2rhw - Revision history

OCA at 09:22, 21 February 2024

OCA — Wed, 21 Feb 2024 09:22:29 GMT

←Older revision		Revision as of 09:22, 21 February 2024
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	<StructureSection load='2rhw' size='340' side='right'caption='[[2rhw]], [[Resolution\|resolution]] 1.57Å' scene=''>		<StructureSection load='2rhw' size='340' side='right'caption='[[2rhw]], [[Resolution\|resolution]] 1.57Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2rhw]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Burkholderia_xenovorans Burkholderia~~ xenovorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RHW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RHW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2rhw]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Paraburkholderia_xenovorans_LB400 Paraburkholderia xenovorans LB400]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RHW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RHW FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C0E:3-FLUORO-6-(4-FLUOROPHENYL)-2-HYDROXY-6-OXOHEXA-2,4-DIENOIC+ACID'>C0E</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene~~></td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.57Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2puh\|2puh]], [[2puj\|2puj]], [[2rht\|2rht]]</div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C0E:3-FLUORO-6-(4-FLUOROPHENYL)-2-HYDROXY-6-OXOHEXA-2,4-DIENOIC+ACID'>C0E</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></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=2rhw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rhw OCA], [https://pdbe.org/2rhw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rhw RCSB], [https://www.ebi.ac.uk/pdbsum/2rhw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rhw 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=2rhw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rhw OCA], [https://pdbe.org/2rhw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rhw RCSB], [https://www.ebi.ac.uk/pdbsum/2rhw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rhw ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~BPHD_BURXL BPHD_BURXL]~~] Catalyzes an unusual C-C bond hydrolysis of 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA) to produce benzoic acid and 2-hydroxy-2,4-pentadienoic acid (HPD).<ref>PMID:16964968</ref>	+	[https://www.uniprot.org/uniprot/BPHD_PARXL BPHD_PARXL] Catalyzes an unusual C-C bond hydrolysis of 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA) to produce benzoic acid and 2-hydroxy-2,4-pentadienoic acid (HPD).<ref>PMID:16964968</ref>
	== 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=2rhw 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=2rhw ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The microbial degradation of polychlorinated biphenyls (PCBs) by the biphenyl catabolic (Bph) pathway is limited in part by the pathway's fourth enzyme, BphD. BphD catalyzes an unusual carbon-carbon bond hydrolysis of 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA), in which the substrate is subject to histidine-mediated enol-keto tautomerization prior to hydrolysis. Chlorinated HOPDAs such as 3-Cl HOPDA inhibit BphD. Here we report that BphD preferentially hydrolyzed a series of 3-substituted HOPDAs in the order H>F>Cl>Me, suggesting that catalysis is affected by steric, not electronic, determinants. Transient state kinetic studies performed using wild-type BphD and the hydrolysis-defective S112A variant indicated that large 3-substituents inhibited His-265-catalyzed tautomerization by 5 orders of magnitude. Structural analyses of S112A.3-Cl HOPDA and S112A.3,10-diF HOPDA complexes revealed a non-productive binding mode in which the plane defined by the carbon atoms of the dienoate moiety of HOPDA is nearly orthogonal to that of the proposed keto tautomer observed in the S112A.HOPDA complex. Moreover, in the 3-Cl HOPDA complex, the 2-hydroxo group is moved by 3.6 A from its position near the catalytic His-265 to hydrogen bond with Arg-190 and access of His-265 is blocked by the 3-Cl substituent. Nonproductive binding may be stabilized by interactions involving the 3-substituent with non-polar side chains. Solvent molecules have poor access to C6 in the S112A.3-Cl HOPDA structure, more consistent with hydrolysis occurring via an acyl-enzyme than a gem-diol intermediate. These results provide insight into engineering BphD for PCB degradation.
-
-	The molecular basis for inhibition of BphD, a C-C bond hydrolase involved in polychlorinated biphenyls degradation: large 3-substituents prevent tautomerization.,Bhowmik S, Horsman GP, Bolin JT, Eltis LD J Biol Chem. 2007 Dec 14;282(50):36377-85. Epub 2007 Oct 11. PMID:17932031<ref>PMID:17932031</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2rhw" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Burkholderia xenovorans]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Bhowmik, S~~]]	+	[[Category: Paraburkholderia xenovorans LB400]]
-	[[Category: ~~Bolin, J T~~]]	+	[[Category: Bhowmik S]]
-	[[Category: ~~Aromatic hydrocarbons catabolism]]~~	+	[[Category: Bolin JT]]
-	~~[[Category: C-c bond hydrolase]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 04:25, 2 July 2021

OCA — Fri, 02 Jul 2021 04:25:58 GMT

←Older revision		Revision as of 04:25, 2 July 2021
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	<StructureSection load='2rhw' size='340' side='right'caption='[[2rhw]], [[Resolution\|resolution]] 1.57Å' scene=''>		<StructureSection load='2rhw' size='340' side='right'caption='[[2rhw]], [[Resolution\|resolution]] 1.57Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2rhw]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Burkholderia_xenovorans Burkholderia xenovorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RHW OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2RHW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2rhw]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Burkholderia_xenovorans Burkholderia xenovorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RHW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RHW FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C0E:3-FLUORO-6-(4-FLUOROPHENYL)-2-HYDROXY-6-OXOHEXA-2,4-DIENOIC+ACID'>C0E</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C0E:3-FLUORO-6-(4-FLUOROPHENYL)-2-HYDROXY-6-OXOHEXA-2,4-DIENOIC+ACID'>C0E</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2puh\|2puh]], [[2puj\|2puj]], [[2rht\|2rht]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2puh\|2puh]], [[2puj\|2puj]], [[2rht\|2rht]]</div></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=2rhw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rhw OCA], [~~http~~://pdbe.org/2rhw PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2rhw RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2rhw PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2rhw 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=2rhw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rhw OCA], [https://pdbe.org/2rhw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rhw RCSB], [https://www.ebi.ac.uk/pdbsum/2rhw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rhw ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/BPHD_BURXL BPHD_BURXL]] Catalyzes an unusual C-C bond hydrolysis of 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA) to produce benzoic acid and 2-hydroxy-2,4-pentadienoic acid (HPD).<ref>PMID:16964968</ref>	+	[[https://www.uniprot.org/uniprot/BPHD_BURXL BPHD_BURXL]] Catalyzes an unusual C-C bond hydrolysis of 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA) to produce benzoic acid and 2-hydroxy-2,4-pentadienoic acid (HPD).<ref>PMID:16964968</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 08:01, 31 July 2019

OCA — Wed, 31 Jul 2019 08:01:43 GMT

←Older revision		Revision as of 08:01, 31 July 2019
Line 1:		Line 1:

	==Crystal Structure of the S112A mutant of a C-C hydrolase, BphD from Burkholderia xenovorans LB400, in complex with 3,10-Di-Fluoro HOPDA==		==Crystal Structure of the S112A mutant of a C-C hydrolase, BphD from Burkholderia xenovorans LB400, in complex with 3,10-Di-Fluoro HOPDA==
-	<StructureSection load='2rhw' size='340' side='right' caption='[[2rhw]], [[Resolution\|resolution]] 1.57Å' scene=''>	+	<StructureSection load='2rhw' size='340' side='right'caption='[[2rhw]], [[Resolution\|resolution]] 1.57Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2rhw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_xenovorans Burkholderia xenovorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RHW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RHW FirstGlance]. <br>		<table><tr><td colspan='2'>[[2rhw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_xenovorans Burkholderia xenovorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RHW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RHW FirstGlance]. <br>
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/rh/2rhw_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rh/2rhw_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 34:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Burkholderia xenovorans]]		[[Category: Burkholderia xenovorans]]
		+	[[Category: Large Structures]]
	[[Category: Bhowmik, S]]		[[Category: Bhowmik, S]]
	[[Category: Bolin, J T]]		[[Category: Bolin, J T]]

OCA at 07:52, 25 October 2017

OCA — Wed, 25 Oct 2017 07:52:25 GMT

←Older revision		Revision as of 07:52, 25 October 2017
Line 1:		Line 1:
		+
	==Crystal Structure of the S112A mutant of a C-C hydrolase, BphD from Burkholderia xenovorans LB400, in complex with 3,10-Di-Fluoro HOPDA==		==Crystal Structure of the S112A mutant of a C-C hydrolase, BphD from Burkholderia xenovorans LB400, in complex with 3,10-Di-Fluoro HOPDA==
	<StructureSection load='2rhw' size='340' side='right' caption='[[2rhw]], [[Resolution\|resolution]] 1.57Å' scene=''>		<StructureSection load='2rhw' size='340' side='right' caption='[[2rhw]], [[Resolution\|resolution]] 1.57Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C0E:3-FLUORO-6-(4-FLUOROPHENYL)-2-HYDROXY-6-OXOHEXA-2,4-DIENOIC+ACID'>C0E</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C0E:3-FLUORO-6-(4-FLUOROPHENYL)-2-HYDROXY-6-OXOHEXA-2,4-DIENOIC+ACID'>C0E</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2puh\|2puh]], [[2puj\|2puj]], [[2rht\|2rht]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2puh\|2puh]], [[2puj\|2puj]], [[2rht\|2rht]]</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=2rhw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rhw OCA], [http://pdbe.org/2rhw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rhw RCSB], [http://www.ebi.ac.uk/pdbsum/2rhw 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=2rhw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rhw OCA], [http://pdbe.org/2rhw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rhw RCSB], [http://www.ebi.ac.uk/pdbsum/2rhw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2rhw ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 21:20, 9 February 2016

OCA — Tue, 09 Feb 2016 21:20:10 GMT

←Older revision		Revision as of 21:20, 9 February 2016
Line 5:		Line 5:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C0E:3-FLUORO-6-(4-FLUOROPHENYL)-2-HYDROXY-6-OXOHEXA-2,4-DIENOIC+ACID'>C0E</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C0E:3-FLUORO-6-(4-FLUOROPHENYL)-2-HYDROXY-6-OXOHEXA-2,4-DIENOIC+ACID'>C0E</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2puh\|2puh]], [[2puj\|2puj]], [[2rht\|2rht]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2puh\|2puh]], [[2puj\|2puj]], [[2rht\|2rht]]</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=2rhw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rhw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rhw RCSB], [http://www.ebi.ac.uk/pdbsum/2rhw 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=2rhw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rhw OCA], [http://pdbe.org/2rhw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rhw RCSB], [http://www.ebi.ac.uk/pdbsum/2rhw PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 17:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2rhw ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2rhw" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:37, 25 December 2014

OCA — Thu, 25 Dec 2014 09:37:02 GMT

←Older revision		Revision as of 09:37, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2rhw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_xenovorans Burkholderia xenovorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RHW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RHW FirstGlance]. <br>		<table><tr><td colspan='2'>[[2rhw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_xenovorans Burkholderia xenovorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RHW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RHW FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C0E:3-FLUORO-6-(4-FLUOROPHENYL)-2-HYDROXY-6-OXOHEXA-2,4-DIENOIC+ACID'>C0E</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C0E:3-FLUORO-6-(4-FLUOROPHENYL)-2-HYDROXY-6-OXOHEXA-2,4-DIENOIC+ACID'>C0E</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2puh\|2puh]], [[2puj\|2puj]], [[2rht\|2rht]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2puh\|2puh]], [[2puj\|2puj]], [[2rht\|2rht]]</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=2rhw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rhw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rhw RCSB], [http://www.ebi.ac.uk/pdbsum/2rhw 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=2rhw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rhw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rhw RCSB], [http://www.ebi.ac.uk/pdbsum/2rhw PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/BPHD_BURXL BPHD_BURXL]] Catalyzes an unusual C-C bond hydrolysis of 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA) to produce benzoic acid and 2-hydroxy-2,4-pentadienoic acid (HPD).<ref>PMID:16964968</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Burkholderia xenovorans]]		[[Category: Burkholderia xenovorans]]
-	[[Category: Bhowmik, S.]]	+	[[Category: Bhowmik, S]]
-	[[Category: Bolin, J T.]]	+	[[Category: Bolin, J T]]
	[[Category: Aromatic hydrocarbons catabolism]]		[[Category: Aromatic hydrocarbons catabolism]]
	[[Category: C-c bond hydrolase]]		[[Category: C-c bond hydrolase]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 18:30, 30 September 2014

OCA — Tue, 30 Sep 2014 18:30:30 GMT

←Older revision		Revision as of 18:30, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2rhw.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of the S112A mutant of a C-C hydrolase, BphD from Burkholderia xenovorans LB400, in complex with 3,10-Di-Fluoro HOPDA==
		+	<StructureSection load='2rhw' size='340' side='right' caption='[[2rhw]], [[Resolution\|resolution]] 1.57Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2rhw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_xenovorans Burkholderia xenovorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RHW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RHW FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C0E:3-FLUORO-6-(4-FLUOROPHENYL)-2-HYDROXY-6-OXOHEXA-2,4-DIENOIC+ACID'>C0E</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2puh\|2puh]], [[2puj\|2puj]], [[2rht\|2rht]]</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=2rhw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rhw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rhw RCSB], [http://www.ebi.ac.uk/pdbsum/2rhw 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/rh/2rhw_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The microbial degradation of polychlorinated biphenyls (PCBs) by the biphenyl catabolic (Bph) pathway is limited in part by the pathway's fourth enzyme, BphD. BphD catalyzes an unusual carbon-carbon bond hydrolysis of 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA), in which the substrate is subject to histidine-mediated enol-keto tautomerization prior to hydrolysis. Chlorinated HOPDAs such as 3-Cl HOPDA inhibit BphD. Here we report that BphD preferentially hydrolyzed a series of 3-substituted HOPDAs in the order H>F>Cl>Me, suggesting that catalysis is affected by steric, not electronic, determinants. Transient state kinetic studies performed using wild-type BphD and the hydrolysis-defective S112A variant indicated that large 3-substituents inhibited His-265-catalyzed tautomerization by 5 orders of magnitude. Structural analyses of S112A.3-Cl HOPDA and S112A.3,10-diF HOPDA complexes revealed a non-productive binding mode in which the plane defined by the carbon atoms of the dienoate moiety of HOPDA is nearly orthogonal to that of the proposed keto tautomer observed in the S112A.HOPDA complex. Moreover, in the 3-Cl HOPDA complex, the 2-hydroxo group is moved by 3.6 A from its position near the catalytic His-265 to hydrogen bond with Arg-190 and access of His-265 is blocked by the 3-Cl substituent. Nonproductive binding may be stabilized by interactions involving the 3-substituent with non-polar side chains. Solvent molecules have poor access to C6 in the S112A.3-Cl HOPDA structure, more consistent with hydrolysis occurring via an acyl-enzyme than a gem-diol intermediate. These results provide insight into engineering BphD for PCB degradation.

-	~~{{STRUCTURE_2rhw\| PDB=2rhw \| SCENE= }}~~	+	The molecular basis for inhibition of BphD, a C-C bond hydrolase involved in polychlorinated biphenyls degradation: large 3-substituents prevent tautomerization.,Bhowmik S, Horsman GP, Bolin JT, Eltis LD J Biol Chem. 2007 Dec 14;282(50):36377-85. Epub 2007 Oct 11. PMID:17932031<ref>PMID:17932031</ref>

-	~~===Crystal Structure~~ of the ~~S112A mutant of a C-C hydrolase, BphD from Burkholderia xenovorans LB400, in complex with 3,10-Di-Fluoro HOPDA===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17932031}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2rhw]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Burkholderia_xenovorans Burkholderia xenovorans]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2RHW OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:017932031<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Burkholderia xenovorans]]		[[Category: Burkholderia xenovorans]]
	[[Category: Bhowmik, S.]]		[[Category: Bhowmik, S.]]

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

OCA — Mon, 07 Jan 2013 21:10:08 GMT

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

←Older revision

Revision as of 21:10, 7 January 2013

OCA at 21:10, 7 January 2013

OCA — Mon, 07 Jan 2013 21:10:05 GMT

←Older revision		Revision as of 21:10, 7 January 2013
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-	{{Seed}}
	[[Image:2rhw.png\|left\|200px]]		[[Image:2rhw.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2rhw", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
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	{{STRUCTURE_2rhw\| PDB=2rhw \| SCENE= }}		{{STRUCTURE_2rhw\| PDB=2rhw \| SCENE= }}

	===Crystal Structure of the S112A mutant of a C-C hydrolase, BphD from Burkholderia xenovorans LB400, in complex with 3,10-Di-Fluoro HOPDA===		===Crystal Structure of the S112A mutant of a C-C hydrolase, BphD from Burkholderia xenovorans LB400, in complex with 3,10-Di-Fluoro HOPDA===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17932031}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17932031 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17932031}}		{{ABSTRACT_PUBMED_17932031}}

	==About this Structure==		==About this Structure==
-	~~2RHW~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Burkholderia_xenovorans Burkholderia xenovorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RHW OCA].	+	[[2rhw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_xenovorans Burkholderia xenovorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RHW OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17932031~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017932031</ref><references group="xtra"/>
	[[Category: Burkholderia xenovorans]]		[[Category: Burkholderia xenovorans]]
	[[Category: Bhowmik, S.]]		[[Category: Bhowmik, S.]]
Line 30:		Line 18:
	[[Category: C-c bond hydrolase]]		[[Category: C-c bond hydrolase]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 12:50:06 2009''

OCA at 10:50, 17 February 2009

OCA — Tue, 17 Feb 2009 10:50:06 GMT

←Older revision		Revision as of 10:50, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2RHW is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Burkholderia_xenovorans Burkholderia xenovorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RHW OCA].	+	2RHW is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Burkholderia_xenovorans Burkholderia xenovorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RHW OCA].

	==Reference==		==Reference==
-	The molecular basis for inhibition of BphD, a C-C bond hydrolase involved in polychlorinated biphenyls degradation: large 3-substituents prevent tautomerization., Bhowmik S, Horsman GP, Bolin JT, Eltis LD, J Biol Chem. 2007 Dec 14;282(50):36377-85. Epub 2007 Oct 11. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17932031 17932031]~~	+	<ref group="xtra">PMID:17932031</ref><references group="xtra"/>
	[[Category: Burkholderia xenovorans]]		[[Category: Burkholderia xenovorans]]
-	[[Category: Single protein]]
	[[Category: Bhowmik, S.]]		[[Category: Bhowmik, S.]]
	[[Category: Bolin, J T.]]		[[Category: Bolin, J T.]]
Line 32:		Line 31:
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jul 28~~ 17:15:~~18 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 12:50:06 2009''