title: Analysis of PCBs degradation abilities of biphenyl dioxygenase derived from Enterobacter sp. LY402 by molecular simulation.
abstract: Enterobacter sp. LY402 is a bacterium isolated from polluted soil. It can efficiently degrade polychlorinated biphenyls (PCBs) under aerobic conditions. However, the degradation was limited when it comes to high chlorine or double para-substituted PCBs. Biphenyl dioxygenase (BDO) is the key enzyme in the PCBs biodegradation process. It has been confirmed that the α-subunit of the iron-sulfur protein of biphenyl 2,3-dioxygenase (BphA1) directly influenced catalytic activities and substrate specificity. To know the degradation characteristics of BDO to PCBs, we analyzed PCBs degradation abilities of BphA1 from Enterobacter sp. LY402 by experiment and molecular simulation. Firstly, the degradation experiment of PCBs was performed, and the degradation rate constants (k) were calculated. Then the three-dimensional model of LY402-BphA1 was constructed. Through further docking studies with 209 PCB congeners, the PCBs binding abilities of LY402-BphA1 were measured and some crucial active site residues were identified. Moreover, the molecular descriptors of PCBs were calculated and analyzed to determine the correlation of molecular properties and degradation. The results showed that the affinity energy of PCBs was well matched with the k values of the different number of chlorine substituents. The binding ability of BphA1 greatly affected the PCBs degradation abilities of BDO. Hydrophobic contact was the main interaction between the residues of active site and PCB substrates. The number and subposition of chlorine substituents would influence the PCBs binding ability of BphA1 significantly. Ser283, Val287, Gly321 and Tyr384 residues in the active site of LY402-BphA1 showed high variability, and the space limitation of the active site of BphA1 had negative influence on the PCBs binding affinity of BDO. The changes of physical, electronic and geometrical properties could influence degradation and binding affinity of PCBs. Analysis of structural information, binding affinity and influences of molecular properties could be used to direct further modification of BDO to enhance biodegradation of PCBs and other toxic compounds.
authors.affiliation: School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116000, People's Republic of China.
authors.forename: Ya-Ming
authors.initials: YM
authors.lastname: Cao
authors.forename: Li
authors.initials: L
authors.lastname: Xu
authors.forename: Ling-Yun
authors.initials: LY
authors.lastname: Jia
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000378:metabolism*; D001673:Biodegradation, Environmental; D020134:Catalytic Domain; D003198:Computer Simulation; D049308:Dioxygenases / Q000378:metabolism*; D004754:Enterobacter / Q000737:chemistry / Q000201:enzymology*; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011078:Polychlorinated Biphenyls / Q000737:chemistry / Q000378:metabolism*; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D013379:Substrate Specificity
chemical_list: D001426:Bacterial Proteins; D011078:Polychlorinated Biphenyls; D049308:Dioxygenases