Figure 1: Regulatory cascade and structure of RamR.

(a) Model for gene regulation by RamR. RamR represses the ramA gene, which encodes the activator protein for the acrAB drug efflux pump genes. RamR binds to the intergenic region between the ramR and ramA genes, and RamA binds to the upstream region to acrAB. (b) Crystal structure of the RamR dimer. Each monomer is coloured as follows: the α-helices are represented in blue (α1), marine (α2), sky blue (α3), cyan (α4), green (α5), limon (α6), yellow (α7a), deep olive (α7b), orange (α8a), brown (α8b) and red (α9). (c) Secondary structure elements and amino acid sequence of the RamR protomer. RamR composes of nine α-helices (α1–α9). Because α7 and α8 are tortuous, they are subdivided into regions denoted α7a, α7b, α8a and α8b based on the borders of this tortuosity. Each of α-helices are coloured according to the scheme used in b. (d) Structures of DNA-binding sites of QacR, CgmR and RamR. Helices α1, α2 and α3 of QacR (amino acids 1–42) are represented in green, of CgmR (2–43) in blue and of RamR (2–42) in red. (e) Structures of the C-termini of TetR family regulators. Structures of helices α5, α6 and α7 of QacR (amino acids 73–130) are represented in green, of CgmR (75–122) in blue and of RamR (73–130) in red. Because α7 of RamR is tortuous, its shape is different from those of QacR and CgmR.