Figure 5: Conformational changes in VcFadR upon DNA binding.

(a) Superposition of the VcFadR–DNA complex and apo-VcFadR shown in two orientations (along and perpendicular to the pseudo twofold axis). The two primary regions that are altered upon DNA binding are shown in colour (green, VcFadR–DNA complex; magenta, apo-VcFadR) and the rest of the protein is white. The tip of the wing (H65) in each DNA wHTH-binding domain is shifted by up to 5 Å between the two structures and the distance between the two DNA recognition helices (R45 at the beginning of helix α3) is wider in apo-VcFadR structure (17 Å) compared with that in the VcFadR–DNA complex (15 Å). (b) Detailed view of the interaction between the insertion region and the wing of wHTH in the absence of the DNA. The N-terminal DNA-binding domain is pale cyan. The region that undergoes a helix-to-loop transition upon DNA binding (helices αI1, αI2 and the C-terminal end of α6 in apo-VcFadR) is magenta and the rest of the 40-residue insertion region is yellow. Residues that are positively charged are blue and those that are negatively charged are red. Helices and residues from chain B are distinguished by a prime. (c) Same view as in b but in the presence of DNA. The colours are the same as in b.