The structure of the Guanidine-III Riboswitch

Lin Huang, Jia Wang, Timothy J. Wilson, David M. J. Lilley (Lead / Corresponding author)

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Abstract

We have determined high resolution crystal structures of the ykkC guanidine III riboswitch from Thermobifida fusca. The riboswitch forms a classic H-type pseudoknot, in which a connecting strand locates in the major groove of one duplex to form a triple helix. This is continuous with a central core of conserved nucleotides forming a left handed helical ramp of internucleotide interactions that generates the guanidinium cation binding site. The ligand is hydrogen bonded to O6 and N7 of two guanine nucleobases, and to the 2'OH of a cytidine, the nucleobase of which stacks with the guanidinium in a π-cation interaction. The binding pocket has a side opening through which a small side chain can pass, and we have determined structures with bound methylguanidine, aminoguanidine, ethylguanidine and agmatine. Comparison of this structure with those of the guanidine I and II riboswitches reveals common aspects and contrasts.
Original languageEnglish
Pages (from-to)1407-1415.e2
Number of pages12
JournalCell Chemical Biology
Volume24
Issue number11
Early online date5 Oct 2017
DOIs
Publication statusPublished - 16 Nov 2017

Keywords

  • Gene regulation
  • RNA structure
  • X-ray crystallography
  • riboregulation

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