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Structure. 2017 Jan 3;25(1):195-202. doi: 10.1016/j.str.2016.11.020. Epub 2016 Dec 22.

Structural Basis for Ligand Binding to the Guanidine-I Riboswitch.

Author information

1
Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA; Chemical Biology Institute, Yale University, West Haven, CT 06516, USA.
2
Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA.
3
Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA; Chemical Biology Institute, Yale University, West Haven, CT 06516, USA. Electronic address: scott.strobel@yale.edu.

Abstract

The guanidine-I riboswitch is a conserved RNA element with approximately 2,000 known examples across four phyla of bacteria. It exists upstream of nitrogen metabolism and multidrug resistance transporter genes and alters expression through the specific recognition of a free guanidinium cation. Here we report the structure of a guanidine riboswitch aptamer from Sulfobacillus acidophilus at 2.7 Å resolution. Helices P1, P1a, P1b, and P2 form a coaxial stack that acts as a scaffold for ligand binding. A previously unidentified P3 helix docks into P1a to form the guanidinium binding pocket, which is completely enclosed. Every functional group of the ligand is recognized through hydrogen bonding to guanine bases and phosphate oxygens. Guanidinium binding is further stabilized through cation-π interactions with guanine bases. This allows the riboswitch to recognize guanidinium while excluding other bacterial metabolites with a guanidino group, including the amino acid arginine.

KEYWORDS:

RNA; X-ray crystallography; bacteria; cation-pi; guanidine; riboswitch; ykkC

PMID:
28017522
PMCID:
PMC5317007
DOI:
10.1016/j.str.2016.11.020
[Indexed for MEDLINE]
Free PMC Article

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