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| | ==Crystal Structure of S112A mutant of a C-C hydrolase, BphD from Burkholderia xenovorans LB400== |
| The line below this paragraph, containing "STRUCTURE_2ri6", creates the "Structure Box" on the page.
| | <StructureSection load='2ri6' size='340' side='right'caption='[[2ri6]], [[Resolution|resolution]] 1.68Å' scene=''> |
| You may change the PDB parameter (which sets the PDB file loaded into the applet)
| | == Structural highlights == |
| or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
| | <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> |
| or leave the SCENE parameter empty for the default display.
| | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.68Å</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> |
| {{STRUCTURE_2ri6| PDB=2ri6 | SCENE= }}
| | <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> |
| | | </table> |
| '''Crystal Structure of S112A mutant of a C-C hydrolase, BphD from Burkholderia xenovorans LB400'''
| | == Function == |
| | | [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 == |
| ==Overview== | | [[Image:Consurf_key_small.gif|200px|right]] |
| BphD of Burkholderia xenovorans LB400 catalyzes an unusual C-C bond hydrolysis of 2-hydroxy-6-oxo-6-phenylhexa-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 (lambda(max) is 434 nm for the free enolate) proceeds via an unidentified intermediate with a red-shifted absorption spectrum (lambda(max) is 492 nm) (Horsman, G. P., Ke, J., Dai, S., Seah, S. Y. K., Bolin, J. T., and Eltis, L. D. (2006) Biochemistry 45, 11071-11086). Here we demonstrate that the S112A variant generates and traps a similar intermediate (lambda(max) is 506 nm) with a similar rate, 1/tau approximately 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, whereas 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.
| | Check<jmol> |
| | | <jmolCheckbox> |
| ==About this Structure== | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ri/2ri6_consurf.spt"</scriptWhenChecked> |
| 2RI6 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Burkholderia_xenovorans Burkholderia xenovorans]. 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].
| | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | | <text>to colour the structure by Evolutionary Conservation</text> |
| ==Reference== | | </jmolCheckbox> |
| 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 Jul 6;282(27):19894-904. Epub 2007 Apr 18. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17442675 17442675]
| | </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]. |
| [[Category: Burkholderia xenovorans]] | | <div style="clear:both"></div> |
| [[Category: Single protein]] | | == References == |
| [[Category: Bhowmik, S.]] | | <references/> |
| [[Category: Bolin, J T.]] | | __TOC__ |
| [[Category: Aromatic hydrocarbons catabolism]] | | </StructureSection> |
| [[Category: C-c bond hydrolase]] | | [[Category: Large Structures]] |
| [[Category: Hydrolase]] | | [[Category: Paraburkholderia xenovorans LB400]] |
| ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 16:57:00 2008''
| | [[Category: Bhowmik S]] |
| | [[Category: Bolin JT]] |
