2pu5: Difference between revisions

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-[[Image:2pu5.gif|left|200px]]<br /><applet load="2pu5" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="2pu5, resolution 2.300&Aring;" />
-'''Crystal Structure of a C-C bond hydrolase, BphD, from Burkholderia xenovorans LB400'''<br />
-==Overview==
+==Crystal Structure of a C-C bond hydrolase, BphD, from Burkholderia xenovorans LB400==
-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.
+<StructureSection load='2pu5' size='340' side='right'caption='[[2pu5]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[2pu5]] is a 2 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=2PU5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PU5 FirstGlance]. <br>
-PU5 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=MLI:'>MLI</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PU5 OCA].
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene></td></tr>
-==Reference==
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2pu5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pu5 OCA], [https://pdbe.org/2pu5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pu5 RCSB], [https://www.ebi.ac.uk/pdbsum/2pu5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pu5 ProSAT]</span></td></tr>
-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]
+</table>
-[[Category: Burkholderia xenovorans]]
+== Function ==
-[[Category: Single protein]]
+[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>
-[[Category: Bhowmik, S.]]
+== Evolutionary Conservation ==
-[[Category: Bolin, J.T.]]
+[[Image:Consurf_key_small.gif|200px|right]]
-[[Category: MLI]]
+Check<jmol>
-[[Category: c-c bond hydrolase]]
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pu/2pu5_consurf.spt"</scriptWhenChecked>
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 14:29:42 2008''
+    <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/main_output.php?pdb_ID=2pu5 ConSurf].
+<div style="clear:both"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Paraburkholderia xenovorans LB400]]
+[[Category: Bhowmik S]]
+[[Category: Bolin JT]]