2dw6 - Revision history

OCA at 08:31, 25 October 2023

OCA — Wed, 25 Oct 2023 08:31:09 GMT

←Older revision		Revision as of 08:31, 25 October 2023
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	<StructureSection load='2dw6' size='340' side='right'caption='[[2dw6]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='2dw6' size='340' side='right'caption='[[2dw6]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2dw6]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"rhizobacterium_japonicum"_kirchner_1896 "rhizobacterium~~ japonicum~~" kirchner 1896~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DW6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DW6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2dw6]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bradyrhizobium_japonicum Bradyrhizobium japonicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DW6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DW6 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TAR:D(~~-~~)-TARTARIC+ACID'>TAR</scene>~~, ~~<scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</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]] 2.3Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[1tzz\|1tzz]], [[2dw7\|2dw7]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TAR:D(-)-TARTARIC+ACID'>TAR</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[https~~:~~//en.wikipedia.org/wiki/D~~(-)-~~tartrate_dehydratase D(-)-tartrate dehydratase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.81 4.2.1.81]~~ </~~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=2dw6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dw6 OCA], [https://pdbe.org/2dw6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dw6 RCSB], [https://www.ebi.ac.uk/pdbsum/2dw6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dw6 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=2dw6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dw6 OCA], [https://pdbe.org/2dw6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dw6 RCSB], [https://www.ebi.ac.uk/pdbsum/2dw6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dw6 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/TARD_BRADU TARD_BRADU]] Catalyzes the dehydration of D-tartrate to oxaloacetate.<ref>PMID:17144653</ref>	+	[https://www.uniprot.org/uniprot/TARD_BRADU TARD_BRADU] Catalyzes the dehydration of D-tartrate to oxaloacetate.<ref>PMID:17144653</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Rhizobacterium~~ japonicum ~~kirchner 1896~~]]	+	[[Category: Bradyrhizobium japonicum]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Almo~~, S C~~]]	+	[[Category: Almo SC]]
-	[[Category: Fedorov~~, A A~~]]	+	[[Category: Fedorov AA]]
-	[[Category: Fedorov~~, E V~~]]	+	[[Category: Fedorov EV]]
-	[[Category: Gerlt~~, J A~~]]	+	[[Category: Gerlt JA]]
-	[[Category: Wood~~, B M~~]]	+	[[Category: Wood BM]]
-	[[Category: Yew~~, W S]]~~	+	[[Category: Yew WS]]
-	~~[[Category: D-tartrate]]~~	+
-	~~[[Category: D-tartrate dehydratase]]~~	+
-	~~[[Category: Enolase superfamily]]~~	+
-	~~[[Category: L-tartrate]]~~	+
-	~~[[Category: Lyase~~]]	+

OCA at 06:51, 10 November 2021

OCA — Wed, 10 Nov 2021 06:51:41 GMT

←Older revision		Revision as of 06:51, 10 November 2021
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	<StructureSection load='2dw6' size='340' side='right'caption='[[2dw6]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='2dw6' size='340' side='right'caption='[[2dw6]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2dw6]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"rhizobacterium_japonicum"_kirchner_1896 "rhizobacterium japonicum" kirchner 1896]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DW6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2DW6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2dw6]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"rhizobacterium_japonicum"_kirchner_1896 "rhizobacterium japonicum" kirchner 1896]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DW6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DW6 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TAR:D(-)-TARTARIC+ACID'>TAR</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TAR:D(-)-TARTARIC+ACID'>TAR</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tzz\|1tzz]], [[2dw7\|2dw7]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1tzz\|1tzz]], [[2dw7\|2dw7]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/D(-)-tartrate_dehydratase D(-)-tartrate dehydratase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.81 4.2.1.81] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/D(-)-tartrate_dehydratase D(-)-tartrate dehydratase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.81 4.2.1.81] </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=2dw6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dw6 OCA], [~~http~~://pdbe.org/2dw6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2dw6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2dw6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2dw6 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=2dw6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dw6 OCA], [https://pdbe.org/2dw6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dw6 RCSB], [https://www.ebi.ac.uk/pdbsum/2dw6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dw6 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/TARD_BRADU TARD_BRADU]] Catalyzes the dehydration of D-tartrate to oxaloacetate.<ref>PMID:17144653</ref>	+	[[https://www.uniprot.org/uniprot/TARD_BRADU TARD_BRADU]] Catalyzes the dehydration of D-tartrate to oxaloacetate.<ref>PMID:17144653</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 08:22, 11 March 2020

OCA — Wed, 11 Mar 2020 08:22:21 GMT

←Older revision		Revision as of 08:22, 11 March 2020
Line 1:		Line 1:

	==Crystal structure of the mutant K184A of D-Tartrate Dehydratase from Bradyrhizobium japonicum complexed with Mg++ and D-tartrate==		==Crystal structure of the mutant K184A of D-Tartrate Dehydratase from Bradyrhizobium japonicum complexed with Mg++ and D-tartrate==
-	<StructureSection load='2dw6' size='340' side='right' caption='[[2dw6]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='2dw6' size='340' side='right'caption='[[2dw6]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dw6]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"rhizobacterium_japonicum"_kirchner_1896 "rhizobacterium japonicum" kirchner 1896]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DW6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DW6 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dw6]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"rhizobacterium_japonicum"_kirchner_1896 "rhizobacterium japonicum" kirchner 1896]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DW6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DW6 FirstGlance]. <br>
Line 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Rhizobacterium japonicum kirchner 1896]]		[[Category: Rhizobacterium japonicum kirchner 1896]]
		+	[[Category: Large Structures]]
	[[Category: Almo, S C]]		[[Category: Almo, S C]]
	[[Category: Fedorov, A A]]		[[Category: Fedorov, A A]]

OCA at 06:51, 6 June 2018

OCA — Wed, 06 Jun 2018 06:51:51 GMT

←Older revision		Revision as of 06:51, 6 June 2018
Line 1:		Line 1:
		+
	==Crystal structure of the mutant K184A of D-Tartrate Dehydratase from Bradyrhizobium japonicum complexed with Mg++ and D-tartrate==		==Crystal structure of the mutant K184A of D-Tartrate Dehydratase from Bradyrhizobium japonicum complexed with Mg++ and D-tartrate==
	<StructureSection load='2dw6' size='340' side='right' caption='[[2dw6]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='2dw6' size='340' side='right' caption='[[2dw6]], [[Resolution\|resolution]] 2.30Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tzz\|1tzz]], [[2dw7\|2dw7]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tzz\|1tzz]], [[2dw7\|2dw7]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D(-)-tartrate_dehydratase D(-)-tartrate dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.81 4.2.1.81] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D(-)-tartrate_dehydratase D(-)-tartrate dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.81 4.2.1.81] </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=2dw6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dw6 OCA], [http://pdbe.org/2dw6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dw6 RCSB], [http://www.ebi.ac.uk/pdbsum/2dw6 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=2dw6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dw6 OCA], [http://pdbe.org/2dw6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dw6 RCSB], [http://www.ebi.ac.uk/pdbsum/2dw6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2dw6 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/dw/2dw6_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dw/2dw6_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 11:28, 8 February 2016

OCA — Mon, 08 Feb 2016 11:28:42 GMT

←Older revision		Revision as of 11:28, 8 February 2016
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=2dw6 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 11:06, 10 September 2015

OCA — Thu, 10 Sep 2015 11:06:38 GMT

←Older revision		Revision as of 11:06, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2dw6' size='340' side='right' caption='[[2dw6]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='2dw6' size='340' side='right' caption='[[2dw6]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2dw6]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bradyrhizobium_japonicum Bradyrhizobium~~ japonicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DW6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DW6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2dw6]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"rhizobacterium_japonicum"_kirchner_1896 "rhizobacterium japonicum" kirchner 1896]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DW6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DW6 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TAR:D(-)-TARTARIC+ACID'>TAR</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TAR:D(-)-TARTARIC+ACID'>TAR</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tzz\|1tzz]], [[2dw7\|2dw7]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tzz\|1tzz]], [[2dw7\|2dw7]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D(-)-tartrate_dehydratase D(-)-tartrate dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.81 4.2.1.81] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D(-)-tartrate_dehydratase D(-)-tartrate dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.81 4.2.1.81] </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=2dw6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dw6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dw6 RCSB], [http://www.ebi.ac.uk/pdbsum/2dw6 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=2dw6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dw6 OCA], [http://pdbe.org/2dw6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dw6 RCSB], [http://www.ebi.ac.uk/pdbsum/2dw6 PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/TARD_BRADU TARD_BRADU]] Catalyzes the dehydration of D-tartrate to oxaloacetate.<ref>PMID:17144653</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 26:		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 2dw6" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bradyrhizobium~~ japonicum]]	+	[[Category: Rhizobacterium japonicum kirchner 1896]]
	[[Category: Almo, S C]]		[[Category: Almo, S C]]
	[[Category: Fedorov, A A]]		[[Category: Fedorov, A A]]

OCA at 18:02, 15 January 2015

OCA — Thu, 15 Jan 2015 18:02:21 GMT

←Older revision		Revision as of 18:02, 15 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dw6]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bradyrhizobium_japonicum Bradyrhizobium japonicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DW6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DW6 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dw6]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bradyrhizobium_japonicum Bradyrhizobium japonicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DW6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DW6 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TAR:D(-)-TARTARIC+ACID'>TAR</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TAR:D(-)-TARTARIC+ACID'>TAR</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tzz\|1tzz]], [[2dw7\|2dw7]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tzz\|1tzz]], [[2dw7\|2dw7]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D(-)-tartrate_dehydratase D(-)-tartrate dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.81 4.2.1.81] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D(-)-tartrate_dehydratase D(-)-tartrate dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.81 4.2.1.81] </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=2dw6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dw6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dw6 RCSB], [http://www.ebi.ac.uk/pdbsum/2dw6 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=2dw6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dw6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dw6 RCSB], [http://www.ebi.ac.uk/pdbsum/2dw6 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 31:		Line 31:
	</StructureSection>		</StructureSection>
	[[Category: Bradyrhizobium japonicum]]		[[Category: Bradyrhizobium japonicum]]
-	[[Category: Almo, S C.]]	+	[[Category: Almo, S C]]
-	[[Category: Fedorov, A A.]]	+	[[Category: Fedorov, A A]]
-	[[Category: Fedorov, E V.]]	+	[[Category: Fedorov, E V]]
-	[[Category: Gerlt, J A.]]	+	[[Category: Gerlt, J A]]
-	[[Category: Wood, B M.]]	+	[[Category: Wood, B M]]
-	[[Category: Yew, W S.]]	+	[[Category: Yew, W S]]
	[[Category: D-tartrate]]		[[Category: D-tartrate]]
	[[Category: D-tartrate dehydratase]]		[[Category: D-tartrate dehydratase]]

OCA at 01:03, 30 September 2014

OCA — Tue, 30 Sep 2014 01:03:36 GMT

←Older revision		Revision as of 01:03, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2dw6.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of the mutant K184A of D-Tartrate Dehydratase from Bradyrhizobium japonicum complexed with Mg++ and D-tartrate==
		+	<StructureSection load='2dw6' size='340' side='right' caption='[[2dw6]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2dw6]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bradyrhizobium_japonicum Bradyrhizobium japonicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DW6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DW6 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TAR:D(-)-TARTARIC+ACID'>TAR</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tzz\|1tzz]], [[2dw7\|2dw7]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D(-)-tartrate_dehydratase D(-)-tartrate dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.81 4.2.1.81] </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=2dw6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dw6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dw6 RCSB], [http://www.ebi.ac.uk/pdbsum/2dw6 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/dw/2dw6_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 ==
		+	We focus on the assignment of function to and elucidation of structure-function relationships for a member of the mechanistically diverse enolase superfamily encoded by the Bradyrhizobium japonicum genome (bll6730; GI:27381841). As suggested by sequence alignments, the active site contains the same functional groups found in the active site of mandelate racemase (MR) that catalyzes a 1,1-proton transfer reaction: two acid/base catalysts, Lys 184 at the end of the second beta-strand, and a His 322-Asp 292 dyad at the ends of the seventh and sixth beta-strands, respectively, as well as ligands for an essential Mg2+, Asp 213, Glu 239, and Glu 265 at the ends of the third, fourth, and fifth beta-strands, respectively. We screened a library of 46 acid sugars and discovered that only d-tartrate is dehydrated, yielding oxaloacetate as product. The kinetic constants (kcat = 7.3 s(-1); kcat/KM = 8.5 x 10(4) M(-1) s(-1)) are consistent with assignment of the d-tartrate dehydratase (TarD) function. The kinetic phenotypes of mutants as well as the structures of liganded complexes are consistent with a mechanism in which Lys 184 initiates the reaction by abstraction of the alpha-proton to generate a Mg2+-stabilized enediolate intermediate, and the vinylogous beta-elimination of the 3-OH group is general acid-catalyzed by the His 322, accomplishing the anti-elimination of water. The replacement of the leaving group by solvent-derived hydrogen is stereorandom, suggesting that the enol tautomer of oxaloacetate is the product; this expectation was confirmed by its observation by 1H NMR spectroscopy. Thus, the TarD-catalyzed reaction is a "simple" extension of the two-step reaction catalyzed by MR: base-catalyzed proton abstraction to generate a Mg2+-stabilized enediolate intermediate followed by acid-catalyzed decomposition of that intermediate to yield the product.

-	~~{{STRUCTURE_2dw6\| PDB=2dw6 \| SCENE= }}~~	+	Evolution of enzymatic activities in the enolase superfamily: D-tartrate dehydratase from Bradyrhizobium japonicum.,Yew WS, Fedorov AA, Fedorov EV, Wood BM, Almo SC, Gerlt JA Biochemistry. 2006 Dec 12;45(49):14598-608. PMID:17144653<ref>PMID:17144653</ref>

-	~~===Crystal structure~~ of the ~~mutant K184A of D-Tartrate Dehydratase from Bradyrhizobium japonicum complexed with Mg++ and D-tartrate===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17144653}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2dw6]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Bradyrhizobium_japonicum Bradyrhizobium japonicum]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2DW6 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:017144653<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Bradyrhizobium japonicum]]		[[Category: Bradyrhizobium japonicum]]
	[[Category: Almo, S C.]]		[[Category: Almo, S C.]]

OCA: Protected "2dw6" [edit=sysop:move=sysop]

OCA — Sun, 06 Jan 2013 10:20:23 GMT

Protected "2dw6" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:20, 6 January 2013

OCA at 10:20, 6 January 2013

OCA — Sun, 06 Jan 2013 10:20:19 GMT

←Older revision		Revision as of 10:20, 6 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2dw6.png\|left\|200px]]		[[Image:2dw6.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2dw6", 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.
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	{{STRUCTURE_2dw6\| PDB=2dw6 \| SCENE= }}		{{STRUCTURE_2dw6\| PDB=2dw6 \| SCENE= }}

	===Crystal structure of the mutant K184A of D-Tartrate Dehydratase from Bradyrhizobium japonicum complexed with Mg++ and D-tartrate===		===Crystal structure of the mutant K184A of D-Tartrate Dehydratase from Bradyrhizobium japonicum complexed with Mg++ and D-tartrate===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17144653}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17144653 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17144653}}		{{ABSTRACT_PUBMED_17144653}}

	==About this Structure==		==About this Structure==
-	~~2DW6~~ is a 4 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Bradyrhizobium_japonicum Bradyrhizobium japonicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DW6 OCA].	+	[[2dw6]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bradyrhizobium_japonicum Bradyrhizobium japonicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DW6 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17144653~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017144653</ref><references group="xtra"/>
	[[Category: Bradyrhizobium japonicum]]		[[Category: Bradyrhizobium japonicum]]
	[[Category: Almo, S C.]]		[[Category: Almo, S C.]]
Line 35:		Line 23:
	[[Category: Enolase superfamily]]		[[Category: Enolase superfamily]]
	[[Category: L-tartrate]]		[[Category: L-tartrate]]
-		+	[[Category: Lyase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Mon Feb 16 21:39:35 2009''~~	+