Escherichia coli dimethylallyl diphosphate:tRNA dimethylallyltransferase: pre-steady-state kinetic studies

Abstract

Escherichia coli dimethylallyl diphosphate:tRNA dimethylallyltransferase (DMAPP-tRNA transferase) catalyzes the first step in the biosynthesis of the hypermodified A37 residue in tRNAs that read codons beginning with uridine. The mechanism of the enzyme-catalyzed reaction was studied by isotope trapping, pre-steady-state rapid quench, and single turnover experiments. Isotope trapping indicated that the enzyme·tRNA complex is catalytically competent, whereas the enzyme·DMAPP complex is not. The results are consistent with an ordered sequential mechanism for substrate binding where tRNA binds first. The association and dissociation rate constants for the enzyme·tRNA binary complex are 1.15±0.33×10 7 M −1 s −1 and 0.06±0.01 s −1, respectively. Addition of DMAPP gives an enzyme·tRNA·DMAPP ternary complex in rapid equilibrium with the binary complex and DMAPP. Rapid quench studies yielded a linear profile ( k cat=0.36±0.01 s −1) with no evidence for buildup of enzyme-bound product. Product release from DMAPP-tRNA transferase is therefore not rate-limiting. The Michaelis constant for tRNA and the equilibrium dissociation constant for DMAPP calculated from the individual rate constants determined here are consistent with values obtained from a steady-state kinetic analysis.