Ab initio determination of the structure of the active site of a metalloenzyme: Metal substitution in phosphotriesterase using density functional methods

A number of previous studies have determined that a metalloenzyme active site is inherently determined by the ligands and metal and only weakly perturbed by the surrounding protein environment. This conclusion is now being tested for several families of bimetallic enzymes. Metal substitution is examined for phosphotriesterase (PTE) with all possible substitutions of zinc and cadmium in the two sites. A new density functional theory (DFT) functional is used in this study which has yielded accurate structures and thermochemistry for molecules made up of first and second row atoms. Comparisons between gradient-optimized Hartree–Fock and DFT structures are in good agreement, suggesting this functional is useful in studying transition metal enzyme active sites. Good agreement between the X-ray and in vacuo optimized structures is also obtained for the Zn–Zn and Cd–Cd enzymes. This supports the analysis of the PTE active site as an inherent complex and suggests that accurate structures can be obtained for other metal substitutions for which no experimental structures are available. A unique zinc/cadmium hybrid was observed experimentally, and the structure of this active site is theoretically predicted. The polarization of bound water at this very polar active site is very large, suggesting it is the reactive nucleophile. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 75: 289–299, 1999