Molecular modelling of xylose isomerase catalysis: The role of electrostatics and charge transfer to metals

The two main steps of the mechanism of xylose-xylulose conversion catalysed by D-xylose isomerase, the ring opening of xylose and the isomerization of the opened product by hydride transfer, were investigated by molecular mechanical and molecular orbital techniques. The activation energies calculated for these reactions clearly showed that hydrogen transfer is the rate-determining step of the enzymatic isomerization and that Mg2+ ions activate whereas Zn2+ ions inhibit the reaction, in agreement with the experiments. The remarkable differences between the net charges of these ions found by molecular orbital calculations and the inspection of the protein electrostatic potential around the reaction intermediates indicate that the main role of bivalent metal ions should be the electrostatic stabilization of the substrate transition states. In order to propose a more detailed mechanism, an attempt was made to clarify the effects of nearby residues (e.g. His54, Asp57, Lys183, Asp257) in the reaction. Different isomerization mechanisms, such as through an enediol intermediate, were examined and could be excluded, in addition to the charge-relay mechanism during the ring opening.