Quantum mechanical studies on the existence of a trigonal bipyramidal phosphorane intermediate in enzymatic phosphate ester hydrolysis

Phosphate ester hydrolysis is a key step in several enzymatic processes, which follow either a dissociative or an associative mechanism. While in the aqueous phase both pathways are favoured to about the same extent, the associative mechanism is relatively rarely observed. In this paper we report on quantum mechanical calculations for three enzymes HIV integrase, β-phosphoglucomutase and dUTPase, and try to find an explanation for the preference of the associative mechanism in a given enzyme. It is reasonable to suppose that the stabilisation of the pentacovalent, trigonal bipyramidal phosphorane moiety by formation of a covalent bond, one or more hydrogen bonds, or by co-ordination of a divalent metal cation with the equatorial oxygen atoms is the key factor. In all three enzymes studied one of the equatorial oxygen atoms is co-ordinated to a magnesium dication, while a second one is involved in a covalent bond. While in HIV integrase the third oxygen atom may only form a weak hydrogen bond with a solvent water molecule, in β-phosphoglucomutase this atom is stabilised by two strong hydrogen bonds with adjacent protein side chains and in dUTPase it is involved in a covalent bond. Contribution to the Fernando Bernardi Memorial Issue.