Homology modeling and docking study of GyrB

Gordonia sp. D2 is an actinomycete strain that can degrade cypermethrin, and GyrB is regarded as a character playing a key role in the process of pyrethroid degradation of Gordonia sp. D2. In order to understand the mechanisms of ligand binding and the interaction between the cypermethrin and the GyrB, a three-dimensional (3D) model of the GyrB is generated based on the crystal structure of the DNA gyrase B (PDB code 1EI1) by using MODELER module. Flexible docking approaches were then employed to dock two conformations of cypermethrin into the active site of GyrB in order to probe the ligand-binding modes. By analyzing the results, active site architecture and certain key residues responsible for substrate specificity including Ile88, Ile91, Leu109, Thr110 and Asp111 were identified on GyrB, which might be very helpful to further determine its biological roles, and provide insights for the metabolic pathways of cypermethrin by GyrB in the water environment.