Structural basis for ligand binding to the guanidine-II riboswitch

Area of Science:

• Molecular Biology
• Biochemistry
• Structural Biology

Background:

• The guanidine-II riboswitch (mini-ykkC) is a conserved bacterial mRNA regulatory element.
• It controls guanidine carboxylase and SugE-like gene expression.
• This riboswitch acts as a translationally controlled on-switch for guanidinium cations.

Purpose of the Study:

• To determine the high-resolution structure of the guanidine-II riboswitch aptamer.
• To elucidate the molecular mechanisms of guanidinium cation binding.
• To compare the structural strategies of guanidine-II with guanidine-I riboswitches.

Main Methods:

• X-ray crystallography at 1.57 Å resolution.
• Structural analysis of the P2 stem-loop from *Pseudomonas aeruginosa* guanidine-II riboswitch aptamer.
• Detailed examination of ligand-RNA interactions.

Main Results:

• The P2 stem-loop forms a dimer through conserved tetraloops, which harbor the guanidinium binding pocket.
• Two guanidinium molecules bind at the dimerization interface, one in each tetraloop.
• Extensive hydrogen bonding (including Hoogsteen face of guanine), cation-π, and ionic interactions stabilize guanidinium binding.

Conclusions:

• The guanidine-II riboswitch employs a compact RNA fold distinct from guanidine-I riboswitches.
• It utilizes similar guanidinium recognition strategies as the guanidine-I riboswitch.
• The structure provides insights into the precise molecular interactions governing riboswitch-mediated gene regulation.