Structural determinants for ligand capture by a class II preQ1 riboswitch

Area of Science:

• Molecular Biology
• Structural Biology
• RNA Biology

Background:

• Prequeuosine (preQ1) riboswitches regulate the biosynthesis of queuosine, a vital modified base in tRNAs.
• The preQ1 class II (preQ1-II) riboswitch controls preQ1 biosynthesis at the translational level.

Purpose of the Study:

• To determine the solution NMR structure and conformational dynamics of the Streptococcus pneumoniae preQ1-II riboswitch bound to preQ1.
• To elucidate the mechanism of preQ1 binding and regulation by the preQ1-II riboswitch.

Main Methods:

• Solution Nuclear Magnetic Resonance (NMR) spectroscopy
• 13C relaxation experiments
• Residual dipolar coupling experiments

Main Results:

• The 59-nucleotide preQ1-II riboswitch forms an unusual H-type pseudoknot structure requiring divalent cations for high-affinity preQ1 binding.
• A P4 hairpin embedded within loop 3 plays a critical role in pseudoknot formation and sequestering the Shine-Dalgarno sequence.
• The P4 helix acts as a "screw cap" to stabilize the preQ1 binding pocket and prevent ligand dissociation.

Conclusions:

• The preQ1-II riboswitch employs a unique mechanism involving a cation-dependent H-type pseudoknot and a P4 helix for precise regulation of queuosine metabolism.
• Structural and dynamic insights reveal distinct preQ1 recognition strategies compared to the preQ1 class I riboswitch.