Spectroscopic demonstration of a linkage between the kinetics of NTP hydrolysis and the conformational state of the recA-single-stranded DNA complex

We recently constructed a mutant recA protein in which His-163 was replaced by a tryptophan residue; the [H163W]recA protein is functionally identical to the wild-type protein, and the Trp-163 side chain serves as a reporter group for the conformational transitions of the [H163W]recA-single- stranded DNA (ssDNA) complex. We have now examined the fluorescence properties of the [H163W]recA-ssDNA complex in the presence of a series of alternate nucleoside triphosphate cofactors. Under standard conditions (pH 7.5), ATP (S_0.5 = 70 μM) and purine riboside triphosphate (PTP) (S_0.5 = 110 μM) effect a 44% decrease in Trp-163 fluorescence and are active as cofactors for the DNA strand exchange reaction. In contrast, ITP (S_0.5 = 400 μM) elicits only a 20% decrease in Trp-163 fluorescence (a level identical to that observed with the nucleoside diphosphates ADP, PDP, and IDP) and is inactive as a strand exchange cofactor. If the S_0.5 (PTP) is increased to 130 μM (by increasing the pH of the reaction solution), the PTP-mediated quenching of Trp-163 fluorescence decreases to 20%, and PTP becomes inactive as a strand exchange cofactor. These results provide direct evidence for a linkage between the S_0.5 value of a nucleoside triphosphate and the conformational state of the recA-ssDNA complex, with an S_0.5 of 100-120 μM or lower required for stabilization of the strand exchange- active conformation.