Comparison of HapR with DNA-bound apo QacR and dequalinium-bound QacR. (A) SSM (27) produced superposition of DNA-bound apo QacR (PDB 1JT0, chain B) shown in cyan and dequalinium-bound QacR (1JT6:A) shown in green. For clarity, only helices α5, α6, and α7 (amino acids 76 to 136) and the DNA-binding domain (amino acids 2 to 4) are shown. Note that in the dequalinium-bound QacR structure, helix α5 is extended by a full turn, causing the DNA-binding domain to move in relation to helices α5 to α7, as indicated by the arrow. (B) Alignment of HapR, shown in orange, and QacR-dequalinium, shown in green, showing that helix α5 is extended in both of these structures to a similar degree and that the DNA-binding domains do not align. The pronounced kink in helix α7 of HapR is indicated. C, Alignment of HapR, in orange, and apo QacR-DNA, in cyan, showing the close alignment of the DNA-binding domains.