THE REACTION PATHWAY OF THE ISOMERIZATION OF D-XYLOSE CATALYZED BY THE ENZYME D-XYLOSE ISOMERASE - A THEORETICAL-STUDY

Different pathways of the metal-induced isomerization of D-xylose to D -xylulose are investigated and compared in detail using energy minimiz ation and molecular dynamics simulation. Two theoretical models are co nstructed for the reaction: in vacuum and in the enzyme D-xylose isome rase, The vacuum model is constructed based on the X-ray structure of the active site of D-xylose isomerase, It contains the atoms directly involved in the reaction and is studied using a semi-empirical molecul ar orbital method (PM3), The model in the enzyme includes the effects of the enzyme environment on the reaction using a combined quantum mec hanical and molecular mechanical potential For both models, the struct ures of the reactants, products, and intermediate complexes along the isomerization pathway are optimized, The effects of the position of th e ''catalytic Mg2+ ion'' on the energies of the reactions are studied. The results indicate: 1) in vacuum, the isomerization reaction is fav ored when the catalytic metal cation is at site A, which is remote fro m the substrate; 2) in the enzyme, the catalytic metal cation, startin g from site A, moves and stays at site B, which is close to the substr ate; analysis of the charge redistribution of the active site during t he catalytic process shows that the metal ion acts as a Lewis acid to polarize the substrate and catalyze the hydride shift; these results a re consistent with previous experimental observations; and 3) Lys183 p lays an important role in the isomerization reaction, The epsilon-NH3 group of its side chain can provide a proton to the carboxide ion of the substrate to form a hydroxyl group after the hydride shift step, T his role of Lys183 has not been suggested before, Based on our calcula tions, we believe that this is a reasonable mechanism and consistent w ith site-directed mutation experiments. (C) 1997 Wiley-Liss, Inc.