Figure 6.

Models of bridge helix and trigger loop mutant effects. Summary of the predicted positions of the bridge helix (green) and trigger loop base helices (dark blue). (a, c, e) The helices are shown as a schematic cross-section (top view, similar to Figure 1c) to indicate their locations relative to each other. The DNA template strand is shown in light blue and the newly synthesized transcript in red. The amino acids specifically labeled refer to M. jannaschii positions in the A' (Q823, S824) and A'' (I98 and G72) subunits, respectively. The position of the catalytic site is represented by the 'Metal A' ion as a magenta dot. (b, d, f) Schematic side views of the bridge helix (similar to Figures 1a, d) to illustrate the proposed equilibrium distribution between straight and kinked conformations in the wild-type and mutant enzymes. (a, b) In the wild-type, the bridge helix and trigger loop base helices are typically in close contact (indicated by the gray dotted lines in (a)) and the bridge helix is predominantly found in the straight conformation (b). The contacts between the bridge helix and trigger loop stabilize the conformation of the trigger loop base helices. (c, d) In some of the bridge helix mutants, and nearly all the trigger loop mutants described here (TL_N-X72 and TL_C-X98), contacts between bridge helix and the trigger loop are diminished, although the bridge helix conformation is unaffected. (e, f) In certain bridge helix mutants (especially Q823D and S824P), the kinked bridge helix is mainly in the 'forward' position and is therefore not capable of maintaining effective contacts with the trigger loop base helices.