RNA recognition by minimal ProQ from Neisseria meningitidis

3′-terminal uridine is specifically recognized through the ribose 2′- and 3′-OH groups when RNA is bound by the N. meningitidis ProQ protein. (A) The fitting of the ProQ binding data using the quadratic equation provided K_d values of 0.6 nM for rpmG-35, while the binding of rpmG-dU, rpmG-P, and rpmG-C did not reach saturation up to 50 nM concentration of the ProQ. The binding of rpmG-ddC was essentially undetectable up to 50 nM concentration of the ProQ. (B) The fitting of the ProQ binding data using the quadratic equation provided K_d values of 4.5 nM for AniS-37 and 10.5 nM for AniS-C, while the binding for AniS-dU, AniS-P, and AniS-ddC was essentially undetectable up to 50 nM concentration of the ProQ. The data in the plots for rpmG-35 and AniS-37 binding to ProQ are the same as in Figure 3. Gels corresponding to the data in the plots are shown in Supplemental Figure S10. The average equilibrium dissociation constant (K_d) values and maximum RNA fraction bound calculated from at least three independent experiments are shown in Table 5.