratase]]
-	[[Category: ~~Streptococcus suis~~]]	+	[[Category: Strsy]]
	[[Category: Gao, F]]		[[Category: Gao, F]]
	[[Category: Gao, G F]]		[[Category: Gao, G F]]

OCA at 10:26, 25 January 2015

OCA — Sun, 25 Jan 2015 10:26:45 GMT

←Older revision		Revision as of 10:26, 25 January 2015
Line 8:		Line 8:
	<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=3dbn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dbn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dbn RCSB], [http://www.ebi.ac.uk/pdbsum/3dbn 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=3dbn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dbn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dbn RCSB], [http://www.ebi.ac.uk/pdbsum/3dbn PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/UXUA_STRSY UXUA_STRSY]] Catalyzes the dehydration of D-mannonate (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 08:20, 12 November 2014

OCA — Wed, 12 Nov 2014 08:20:53 GMT

←Older revision		Revision as of 08:20, 12 November 2014
Line 1:		Line 1:
-	[[~~Image:~~3dbn.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of the Streptoccocus suis serotype2 D-mannonate dehydratase in complex with its substrate==
		+	<StructureSection load='3dbn' size='340' side='right' caption='[[3dbn]], [[Resolution\|resolution]] 2.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3dbn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptococcus_suis Streptococcus suis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DBN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DBN FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CS2:D-MANNONIC+ACID'>CS2</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">uxuA, SSU05_1157 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1307 Streptococcus suis])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Mannonate_dehydratase Mannonate dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.8 4.2.1.8] </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=3dbn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dbn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dbn RCSB], [http://www.ebi.ac.uk/pdbsum/3dbn 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/db/3dbn_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 ==
		+	Mannonate dehydratase (ManD) is found only in certain bacterial species, where it participates in the dissimilation of glucuronate. ManD catalyzes the dehydration of d-mannonate to yield 2-keto-3-deoxygluconate (2-KDG), the carbon and energy source for growth. Selective inactivation of ManD by drug targeting is of therapeutic interest in the treatment of human Streptococcus suis infections. Here, we report the overexpression, purification, functional characterization, and crystallographic structure of ManD from S. suis. Importantly, by Fourier transform mass spectrometry, we show that 2-KDG is formed when the chemically synthesized substrate (d-mannonate) is incubated with ManD. Inductively coupled plasma-mass spectrometry revealed the presence of Mn(2+) in the purified protein, and in the solution state catalytically active ManD exists as a homodimer of two 41-kDa subunits. The crystal structures of S. suis ManD in native form and in complex with its substrate and Mn(2+) ion have been solved at a resolution of 2.9 A. The core structure of S. suis ManD is a TIM barrel similar to that of other members of the xylose isomerase-like superfamily. Structural analyses and comparative amino acid sequence alignments provide evidence for the importance of His311 and Tyr325 in ManD activity. The results of site-directed mutagenesis confirmed the functional role(s) of these residues in the dehydration reaction and a plausible mechanism for the ManD-catalyzed reaction is proposed.

-	~~{{STRUCTURE_3dbn\| PDB=3dbn \| SCENE= }}~~	+	Crystal structures of Streptococcus suis mannonate dehydratase (ManD) and its complex with substrate: genetic and biochemical evidence for a catalytic mechanism.,Zhang Q, Gao F, Peng H, Cheng H, Liu Y, Tang J, Thompson J, Wei G, Zhang J, Du Y, Yan J, Gao GF J Bacteriol. 2009 Sep;191(18):5832-7. Epub 2009 Jul 17. PMID:19617363<ref>PMID:19617363</ref>

-	~~===Crystal structure~~ of the ~~Streptoccocus suis serotype2 D-mannonate dehydratase in complex with its substrate===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19617363}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[3dbn]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Streptococcus_suis Streptococcus suis]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3DBN OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:019617363<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Mannonate dehydratase]]		[[Category: Mannonate dehydratase]]
	[[Category: Streptococcus suis]]		[[Category: Streptococcus suis]]
-	[[Category: Gao, F.]]	+	[[Category: Gao, F]]
-	[[Category: Gao, G F.]]	+	[[Category: Gao, G F]]
-	[[Category: Peng, H.]]	+	[[Category: Peng, H]]
-	[[Category: Zhang, Q.]]	+	[[Category: Zhang, Q]]
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Tim barrel]]		[[Category: Tim barrel]]

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

OCA — Mon, 07 Jan 2013 22:09:24 GMT

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

←Older revision

Revision as of 22:09, 7 January 2013

OCA at 22:09, 7 January 2013

OCA — Mon, 07 Jan 2013 22:09:21 GMT

←Older revision		Revision as of 22:09, 7 January 2013
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-	{{Seed}}
	[[Image:3dbn.png\|left\|200px]]		[[Image:3dbn.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3dbn", creates the "Structure Box" on the page.
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	{{STRUCTURE_3dbn\| PDB=3dbn \| SCENE= }}		{{STRUCTURE_3dbn\| PDB=3dbn \| SCENE= }}

	===Crystal structure of the Streptoccocus suis serotype2 D-mannonate dehydratase in complex with its substrate===		===Crystal structure of the Streptoccocus suis serotype2 D-mannonate dehydratase in complex with its substrate===

		+	{{ABSTRACT_PUBMED_19617363}}

	==About this Structure==		==About this Structure==
-	~~3DBN~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Streptococcus_suis Streptococcus suis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DBN OCA].	+	[[3dbn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptococcus_suis Streptococcus suis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DBN OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:019617363</ref><references group="xtra"/>
	[[Category: Mannonate dehydratase]]		[[Category: Mannonate dehydratase]]
	[[Category: Streptococcus suis]]		[[Category: Streptococcus suis]]
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	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Tim barrel]]		[[Category: Tim barrel]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 9 20:19:38 2009''

OCA at 17:12, 9 September 2009

OCA — Wed, 09 Sep 2009 17:12:23 GMT

←Older revision		Revision as of 17:12, 9 September 2009
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	===Crystal structure of the Streptoccocus suis serotype2 D-mannonate dehydratase in complex with its substrate===		===Crystal structure of the Streptoccocus suis serotype2 D-mannonate dehydratase in complex with its substrate===

-
-	<!--
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-	(as it appears on PubMed at http://www.pubmed.gov), where 19617363 is the PubMed ID number.
-	-->
-	{{ABSTRACT_PUBMED_19617363}}

	==About this Structure==		==About this Structure==
	3DBN is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Streptococcus_suis Streptococcus suis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DBN OCA].		3DBN is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Streptococcus_suis Streptococcus suis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DBN OCA].
-
-	==Reference==
-	<ref group="xtra">PMID:19617363</ref><references group="xtra"/>
	[[Category: Mannonate dehydratase]]		[[Category: Mannonate dehydratase]]
	[[Category: Streptococcus suis]]		[[Category: Streptococcus suis]]
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	[[Category: Tim barrel]]		[[Category: Tim barrel]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu~~ Sep ~~3 16~~:01:34 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 9 20:19:38 2009''

OCA at 13:01, 3 September 2009

OCA — Thu, 03 Sep 2009 13:01:36 GMT

←Older revision		Revision as of 13:01, 3 September 2009
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	{{Seed}}		{{Seed}}
-	[[Image:3dbn.~~jpg~~\|left\|200px]]	+	[[Image:3dbn.png\|left\|200px]]

	<!--		<!--
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	===Crystal structure of the Streptoccocus suis serotype2 D-mannonate dehydratase in complex with its substrate===		===Crystal structure of the Streptoccocus suis serotype2 D-mannonate dehydratase in complex with its substrate===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_19617363}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 19617363 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_19617363}}

	==About this Structure==		==About this Structure==
	3DBN is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Streptococcus_suis Streptococcus suis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DBN OCA].		3DBN is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Streptococcus_suis Streptococcus suis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DBN OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:19617363</ref><references group="xtra"/>
	[[Category: Mannonate dehydratase]]		[[Category: Mannonate dehydratase]]
	[[Category: Streptococcus suis]]		[[Category: Streptococcus suis]]
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	[[Category: Tim barrel]]		[[Category: Tim barrel]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu ~~Jun 25 11:~~16:56 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Sep 3 16:01:34 2009''