2ri6

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[[Image:2ri6.jpg|left|200px]]
 
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{{Structure
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==Crystal Structure of S112A mutant of a C-C hydrolase, BphD from Burkholderia xenovorans LB400==
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|PDB= 2ri6 |SIZE=350|CAPTION= <scene name='initialview01'>2ri6</scene>, resolution 1.680&Aring;
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<StructureSection load='2ri6' size='340' side='right'caption='[[2ri6]], [[Resolution|resolution]] 1.68&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>
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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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|ACTIVITY=
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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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|GENE=
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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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|DOMAIN=
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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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|RELATEDENTRY=[[2og1|2OG1]], [[1j1i|1J1I]], [[1u2e|1U2E]], [[2pu7|2PU7]], [[1c4x|1C4X]], [[2d0d|2D0D]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ri6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ri6 OCA], [http://www.ebi.ac.uk/pdbsum/2ri6 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2ri6 RCSB]</span>
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== Function ==
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}}
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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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== Evolutionary Conservation ==
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'''Crystal Structure of S112A mutant of a C-C hydrolase, BphD from Burkholderia xenovorans LB400'''
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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==Overview==
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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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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.
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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==About this Structure==
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</jmolCheckbox>
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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 2PU6. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RI6 OCA].
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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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==Reference==
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== References ==
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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 Jul 6;282(27):19894-904. Epub 2007 Apr 18. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17442675 17442675]
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<references/>
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[[Category: Burkholderia xenovorans]]
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__TOC__
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[[Category: Single protein]]
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</StructureSection>
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[[Category: Bhowmik, S.]]
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[[Category: Large Structures]]
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[[Category: Bolin, J T.]]
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[[Category: Paraburkholderia xenovorans LB400]]
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[[Category: aromatic hydrocarbons catabolism]]
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[[Category: Bhowmik S]]
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[[Category: c-c bond hydrolase]]
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[[Category: Bolin JT]]
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[[Category: hydrolase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:00:43 2008''
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Current revision

Crystal Structure of S112A mutant of a C-C hydrolase, BphD from Burkholderia xenovorans LB400

PDB ID 2ri6

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