Fig. 8.

Local-to-global signal transduction pathway in the core of the Xory Mn²⁺ sensing riboswitch. The Xory riboswitch exists in an “X-shaped” extended SU conformation in the absence of Mg²⁺, with very rare transitions into docked “H-shaped” conformations. In the SU state, the legs are far apart in the absence of a stable A-minor tertiary interaction and loops L3 and L1 are less structured under these conditions. In the presence of physiological Mg²⁺ concentrations (mM), the riboswitch samples docked conformations with distinct kinetics, indicative of differences in L3 stacking as observed in our crystal structures. L1 adopts an S-turn conformation (as indicated by the yellow box in the inset) and L3 is partially stacked under these conditions, aided by the presence of Mg²⁺ ions in M_A,Mg and transiently in M_B,Mn. In the presence of sufficient Mn²⁺, binding of the metal ion by A48 reinforces L3 stacking and stability of the A-minor interaction. This maintains L1 in a rigid noncanonical SRL-like conformation that enables co-axial stacking between P1.2 and the switch helix P1.1. In turn, this cascade of interactions stabilizes P1.1, thereby preventing strand invasion to favor formation of the antiterminator required for transcriptional read-through