Tying the knot in the tetrahydrofolate (THF) riboswitch: A molecular basis for gene regulation

Conference: 2022: 72nd ACA Annual Meeting
Jason Stagno Poster Author
Center for Structural Biology, Center for Cancer Research, National Cancer Institute
Frederick, MD 
Haley Wilt Additional Author
Frederick, MD 
Ping Yu Additional Author
National Cancer Institute
Frederick, MD 
Kemin Tan Additional Author
Argonne National Laboratory
Argonne, IL 
Yun-Xing Wang Additional Author
Structural Biophysics Laboratory, National Cancer Institute
07/30/2022: 5:30 PM - 7:30 PM
Poster Session 
Portland Marriott Downtown Waterfront 
Room: Exhibit Hall 


Effective gene regulation by the THF riboswitch has shown dependencies on both ligand affinity and the kinetics of ligand association. Moreover, crystal structures of the aptamer in the ligand-bound conformation have revealed two ligand-binding sites. Knowledge of ligand-free aptamer conformations that are distinct from the ligand-bound form, therefore, can aid in determining the mechanism by which the absence or presence of ligand elicits conformational switching. We have determined a 1.9 Å-resolution crystal structure of the THF riboswitch aptamer domain in the absence of ligand that shows significant differences from previously reported apo and holo structures, particularly in the conformation of the P1 and P3 helices. The pseudoknot binding site 'unwinds' in the absence of ligand, causing rotation and misalignment of the gene-regulatory P1 helix with respect to P3. The second binding site, however, located at the three-way junction, is structurally conserved between apo and holo forms. This suggests cooperativity for the two binding sites, one which is preformed to elicit kinetic control, and the other which is directly involved in conformational switching through winding and unwinding of the pseudoknot.

Wilt, H.M. et al. Journal of Structural Biology 213 (2021) 107703. https://doi.org/10.1016/j.jsb.2021.107703