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| | ==Crystal structure of the S105A mutant of a C-C hydrolase, DxnB2 from Sphingomonas wittichii RW1== | | ==Crystal structure of the S105A mutant of a C-C hydrolase, DxnB2 from Sphingomonas wittichii RW1== |
| - | <StructureSection load='4lyd' size='340' side='right' caption='[[4lyd]], [[Resolution|resolution]] 2.26Å' scene=''> | + | <StructureSection load='4lyd' size='340' side='right'caption='[[4lyd]], [[Resolution|resolution]] 2.26Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4lyd]] 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=4LYD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4LYD FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4lyd]] 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=4LYD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LYD FirstGlance]. <br> |
| - | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4lxg|4lxg]], [[4lxh|4lxh]], [[4lxi|4lxi]]</td></tr> | + | </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=4lyd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lyd OCA], [https://pdbe.org/4lyd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4lyd RCSB], [https://www.ebi.ac.uk/pdbsum/4lyd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4lyd 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>
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| - | <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>
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| - | <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=4lyd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lyd OCA], [http://pdbe.org/4lyd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4lyd RCSB], [http://www.ebi.ac.uk/pdbsum/4lyd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4lyd 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: Bhowmik, S]] | + | [[Category: Bhowmik S]] |
| - | [[Category: Bolin, J T]] | + | [[Category: Bolin JT]] |
| - | [[Category: Ghosh, S]] | + | [[Category: Ghosh S]] |
| - | [[Category: Alpha-beta hydrolase]]
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| - | [[Category: C-c bond hydrolase]]
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| - | [[Category: Dibenzo-p-dioxin degradation]]
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| - | [[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
DxnB2 and BphD are meta-cleavage product (MCP) hydrolases that catalyze C-C bond hydrolysis of the biphenyl metabolite 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA). BphD is a bottleneck in the bacterial degradation of polychlorinated biphenyls (PCBs) by the Bph catabolic pathway due in part to inhibition by 3-Cl HOPDAs. By contrast, DxnB2 from Sphingomonas wittichii RW1 catalyzes the hydrolysis of 3-Cl HOPDAs more efficiently. X-ray crystallographic studies of the catalytically inactive S105A variant of DxnB2 complexed with 3-Cl HOPDA revealed a binding mode in which C1 through C6 of the dienoate are coplanar. The chlorine substituent is accommodated by a hydrophobic pocket that is larger than the homologous site in BphDLB400 from Burkholderia xenovorans LB400. The planar binding mode observed in the crystalline complex was consistent with the hyper- and hypsochromically shifted absorption spectra of 3-Cl and 3,9,11-triCl HOPDA, respectively, bound to S105A in solution. Moreover, ES(red), an intermediate possessing a bathochromically shifted spectrum observed in the turnover of HOPDA, was not detected, suggesting that substrate destabilization was rate-limiting in the turnover of these PCB metabolites. Interestingly, electron density for the first alpha-helix of the lid domain was poorly defined in the dimeric DxnB2 structures, unlike in the tetrameric BphDLB400. Structural comparison of MCP hydrolases identified the NC-loop, connecting the lid to the alpha/beta-hydrolase core domain, as a determinant in the oligomeric state and suggests its involvement in catalysis. Finally, an increased mobility of the DxnB2 lid may contribute to the enzyme's ability to hydrolyze PCB metabolites, highlighting how lid architecture contributes to substrate specificity in alpha/beta-hydrolases.
The Lid Domain of the MCP Hydrolase DxnB2 Contributes to the Reactivity toward Recalcitrant PCB Metabolites.,Ruzzini AC, Bhowmik S, Yam KC, Ghosh S, Bolin JT, Eltis LD Biochemistry. 2013 Aug 20;52(33):5685-95. doi: 10.1021/bi400774m. Epub 2013 Aug, 9. PMID:23879719[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Ruzzini AC, Bhowmik S, Yam KC, Ghosh S, Bolin JT, Eltis LD. The Lid Domain of the MCP Hydrolase DxnB2 Contributes to the Reactivity toward Recalcitrant PCB Metabolites. Biochemistry. 2013 Aug 20;52(33):5685-95. doi: 10.1021/bi400774m. Epub 2013 Aug, 9. PMID:23879719 doi:10.1021/bi400774m
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