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Structural Basis for Ligand Binding to the Guanidine-I Riboswitch
Caroline W Reiss1, Yong Xiong2, Scott A Strobel1
1Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA; Chemical Biology Institute, Yale University, West Haven, CT 06516, USA.
Structure (London, England : 1993)
|December 27, 2016
Summary
The guanidine-I riboswitch, found in bacteria, binds guanidinium cations to regulate gene expression. Its structure reveals a unique binding pocket that precisely recognizes guanidinium, excluding similar molecules.
Area of Science:
- Structural Biology
- RNA Biology
- Bacterial Genetics
Background:
- The guanidine-I riboswitch is a conserved RNA element regulating nitrogen metabolism and multidrug resistance transporter genes in bacteria.
- It functions by specifically recognizing and binding a free guanidinium cation.
Purpose of the Study:
- To determine the high-resolution structure of a guanidine riboswitch aptamer.
- To elucidate the molecular mechanism of guanidinium recognition and binding.
Main Methods:
- X-ray crystallography was used to determine the aptamer structure at 2.7 Å resolution.
- Analysis of the bound ligand interactions within the RNA structure.
Main Results:
- A novel structural model reveals helices P1, P1a, P1b, and P2 forming a ligand-binding scaffold.
- An uncharacterized P3 helix docks into P1a, creating an enclosed guanidinium binding pocket.
- Specific hydrogen bonds and cation-π interactions with guanine bases and phosphate oxygens ensure selective guanidinium binding, excluding arginine.
Conclusions:
- The determined structure provides atomic-level insight into guanidinium-I riboswitch function.
- The unique binding pocket architecture explains the riboswitch's high specificity for guanidinium.
- This understanding can inform the design of novel regulatory elements or therapeutic agents.
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