Characterization of a C—C Bond Hydrolase fromSphingomonas wittichiiRW1 with Novel Specificities towards Polychlorinated Biphenyl Metabolites

Abstract

Sphingomonas wittichii RW1 degrades chlorinated dibenzofurans and dibenzo-p-dioxins via meta cleavage. We used inverse PCR to amplify dxnB2, a gene encoding one of three meta-cleavage product (MCP) hydrolases identified in the organism that are homologues of BphD involved in biphenyl catabolism. Purified DxnB2 catalyzed the hydrolysis of 8-OH 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate (HOPDA) approximately six times faster than for HOPDA at saturating substrate concentrations. Moreover, the specificity of DxnB2 for HOPDA (k cat /K m ‫؍‬ 1.2 ؋ 10 7 M ؊1 s ؊1 ) was about half that of the BphDs of Burkholderia xenovorans LB400 and Rhodococcus globerulus P6, two potent polychlorinated biphenyl (PCB)-degrading strains. Interestingly, DxnB2 transformed 3-Cl and 4-OH HOPDAs, compounds that inhibit the BphDs and limit PCB degradation. DxnB2 had a higher specificity for 9-Cl HOPDA than for HOPDA but a lower specificity for 8-Cl HOPDA (k cat /K m ‫؍‬ 1.7 ؋ 10 6 M ؊1 s ؊1 ), the chlorinated analog of 8-OH HOPDA produced during dibenzofuran catabolism. Phylogenetic analyses based on structure-guided sequence alignment revealed that DxnB2 belongs to a previously unrecognized class of MCP hydrolases, evolutionarily divergent from the BphDs although the physiological substrates of both enzyme types are HOPDAs. However, both classes of enzymes have mainly small hydrophobic residues lining the subsite that binds the C-6 phenyl of HOPDA, in contrast to the bulky hydrophobic residues (Phe106, Phe135, Trp150, and Phe197) found in the class II enzymes that prefer substrates possessing a C-6 alkyl. Thr196 and/or Asn203 appears to be an important determinant of specificity for DxnB2, potentially forming hydrogen bonds with the 8-OH substituent. This study demonstrates that the substrate specificities of evolutionarily divergent hydrolases may be useful for degrading mixtures of pollutants, such as PCBs.Chlorinated aromatic compounds, such as polychlorinated biphenyls (PCBs) and dibenzofurans, are among the most widespread, toxic, and/or persistent environmental pollutants. The Bph and Dxn/Dbf pathways responsible for the aerobic bacterial catabolism of biphenyl and dibenzofuran, respectively, have been extensively studied, in part due to their potential for remediating environments contaminated with the polychlorinated compounds (2, 10). The pathways share three homologous enzymes ( Fig. 1): a multicomponent dioxygenase that catalyzes the initial step of ring hydroxylation, an extradiol dioxygenase that catalyzes oxygenolytic cleavage of the catecholic intermediate at the meta position to yield 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate (HOPDA) or ortho-substituted HOPDA, and a metacleavage product (MCP) hydrolase that catalyzes an unusual COC bond cleavage of the HOPDA.A general limitation of bacterial catabolic pathways for the degradation of complex industrial mixtures is that one or more pathway enzymes lack the requisite broad substrate specificity to degrade all man-made (xenobiotic) congeners of the naturally occurring compounds,...

Characterization of a Carbon-Carbon Hydrolase from Mycobacterium tuberculosis Involved in Cholesterol Metabolism

“…Similarly, the structural data indicate that the substrate-binding pocket is best adapted to the steroid substrate. Although the specificity of HsaD is ϳ2-3 orders of magnitude lower than other MCP hydrolases for their physiological substrates (13,23,35), this is consistent with what has been reported for other M. tuberculosis enzymes involved in cholesterol metabolism, including KshAB (36) and HsaC (8).…”

The Molecular Basis for Inhibition of BphD, a C-C Bond Hydrolase Involved in Polychlorinated Biphenyls Degradation

“…With respect to the former, the ability of the BphD homologue DxnB2 to hydrolyze 3-Cl HOPDA with a ϳ13-fold higher specificity may provide an opportunity to overcome this block in the Bph pathway (9). Nevertheless, the structural basis for the different activities of these enzymes is unclear: Gly-42 and Gly-43, which are proposed to clash with the 3-Cl substituent in the E⅐S red conformation, as well as the flanking residues are conserved between the two enzymes, as is Phe-74, the residue closest in space to Gly-43.…”

Quantitative PCR for Tracking the Megaplasmid-Borne Biodegradation Potential of a Model Sphingomonad

“…likely because the chlorinated metabolites, especially chlorocatechols, can inhibit enzymes in this and other catabolic pathways (5,19). The tubes were incubated horizontally at room temperature without agitation and sampled daily with three replicate samples taken 3, 6, 9, 12, and 14 days postinoculation.…”

“…These downstream metabolites can then be funneled into the citric acid cycle and used for carbon and energy. The dioxin dioxygenase also transforms chlorinated congeners of dibenzo-p-dioxin, resulting in the formation of chlorinated salicylates (19). This initial transformation destroys and detoxifies the planar structure of the molecule (15), but the resultant chlorinated intermediates typically do not support growth.…”

“…This enzyme catalyzes the initial dihydroxylation of the aromatic ring (18), leading to its spontaneous cleavage into 2,2=,3-trihydroxybiphenyl, which is dihydroxylated by a second enzyme into 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate and then hydrolyzed to form salicylic acid (19). These downstream metabolites can then be funneled into the citric acid cycle and used for carbon and energy.…”