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Cell Chem Biol. 2017 Nov 16;24(11):1407-1415.e2. doi: 10.1016/j.chembiol.2017.08.021. Epub 2017 Oct 5.

Structure of the Guanidine III Riboswitch.

Author information

1
Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK.
2
Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK. Electronic address: d.m.j.lilley@dundee.ac.uk.

Abstract

Riboswitches are structural elements found in mRNA molecules that couple small-molecule binding to regulation of gene expression, usually by controlling transcription or translation. We have determined high-resolution crystal structures of the ykkC guanidine III riboswitch from Thermobifida fusca. The riboswitch forms a classic H-type pseudoknot that includes a triple helix that is continuous with a central core of conserved nucleotides. These form a left-handed helical ramp of inter-nucleotide interactions, generating the guanidinium cation binding site. The ligand is hydrogen bonded to the Hoogsteen edges of two guanine bases. The binding pocket has a side opening that can accommodate a small side chain, shown by structures with bound methylguanidine, aminoguanidine, ethylguanidine, and agmatine. Comparison of the new structure with those of the guanidine I and II riboswitches reveals that evolution generated three different structural solutions for guanidine binding and subsequent gene regulation, although with some common elements.

KEYWORDS:

RNA structure; X-ray crystallography; gene regulation; riboregulation

PMID:
28988949
PMCID:
PMC5696562
DOI:
10.1016/j.chembiol.2017.08.021
[Indexed for MEDLINE]
Free PMC Article

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