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| | <StructureSection load='3v1m' size='340' side='right'caption='[[3v1m]], [[Resolution|resolution]] 1.92Å' scene=''> | | <StructureSection load='3v1m' size='340' side='right'caption='[[3v1m]], [[Resolution|resolution]] 1.92Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3v1m]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Burkholderia_cepacia_lb400 Burkholderia cepacia lb400]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V1M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3V1M FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3v1m]] is a 1 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=3V1M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3V1M FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HPK:(3E)-2,6-DIOXO-6-PHENYLHEX-3-ENOATE'>HPK</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.92Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2og1|2og1]], [[2ri6|2ri6]], [[2pu7|2pu7]], [[2puh|2puh]], [[2puj|2puj]], [[2rhw|2rhw]], [[2rht|2rht]], [[3v1k|3v1k]], [[3v1l|3v1l]], [[3v1n|3v1n]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HPK:(3E)-2,6-DIOXO-6-PHENYLHEX-3-ENOATE'>HPK</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">bphD, Bxeno_C1120, Bxe_C1186 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266265 Burkholderia cepacia LB400])</td></tr> | + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/2,6-dioxo-6-phenylhexa-3-enoate_hydrolase 2,6-dioxo-6-phenylhexa-3-enoate hydrolase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.7.1.8 3.7.1.8] </span></td></tr>
| + | |
| | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3v1m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v1m OCA], [https://pdbe.org/3v1m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3v1m RCSB], [https://www.ebi.ac.uk/pdbsum/3v1m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3v1m ProSAT]</span></td></tr> | | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3v1m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v1m OCA], [https://pdbe.org/3v1m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3v1m RCSB], [https://www.ebi.ac.uk/pdbsum/3v1m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3v1m ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/BPHD_BURXL BPHD_BURXL]] 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>
| + | [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> |
| - | <div style="background-color:#fffaf0;">
| + | |
| - | == Publication Abstract from PubMed ==
| + | |
| - | Meta-cleavage product (MCP) hydrolases are members of the alpha/beta-hydrolase superfamily that utilize a Ser-His-Asp triad to catalyze the hydrolysis of a C-C bond. BphD, the MCP hydrolase from the biphenyl degradation pathway, hydrolyzes 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA) to 2-hydroxypenta-2,4-dienoic acid (HPD) and benzoate. A 1.6 A resolution crystal structure of BphD H265Q incubated with HOPDA revealed that the enzyme's catalytic serine was benzoylated. The acyl-enzyme is stabilized by hydrogen bonding from the amide backbone of 'oxyanion hole' residues, consistent with formation of a tetrahedral oxyanion during nucleophilic attack by Ser112. Chemical quench and mass spectrometry studies substantiated the formation and decay of a Ser112-benzoyl species in wild-type BphD on a time scale consistent with turnover and incorporation of a single equivalent of (18)O into the benzoate produced during hydrolysis in H(2)(18)O. Rapid-scanning kinetic studies indicated that the catalytic histidine contributes to the rate of acylation by only an order of magnitude, but affects the rate of deacylation by over 5 orders of magnitude. The orange-colored catalytic intermediate, ES(red), previously detected in the wild-type enzyme and proposed herein to be a carbanion, was not observed during hydrolysis by H265Q. In the newly proposed mechanism, the carbanion abstracts a proton from Ser112, thereby completing tautomerization and generating a serinate for nucleophilic attack on the C6-carbonyl. Finally, quantification of an observed pre-steady-state kinetic burst suggests that BphD is a half-site reactive enzyme. While the updated catalytic mechanism shares features with the serine proteases, MCP hydrolase-specific chemistry highlights the versatility of the Ser-His-Asp triad.
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| - | Identification of an Acyl-Enzyme Intermediate in a meta-Cleavage Product Hydrolase Reveals the Versatility of the Catalytic Triad.,Ruzzini AC, Ghosh S, Horsman GP, Foster LJ, Bolin JT, Eltis LD J Am Chem Soc. 2012 Mar 14;134(10):4615-24. Epub 2012 Mar 5. PMID:22339283<ref>PMID:22339283</ref>
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| - | | + | |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| + | |
| - | </div>
| + | |
| - | <div class="pdbe-citations 3v1m" style="background-color:#fffaf0;"></div>
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| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: 2,6-dioxo-6-phenylhexa-3-enoate hydrolase]] | |
| - | [[Category: Burkholderia cepacia lb400]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Bolin, J T]] | + | [[Category: Paraburkholderia xenovorans LB400]] |
| - | [[Category: Ghosh, S]] | + | [[Category: Bolin JT]] |
| - | [[Category: 2-hydroxy-6-oxo-6-phenyl-hexa-2]] | + | [[Category: Ghosh S]] |
| - | [[Category: 4-dienoate hydrolase]]
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| - | [[Category: Alpha/beta hydrolase]]
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| - | [[Category: Alpha/beta hydrolase fold]]
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| - | [[Category: Bphd]]
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| - | [[Category: C-c bond hydrolase]]
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| - | [[Category: Hydrolase]]
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| - | [[Category: Mcp hydrolase]]
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| - | [[Category: Meta cleavage product hydrolase]]
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| - | [[Category: Pcb degradation]]
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