Tetrahydrofolate
Tetrahydrofolate riboswitches: PDB ID,
The THF riboswitch is found mainly in Firmicutes and specifically binds reduced folates (dihydrofolate and various forms of tetrahydrofolate). We solved the biologically relevant form of the aptamer, which surprisingly showed TWO ligand binding sites. The first in a three-way junction and the second is in a pseudoknot.
The binding pockets for each of the two sites is remarkably similar, despite being embedded in two different structural contexts.
In both cases, the RNA primarily recognizes the pterin moiety using a set of conserved pyrimidine residues. The p-aminobenzoic acid (PABA) moiety interacts with the RNA through stacking interactions, while the glutamyl moiety is disordered in the crystals (and thus not built).
Both sites are not equal with regards to their affect upon regulatory activity. Using an in vitro transcription approach, it is clear that the psuedoknot site is more important than the three-way junction site.
Therefore, we conclude that the pseudoknot site is the primary site required for activity and that the three way junction site serves a supporting role.