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| - | [[Image:2pu5.gif|left|200px]] | |
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| - | {{Structure
| + | ==Crystal Structure of a C-C bond hydrolase, BphD, from Burkholderia xenovorans LB400== |
| - | |PDB= 2pu5 |SIZE=350|CAPTION= <scene name='initialview01'>2pu5</scene>, resolution 2.300Å
| + | <StructureSection load='2pu5' size='340' side='right'caption='[[2pu5]], [[Resolution|resolution]] 2.30Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>
| + | <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> |
| - | |ACTIVITY=
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3Å</td></tr> |
| - | |GENE= bphD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=36873 Burkholderia xenovorans])
| + | <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> |
| - | |DOMAIN=
| + | <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> |
| - | |RELATEDENTRY=[[1u2e|1U2E]], [[1j1i|1J1I]], [[1c4x|1C4X]], [[2d0d|2D0D]], [[2pu6|2PU6]], [[2pu7|2PU7]], [[2puh|2PUH]], [[2puj|2PUJ]]
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2pu5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pu5 OCA], [http://www.ebi.ac.uk/pdbsum/2pu5 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2pu5 RCSB]</span>
| + | == 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 == |
| - | '''Crystal Structure of a C-C bond hydrolase, BphD, from Burkholderia xenovorans LB400'''
| + | [[Image:Consurf_key_small.gif|200px|right]] |
| - | | + | Check<jmol> |
| - | | + | <jmolCheckbox> |
| - | ==Overview== | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pu/2pu5_consurf.spt"</scriptWhenChecked> |
| - | 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.
| + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| - | | + | <text>to colour the structure by Evolutionary Conservation</text> |
| - | ==About this Structure== | + | </jmolCheckbox> |
| - | 2PU5 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Burkholderia_xenovorans Burkholderia xenovorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PU5 OCA].
| + | </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> |
| - | ==Reference== | + | == References == |
| - | 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]
| + | <references/> |
| - | [[Category: Burkholderia xenovorans]] | + | __TOC__ |
| - | [[Category: Single protein]] | + | </StructureSection> |
| - | [[Category: Bhowmik, S.]] | + | [[Category: Large Structures]] |
| - | [[Category: Bolin, J T.]] | + | [[Category: Paraburkholderia xenovorans LB400]] |
| - | [[Category: c-c bond hydrolase]]
| + | [[Category: Bhowmik S]] |
| - | | + | [[Category: Bolin JT]] |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:40:46 2008''
| + | |
