Figure 5.

Conformational differences between the apo and two drug-bound structures of LmrR. (A) Superposition (in ribbon representation) of the apo–LmrR subunit structure (yellow) and the subunit structures of H33342-bound (green) and daunomycin-bound LmrR (salmon). The superposition was carried out using the Cα atoms of the wHTH domain. (B) Superposition of the three LmrR dimers, showing the difference in relative position of the two wHTH domains. Only one of the two subunits (light colors) was used for the superposition (identical to the superposition in Figure 5A). The range of distances between the two DNA recognition helices in the different dimers, and the largest rotational shift of the wHTH domains (based on comparing the H33342- and daunomycin-bound dimers) are indicated. (C) The same superposition as in Figure 5B, but from a different view, showing the relative shifts of helix pair α1–α4′ with respect to helix pair α1′–α4. H33342 (green) and daunomycin (salmon), as well as the W96/W96′ tryptophan pair, are also shown in sticks. The amino sugar moiety of daunomycin is shown in a solvent-exposed position at the front entrance of the pore, but it should be noted that its binding is highly disordered, as evident from the weak electron density associated with this substituent.