Full Structure Modeling of Three-Domains Monooxygenase CYP102A1 ВМ3 from Bacillus megaterium

Abstract

The 3D full-atom model of the whole-size CYP102A1 from Bacillus megaterium (cytochrome P450 BM3) has been constructed using molecular modeling methods. The structure model was constructed using crystal structures of the separate FAD-binding domain (PDB ID: 4DQK) and the complex of FMN-binding and monooxygenase domains (PDB ID: 1BVY). Modeling procedure included analysis of the domains’ surfaces to find the orientation with maximum inter-subunit contacts. The overall configuration of the obtained complex was optimized using molecular dynamics. The final full-atom structure model shows rather tight interactions between FAD- and FMN-binding domains due to 10 inter-domain hydrogen bonds and hydrophobic interactions between three pairs of amino acid residues. This 3D model can be used for structure-function studies and rational design of the enzyme as well as for construction of hybrid supramolecular structures of biocatalysts with cytochrome P450 BM3.