Chemical Rescue of Phosphoryl Transfer in a Cavity Mutant:  A Cautionary Tale for Site-Directed Mutagenesis^,

Abstract

We have explored the ability of a nucleoside diphosphate kinase (NDPK) mutant in which the nucleophilic histidine has been replaced by glycine (H122G) to transfer phosphate from ATP to alcohols of varying pK a , size, shape, and polarity. This cavity mutant does indeed act as a primitive alcohol kinase. The rate of its phosphoryl transfer to alcohols varies considerably, with values spanning a ∆∆G ‡ range of 4 kcal/mol, whereas the alcohols have very similar intrinsic reactivities. Analysis of these results suggests that the ability to carry out phosphoryl transfer within the cavity is not a simple function of being small enough to enter the cavity, but rather is a complex function of steric, solvation, entropic, van der Waals packing, and electrostatic properties of the alcohol. In addition, large differences are observed between the reactivities of alcohols within the nucleophile cavity of H122G and the reactivities of the same alcohols within the nucleophile cavity of H122A, a mutant NDPK that differs from H122G by a single methyl group within the cavity. The crystal structures of the two cavity mutants are very similar to one another and to wild-type NDPK, providing no evidence for a structurally perturbed active site. The differences in reactivity between the two mutant proteins illustrate a fundamental limitation of energetic analysis from site-directed mutagenesis: although removal of a side chain is generally considered to be a conservative change, the energetic effects of any given mutation are inextricably linked to the molecular properties of the created cavity and the surrounding protein environment.Previous studies of small molecule rescue of either the reactivity or stability of cavity mutants have provided insights into protein energetics. Mutagenesis of the lysine general base of aspartate aminotransferase to an alanine allowed Toney and Kirsch to investigate the ability of exogenous amines to restore catalytic activity to this cavity mutant (7). Matthews and co-workers demonstrated that a variety of small, mainly nonpolar ligands stabilize a cavity mutant of T4 lysozyme (8-10). In both studies, the authors obtained an energetic picture of the primarily hydrophobic cavities that were investigated by varying the small molecule that occupied those cavities. These earlier results suggested that a systematic study of rescue in a more complex cavity that is accessible to solvent and bordered by charged residues could provide information about the energetic features of protein crevices such as those often present at active sites.We have explored the energetic features of such a protein cavity using H122G, a site-directed mutant of nucleoside diphosphate kinase (NDPK) 1 in which the nucleophilic histidine has been replaced by a glycine. Wild-type NDPK interconverts NTPs and NDPs by catalyzing successive phosphoryl transfers, first transferring a phosphoryl group from an NTP to histidine 122 to form a phosphorylated enzyme and an NDP, then catalyzing a second transfer between the phosphorylated...

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