2rht

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[[Image:2rht.jpg|left|200px]]<br /><applet load="2rht" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2rht, resolution 1.700&Aring;" />
 
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'''Crystal Structure of the S112A mutant of a C-C hydrolase, BphD from Burkholderia xenovorans LB400, in complex with 3-Cl HOPDA'''<br />
 
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==Overview==
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==Crystal Structure of the S112A mutant of a C-C hydrolase, BphD from Burkholderia xenovorans LB400, in complex with 3-Cl HOPDA==
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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&gt;F&gt;Cl&gt;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.
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<StructureSection load='2rht' size='340' side='right'caption='[[2rht]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[2rht]] 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=2RHT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RHT FirstGlance]. <br>
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2RHT is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Burkholderia_xenovorans Burkholderia xenovorans] with <scene name='pdbligand=NA:'>NA</scene>, <scene name='pdbligand=C1E:'>C1E</scene> and <scene name='pdbligand=MLI:'>MLI</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RHT OCA].
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C1E:(2Z,4E)-3-CHLORO-2-HYDROXY-6-OXO-6-PHENYLHEXA-2,4-DIENOIC+ACID'>C1E</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
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==Reference==
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2rht FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rht OCA], [https://pdbe.org/2rht PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rht RCSB], [https://www.ebi.ac.uk/pdbsum/2rht PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rht ProSAT]</span></td></tr>
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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://ispc.weizmann.ac.il//pmbin/getpm?pmid=17932031 17932031]
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</table>
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[[Category: Burkholderia xenovorans]]
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== Function ==
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[[Category: Single protein]]
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[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>
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[[Category: Bhowmik, S.]]
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== Evolutionary Conservation ==
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[[Category: Bolin, J T.]]
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[[Image:Consurf_key_small.gif|200px|right]]
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[[Category: C1E]]
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Check<jmol>
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[[Category: MLI]]
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<jmolCheckbox>
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[[Category: NA]]
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rh/2rht_consurf.spt"</scriptWhenChecked>
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[[Category: aromatic hydrocarbons catabolism]]
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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[[Category: c-c bond hydrolase ]]
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<text>to colour the structure by Evolutionary Conservation</text>
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[[Category: hydrolase]]
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</jmolCheckbox>
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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=2rht ConSurf].
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 18:47:26 2008''
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<div style="clear:both"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Paraburkholderia xenovorans LB400]]
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[[Category: Bhowmik S]]
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[[Category: Bolin JT]]

Current revision

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

PDB ID 2rht

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