Structural studies of the 1,2-dihydroxynaphthalene dioxygenase, DoxG, reveal features that permit the cleavage of 4-substituted catechols
Abstract
Failure in the processing of PCBs and PCB metabolites by bacterial bph pathways limits prospects for bioremediation of these notorious pollutants. One cause of failure is the generation of 4-substituted catechols, which are not processed by key ring-cleaving dioxygenases. Earlier research has demonstrated that the ring-cleaving dioxygenases from other pathways succeeded in the processing of 4-substituted catechols where enzymes from the bph pathway failed. This study defines a structural basis for this failure comparing the structures of ring-cleaving dioxygenases that succeed and fail in the cleavage of 4-substituted catechols. DoxGC18 is a 1,2-dihydroxnaphthalene dioxygenases from Pseudomonas strain C18. BphCLB400 is the homologous 2,3-dihydroxybiphenyl dioxygenase from the bph pathway of Burkholderia strain LB400. DoxGC18 cleaves 3,4-dihydroxybiphenyl (4-phenylcatechol), whereas BphCLB400 does not do so. I determined the high resolution structure of DoxGC18 and its binary complexes with four substrates: 3,4-dihydroxybiphenyl, 2,3-dihydroxybiphenyl, 4-methylcatechol, and 1,2-dihydroxynaphthalene. Comparisons to previously determined substrate complexes of BphCLB400 revealed variations in enzyme:substate interactions and dynamic features of enzyme structure that correlate with competency for cleavage of 4-substituted catechols and, presumably, related PCB metabolites. In particular, a key hydrogen bond to a histidine involved in catalysis is formed in DoxGC18 by the side chain carboxylate of an aspartate residue, whereas in BphC LB400 the bond is formed by the backbone carbonyl of a proline residue. Utilization of the aspartate in this hydrogen bond generates more room for the binding of 4-substituted catechols and flexibility in the hydrogen bond network. This leads to ability of DoxGC18 to degrade these substrate where BphCLB400 fails.
Degree
Ph.D.
Advisors
Bolin, Purdue University.
Subject Area
Biophysics
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