Figure 1

(a) Overview of one monomer of DntR with the seven residues that are replaced in this study marked in red, with the number of the residue next to it. Model (see Smirnova et al. [8]) of the DNA-binding domain (DBD) and linker connected to the structure of the inducer-binding domain (IBD) are shown as grey ribbons. The previously identified inducer-binding pocket is situated in the region between subdomains 1 (SD1) and 2 (SD2) and its position is encircled (see b). One monomer is packed with another monomer in a head-to-tail orientation so that the β-strands seen to the right under the inducer-binding pocket in SD2 forms a parallel β-sheet together with the β-strands seen to the upper left in SD1. (b) The inducer-binding pocket shown in detail, with the position of a salicylate (shown in yellow, oxygens marked in red) modelled based on the position of the acetate ion found in the crystal structure. The side-chains of all residues within 4Å of the modelled salicylate molecule are displayed (with oxygens in red and nitrogens in blue, the carbons of His 169 are marked in red). In this model, the hydroxyl group points away from His 169. The His169 residue is the only substituteded residue in this study within 5 Å from the modelled salicylate. Below the pictures, the differences in sequence for NtdR and NagR, compared to DntR, are indicated. In bold are the amino-acid residues in the DBD, while the other five amino-acid residue substitutions are found in the IBD.