Homology modeling and docking studies of Comamonas testosteroni B-356 biphenyl-2,3-dioxygenase involved in degradation of polychlorinated biphenyls

• Published in: International journal of biological macromolecules Vol. 46; no. 1; pp. 47 - 53
• Main Authors: Baig, M.S., Manickam, N.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 2010
• Subjects: Amino Acid Sequence; Biodegradation, Environmental; Biphenyl dioxygenase; Catalytic Domain; Comamonas testosteroni; Comamonas testosteroni - enzymology; Docking; Environmental contaminants; Iron-Sulfur Proteins - chemistry; Iron-Sulfur Proteins - metabolism; Models, Molecular; Molecular Sequence Data; Oxygenases - chemistry; Oxygenases - metabolism; Polychlorinated Biphenyls - metabolism; Protein Structure, Secondary; Protein Subunits - chemistry; Reproducibility of Results; Sequence Alignment; Structural Homology, Protein; Three-dimensional model; Validation; Validation; Three-dimensional model; Docking; Biphenyl dioxygenase; Environmental contaminants
• ISSN: 0141-8130; 1879-0003
• DOI: 10.1016/j.ijbiomac.2009.10.014

Biphenyl dioxygenase is a microbial enzyme which catalyzes the stereospecific dioxygenation of aromatic rings of biphenyl congeners leading to their degradation. Hence, it has attracted the attention of researchers due to its ability to oxidize chlorinated biphenyls, which are one of the serious environmental contaminants. In the present study, the three-dimensional model of α-subunit of biphenyl dioxygenase (BphA) from Comamonas testosteroni B-356 has been constructed. The resulting model was further validated and used for docking studies with a class of chlorinated biphenyls such as biphenyl,3,3′-dichlorobiphenyl and 4,4′-dichlorobiphenyl. The kinetic parameters of these biphenyl compounds were well matched with the docking results in terms of conformational and distance constraints. The binding properties of these biphenyl compounds along with identification of critical active site residues could be used for further site-directed mutagenesis experiments in order to identify their role in activity and substrate specificity, ultimately leading to improved mutants for degradation of these toxic compounds.