Comparison of the Structures and Mechanisms of the Pistol and Hammerhead Ribozymes

Timothy J. Wilson, Yijin Liu, Nan-Sheng Li, Qing Dai, Joseph A. Piccirilli, David M. J. Lilley (Lead / Corresponding author)

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33 Citations (Scopus)
138 Downloads (Pure)


Comparison of the secondary and three-dimensional structures of the hammerhead and pistol ribozymes reveals many close similarities, so in this work we have asked if they are mechanistically identical. We have determined a new crystal structure of the pistol ribozyme and have shown that G40 acts as general base in the cleavage reaction. The conformation in the active site ensures an in-line attack of the O2′ nucleophile, and the conformation at the scissile phosphate and the position of the general base are closely similar to those in the hammerhead ribozyme. However, the two ribozymes differ in the nature of the general acid. 2′-Amino substitution experiments indicate that the general acid of the hammerhead ribozyme is the O2′ of G8, while that of the pistol ribozyme is a hydrated metal ion. The two ribozymes are related but mechanistically distinct.

Original languageEnglish
Pages (from-to)7865-7875
Number of pages11
JournalJournal of the American Chemical Society
Issue number19
Early online date24 Apr 2019
Publication statusPublished - 15 May 2019


  • RNA catalysis
  • general acid-base catalysis
  • metal ions
  • atomic mutagenesis
  • X-ray crystallography

ASJC Scopus subject areas

  • Chemistry(all)
  • Biochemistry
  • Catalysis
  • Colloid and Surface Chemistry


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