FIGURE 3.

Interactions between the OmpR DNA binding domain and two DNA sites. A, OmpR_C in the presence of an SsrB DNA-binding site (green, 1:2 ratio of OmpR_C to DNA). The label identifying Gln²²³ is above the black spectrum; it is completely shifted in the presence of SsrB DNA. B, OmpR_C in the presence of the OmpR DNA half-site C1b (red, 1:2 ratio of OmpR_C to DNA). The HSQC spectrum in black is the spectrum of the DNA-free OmpR_C. The spectra were acquired at 35 °C, and in 25 mm phosphate buffer, pH 6.5. The data indicate that the chemical shift perturbation is greater when the C1 site is used, and that the monomeric OmpR DNA binding domain can form a stable complex with a strong OmpR half-site. The perturbed residues that are well resolved in each spectrum are labeled, and the arrows trace the positions of the perturbed residues. C, summary of the chemical shift changes observed with OmpR_C in the presence of a C1b site. The vertical axis corresponds to average chemical variations measured on the spectra of the DNA-free OmpR_C and the OmpR_C-C1b DNA complex. The amino acid residue number is listed on the x axis and the secondary structure element is at the top of the graph, where S signifies a β-strand and α is α-helix. D, OmpR_C in the presence of the DNA half-site C1a overlaid with the spectrum of OmpR_C in the presence of the DNA half-site C1b at a 1:2 ratio of OmpR_C to DNA (red, C1b site; black, C1a site).