Figure 4.

NMR investigations of PmrA_C–DNA complexes. (A) The regions of amide resonances and N_εH resonances of Arg side-chains (inset) of overlaid 2D ¹H, ¹⁵N TROSY-HSQC spectra for PmrA_C in the absence (black) or presence (red) of box1a DNA. The amide resonances in complex state are indicated. (B) Weighted chemical shift perturbations for backbone ¹⁵N and ¹H_N resonances as calculated by the equation Δδ = {[(Δδ_HN)²+(Δδ_N/5)²]/2}^0.5. The solid black bar represents the Δδ values for the box1a complex, green x for box1 and orange x for box1b. The black line indicates 0.33 ppm (the mean Δδ value of box1a complex plus 1 SD). (C) Structural mapping of chemical shift perturbations of the box1a complex. The residues with chemical shift perturbation >0.33 ppm are in red, <0.14 ppm (the mean Δδ value of the box1a complex) green and 0.14 to 0.33 ppm blue. The proline residues and the residues without data are in white. The top two most-perturbed residues, Gly²¹¹ and Glu¹⁹¹, are indicated. Side-chains of the three Arg residues are shown as magenta sticks with nitrogen atoms in blue. The DNA-binding site of PmrA_C consists of the α3 helix, the transactivation loop, the C-terminal β-hairpin and adjacent residues.