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Characterization of a C—C Bond Hydrolase from Sphingomonas wittichii RW1 with Novel Specificities towards Polychlorinated Biphenyl Metabolites

Stephen Y. K. Seah,^1,2,3 Jiyuan Ke,⁴ Geoffroy Denis,¹ Geoff P. Horsman,² Pascal D. Fortin,^2, Cheryl J. Whiting,² and Lindsay D. Eltis^1,2*

Department of Biochemistry, Université Laval, Québec City, Québec, Canada,¹ Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada,² Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada,³ Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky, Lexington, Kentucky 40536⁴

Received 22 December 2006/ Accepted 6 March 2007

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 x 10⁷ 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 x 10⁶ 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.

Published ahead of print on 6 April 2007.

Present address: Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115.

This article has been cited by other articles:

• Bhowmik, S., Horsman, G. P., Bolin, J. T., Eltis, L. D. (2007). The Molecular Basis for Inhibition of BphD, a C-C Bond Hydrolase Involved in Polychlorinated Biphenyls Degradation: LARGE 3-SUBSTITUENTS PREVENT TAUTOMERIZATION. J. Biol. Chem. 282: 36377-36385 [Abstract] [Full Text]