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A. V. Krivitskaya, A. A. Pometun, P. D. Parshin, M. G. Khrenova, V. B. Urlacher, V. I. Tishkov
Full structure modeling of three-domains
monooxygenase CYP102A1 BM3 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.
Key words: cytochrome P450 BM3, molecular
modeling, 3D structure.
Copyright (C) Chemistry Dept., Moscow State University, 2002
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