Figure 4.

Schemes illustrating the proposed mechanism for the ligand (nickel)-induced transcription factor (NikR) binding to DNA. (a) Simple, incorrect model for depicting the mechanism described for most ligand-binding transcription factors. (b) Alternate model for NikR−DNA binding indicating the importance of the high-affinity nickel ions in ordering the central α3 helices. (c) Expansion of the model shown in panel b, which considers the role that excess nickel ions may play in enhancing NikR’s affinity for DNA by binding NikR either before or after it has bound to DNA. The tetrameric metal binding domain is represented with a gray rectangle. The dimeric ribbon−helix−helix domains are represented as triangles. The DNA is represented as a ladder. Nickel ions are represented as black circles. Potassium ions are represented as gray circles. α3 helices are represented as ovals.