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The structure-function dilemma of the hammerhead ribozyme.

Kenneth F Blount1, Olke C Uhlenbeck

  • 1Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0358, USA. kblount@ucsd.edu

Annual Review of Biophysics and Biomolecular Structure
|May 5, 2005
PubMed
Summary

Investigating the hammerhead ribozyme reveals inconsistencies between its structure and function. This suggests a significant conformational change is necessary for RNA enzyme catalysis.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • RNA catalysis

Background:

  • Understanding enzyme catalysis often involves examining essential amino acid side chains in proteins.
  • RNA enzymes (ribozymes) offer unique opportunities due to modified nucleotides, but the hammerhead ribozyme presents a structural and functional data anomaly.
  • Previous studies confirm the utility of structure-function analysis for ribozyme function.

Purpose of the Study:

  • To reconcile discrepancies between structural and functional data for the hammerhead ribozyme.
  • To establish a unifying view of the hammerhead ribozyme's catalytic mechanism.
  • To identify key functional groups essential for hammerhead ribozyme catalysis.

Main Methods:

  • Distilled extensive biochemical data into a consensus set of essential functional groups.

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  • Examined the structural context of these functional groups in available hammerhead ribozyme structures.
  • Compared and contrasted structural data with functional requirements.

    • Main Results:

    • Identified a concise set of disagreements between hammerhead ribozyme structural and functional data.
    • Observed inconsistencies distributed throughout the ribozyme structure.
    • These findings indicate a necessary conformational rearrangement for catalysis.

    Conclusions:

    • The hammerhead ribozyme undergoes an extensive conformational rearrangement for cleavage.
    • Crystal structure folds do not fully represent the active catalytic state.
    • The nature and energetic driving force of this conformational isomerization are critical for catalysis.