title: Homology modeling and docking studies of Comamonas testosteroni B-356 biphenyl-2,3-dioxygenase involved in degradation of polychlorinated biphenyls.
abstract: 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 alpha-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.
authors.affiliation: Environmental Biotechnology Division, Indian Institute of Toxicology Research, Council of Scientific and Industrial Research, Lucknow, Uttar Pradesh 226001, India.
authors.forename: M S
authors.initials: MS
authors.lastname: Baig
authors.forename: N
authors.initials: N
authors.lastname: Manickam
mesh_terms: D000595:Amino Acid Sequence; D001673:Biodegradation, Environmental; D020134:Catalytic Domain; D020604:Comamonas testosteroni / Q000201:enzymology*; D007506:Iron-Sulfur Proteins / Q000737:chemistry* / Q000378:metabolism*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010105:Oxygenases / Q000737:chemistry* / Q000378:metabolism*; D011078:Polychlorinated Biphenyls / Q000378:metabolism*; D017433:Protein Structure, Secondary; D021122:Protein Subunits / Q000737:chemistry; D015203:Reproducibility of Results; D016415:Sequence Alignment; D040681:Structural Homology, Protein
chemical_list: D007506:Iron-Sulfur Proteins; D021122:Protein Subunits; D011078:Polychlorinated Biphenyls; D010105:Oxygenases; C074161:biphenyl-2,3-dioxygenase