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| | ==Crystal structure of the S105A mutant of a C-C hydrolase, DxnB2 from Sphingomonas wittichii RW1, in complex with substrate HOPDA== | | ==Crystal structure of the S105A mutant of a C-C hydrolase, DxnB2 from Sphingomonas wittichii RW1, in complex with substrate HOPDA== |
| - | <StructureSection load='4lye' size='340' side='right' caption='[[4lye]], [[Resolution|resolution]] 2.33Å' scene=''> | + | <StructureSection load='4lye' size='340' side='right'caption='[[4lye]], [[Resolution|resolution]] 2.33Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4lye]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sphww Sphww]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LYE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4LYE FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4lye]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhizorhabdus_wittichii_RW1 Rhizorhabdus wittichii RW1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LYE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LYE FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HPK:(3E)-2,6-DIOXO-6-PHENYLHEX-3-ENOATE'>HPK</scene></td></tr> | + | </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></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4lxg|4lxg]], [[4lyd|4lyd]], [[4lxh|4lxh]], [[4lxi|4lxi]]</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=4lye FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lye OCA], [https://pdbe.org/4lye PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4lye RCSB], [https://www.ebi.ac.uk/pdbsum/4lye PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4lye ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dxnB2, Swit_3055 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=392499 SPHWW])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2,6-dioxo-6-phenylhexa-3-enoate_hydrolase 2,6-dioxo-6-phenylhexa-3-enoate hydrolase], with EC number [http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4lye FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lye OCA], [http://pdbe.org/4lye PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4lye RCSB], [http://www.ebi.ac.uk/pdbsum/4lye PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4lye ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: 2,6-dioxo-6-phenylhexa-3-enoate hydrolase]] | + | [[Category: Large Structures]] |
| - | [[Category: Sphww]] | + | [[Category: Rhizorhabdus wittichii RW1]] |
| - | [[Category: Bolin, J T]] | + | [[Category: Bolin JT]] |
| - | [[Category: Ghosh, S]] | + | [[Category: Ghosh S]] |
| - | [[Category: Alpha-beta hydrolase]]
| + | |
| - | [[Category: C-c bond hydrolase]]
| + | |
| - | [[Category: Dibenzo-p-dioxin degradation]]
| + | |
| - | [[Category: Dibenzofuran degradation]]
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| - | [[Category: Hydrolase]]
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| - | [[Category: Meta-cleavage product hydrolase]]
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| Structural highlights
Publication Abstract from PubMed
The meta-cleavage product (MCP) hydrolases utilize a Ser-His-Asp triad to hydrolyze a carbon-carbon bond. Hydrolysis of the MCP substrate has been proposed to proceed via an enol-to-keto tautomerization followed by a nucleophilic mechanism of catalysis. Ketonization involves an intermediate, ESred, possessing a remarkable bathochromically-shifted absorption spectrum. We investigated the catalytic mechanism of the MCP hydrolases using DxnB2 from Sphingomonas wittichii RW1. Pre-steady-state kinetic and LC ESI/MS evaluation of the DxnB2-mediated hydrolysis of 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA) to 2-hydroxy-2,4-pentadienoic acid (HPD) and benzoate support a nucleophilic mechanism catalysis. In DxnB2, the rate of ESred decay and product formation showed a solvent kinetic isotope effect of 2.5 indicating that a proton transfer reaction, assigned here to substrate ketonization, limits the rate of acylation. For a series of substituted MCPs, this rate was linearly dependent on MCP pKa2 (betanuc ~1). Structural characterization of DxnB2 S105A:MCP complexes revealed that the catalytic histidine is displaced upon substrate-binding. The results provide evidence for enzyme-catalyzed ketonization in which the catalytic His-Asp pair does not play an essential role. The data further suggest that ESred represents a dianionic intermediate that acts as a general base to activate the serine nucleophile. This substrate-assisted mechanism of nucleophilic catalysis distinguishes MCP hydrolases from other serine hydrolases.
A substrate-assisted mechanism of nucleophile activation in a Ser-His-Asp containing C-C bond hydrolase.,Ruzzini AC, Bhowmik S, Ghosh S, Yam KC, Bolin JT, Eltis LD Biochemistry. 2013 Sep 25. PMID:24067021[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Ruzzini AC, Bhowmik S, Ghosh S, Yam KC, Bolin JT, Eltis LD. A substrate-assisted mechanism of nucleophile activation in a Ser-His-Asp containing C-C bond hydrolase. Biochemistry. 2013 Sep 25. PMID:24067021 doi:http://dx.doi.org/10.1021/bi401156a
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