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2ri6

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(New page: 200px<br /><applet load="2ri6" size="450" color="white" frame="true" align="right" spinBox="true" caption="2ri6, resolution 1.680&Aring;" /> '''Crystal Structure o...)
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[[Image:2ri6.jpg|left|200px]]<br /><applet load="2ri6" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2ri6, resolution 1.680&Aring;" />
 
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'''Crystal Structure of S112A mutant of a C-C hydrolase, BphD from Burkholderia xenovorans LB400'''<br />
 
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==Overview==
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==Crystal Structure of S112A mutant of a C-C hydrolase, BphD from Burkholderia xenovorans LB400==
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BphD of Burkholderia xenovorans LB400 catalyzes an unusual C-C bond, hydrolysis of 2-hydroxy-6-oxo-6-phenyl-hexa-2,4-dienoic acid (HOPDA) to, afford benzoic acid and 2-hydroxy-2,4-pentadienoic acid (HPD). An, enol-keto tautomerization has been proposed to precede hydrolysis via a, gem-diol intermediate. The role of the canonical 'catalytic triad', (Ser-112, His-265, Asp-237) in mediating these two half-reactions remains, unclear. We previously reported that the BphD-catalyzed hydrolysis of, HOPDA (max = 434 nm for the free enolate) proceeds via an unidentified, intermediate with a red-shifted absorption spectrum (max = 492 nm), (Horsman et al. (2006), Biochemistry 45, 11071). Here we demonstrate that, the Ser112Ala variant (S112A) generates and traps a similar intermediate, (max = 506 nm) with a similar rate, 1/t ~ 500 s-1. The crystal structure, of the S112A:HOPDA complex at 1.8 A resolution identified this, intermediate as the keto tautomer, (E)-2,6-dioxo-6-phenyl-hex-3-enoate., This keto tautomer did not accumulate in either the H265A or the, S112A/H265A double variants, indicating that His-265 catalyzes, tautomerization. Consistent with this role, the wild type and S112A, enzymes catalyzed tautomerization of the product HPD, while H265A variants, did not. This study thus identifies a keto intermediate, and demonstrates, that the catalytic triad histidine catalyzes the tautomerization, half-reaction, expanding the role of this residue from its purely, hydrolytic function in other serine hydrolases. Finally, the S112A:HOPDA, crystal structure is more consistent with hydrolysis occurring via an, acyl-enzyme intermediate than a gem-diol intermediate as solvent molecules, have poor access to C6, and the closest ordered water is 7 A away.
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<StructureSection load='2ri6' size='340' side='right'caption='[[2ri6]], [[Resolution|resolution]] 1.68&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[2ri6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Paraburkholderia_xenovorans_LB400 Paraburkholderia xenovorans LB400]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2pu6 2pu6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RI6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RI6 FirstGlance]. <br>
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2RI6 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 NA and MLI as [http://en.wikipedia.org/wiki/ligands ligands]. This structure superseeds the now removed PDB entry 2PU6. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2RI6 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]] 1.68&#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=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=2ri6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ri6 OCA], [https://pdbe.org/2ri6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ri6 RCSB], [https://www.ebi.ac.uk/pdbsum/2ri6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ri6 ProSAT]</span></td></tr>
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The tautomeric half-reaction of BphD, A C-C bond hydrolase: Kinetic and structural evidence supporting a key role for histidine 265 of the catalytic triad., Horsman GP, Bhowmik S, Seah SY, Kumar P, Bolin JT, Eltis LD, J Biol Chem. 2007 Apr 18;. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17442675 17442675]
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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: MLI]]
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Check<jmol>
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[[Category: NA]]
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<jmolCheckbox>
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[[Category: aromatic hydrocarbons catabolism]]
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ri/2ri6_consurf.spt"</scriptWhenChecked>
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[[Category: c-c bond hydrolase]]
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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[[Category: hydrolase]]
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 08:56:18 2007''
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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=2ri6 ConSurf].
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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 S112A mutant of a C-C hydrolase, BphD from Burkholderia xenovorans LB400

PDB ID 2ri6

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