Fig. 4.

FMN stabilizes helix P1 by inducing coaxial alignment with helix P6. (A-C) Cartoon depicting the P1 and P6 helices as observed in (A) apo-6WJR (cyan), (B) holo-3F2Q (magenta), and (C) apo-2YIF (gray). The orientation relative to Fig. 3 is ~180° around the vertical axis. Approximate helical axes (depicted as dotted lines) for P1 and P6 are aligned in holo-3F2Q (B) and apo-2YIF (C), and misaligned in apo-6WJR (A). (D-F) Expanded view of the P1/P6 helical junction in (A), (B), and (C), respectively, whose area is indicated by the black box in (A). (D) The absence of FMN in apo-6WJR creates a gap and kink between the P1 and P6 helices. Junction residues, A48, A49, and A104 reorient to propagate stacking between P3 and P4 helices, resulting in the partial instability of P1. (E) In the presence of ligand, the continuity and alignment of P1 and P6 is facilitated by the isoalloxazine ring of FMN (yellow ball-and-stick) through base-stacking with A85 and A48, thereby stabilizing P1. (F) In apo-2YIF, A48, A49, and A104 exhibit changes similar to those in apo-6WJR. However, the alignment of P1 and P6 is reminiscent of a bound-like conformation.