Computational study of phosphatase activity in soluble epoxide hydrolase: high efficiency through a water bridge mediated proton shuttle.
Recently, a new branch of fatty acid metabolism has been opened by the novel phosphatase activity found in the N-terminal domain of the, hence bifunctional, soluble epoxide hydrolase (sEH). Importantly, this finding has also provided a new site for drug targeting in sEH's activity regulation. Classical MD and hybrid Car-Parrinello QM/MM calculations have been performed to investigate the reaction mechanism of the phosphoenzyme intermediate formation in the first step of the catalysis. The results support a concerted multi-event reaction mechanism: (1) a dissociative in-line nucleophilic substitution for the phosphoryl transfer reaction; (2) a double proton transfer involved in the formation of a good leaving group in the transition state. The presence of a water bridge in the substrate/enzyme complex allowed an efficient proton shuttle, showing its key role in speeding up the catalysis. The calculated free energy of the favored catalytic pathway is approximately 19 kcal/mol, in excellent agreement with experimental data.
De Vivo
Marco
M
Center for Molecular Modeling, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, USA. mdevivo@cmm.upenn.edu
Ensing
Bernd
B
Klein
Michael L
ML
D000818:Animals; D002384:Catalysis; D019295:Computational Biology; D003198:Computer Simulation; D004851:Epoxide Hydrolases / Q000737:chemistry*; D008958:Models, Molecular; D010744:Phosphoric Monoester Hydrolases / Q000737:chemistry*; D011522:Protons; D014867:Water / Q000737:chemistry
D011522:Protons; D014867:Water; D010744:Phosphoric Monoester Hydrolases; D004851:Epoxide Hydrolases