2rht

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(New page: 200px<br /><applet load="2rht" size="350" color="white" frame="true" align="right" spinBox="true" caption="2rht, resolution 1.700&Aring;" /> '''Crystal Structure o...)
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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 WT 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, nonproductive binding mode in which the plane defined by the C atoms of, HOPDA's dienoate moiety 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 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 Wed Jan 23 11:24:29 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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