Functional groups on the cleavage site pyrimidine nucleotide are required for stabilization of the hammerhead transition state

Narayan Baidya, Glenyss E. Ammons, Jasenka Matulic-Adamic, Alexander M. Karpeisky, Leonid Beigelman, Olke C. Uhlenbeck*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

17 Scopus citations

Abstract

The role of individual functional groups on cytidine 17 in the hammerhead ribozyme was assessed by introducing modified pyrimidines into two kinetically well-characterized hammerheads. As long as the pyrimide ring size was maintained, the modifications had no effect on substrate binding, suggesting that the C17-C3 hydrogen bond observed in the X-ray structure is energetically neutral. However, modification of the exocyclic amino group and the cerbonyl of C17 reduced the cleavage rate significantly, indicating that these groups are important in stabilizing the transition-state structure. C17 modifications did not affect the ratio of the forward and reverse reaction rates. Thus, unlike that believed previously, C17 is another one of many hammerhead residues critical in maintaining iIts active structure.

Original languageEnglish (US)
Pages (from-to)1135-1142
Number of pages8
JournalRNA
Volume3
Issue number10
StatePublished - Oct 1997

Keywords

  • Catalytic RNA
  • Ribozyme
  • Structure-function

ASJC Scopus subject areas

  • Molecular Biology

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