Nucleoside-diphosphate kinase: Structural and kinetic analysis of reaction pathway and phosphohistidine intermediate

This chapter describes the structural and kinetic analysis of reaction pathway and phosphohistidine intermediate. The structural studies of enzymes have made major contributions to understanding of catalytic mechanisms. Unstable chemical species—such as a Michaelis complex or a covalent intermediate—that form and vanish on the millisecond to second time scale, and the even more elusive transition state that lives a few femto- or picoseconds, may be made accessible to study. In practice, their impact has been marginal and much more structural information on enzyme catalysis has come from experiments, where the time scale of the chemistry has been changed to that of crystallography rather than the converse. There are many ways to slow enzymatic catalysis: by low temperature trapping, by removing catalytic groups through site-directed mutagenesis of the protein or chemical modification of the substrate, by replacing substrates with unreactive analogs of either the ground state or the transition state.