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Solvent structure and hammerhead ribozyme catalysis.

Monika Martick1, Tai-Sung Lee, Darrin M York

  • 1Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.

Chemistry & Biology
|April 19, 2008
PubMed
Summary
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This study clarifies the roles of metal ions and water in hammerhead ribozyme catalysis. A manganese ion and a specific water molecule facilitate proton transfer for RNA cleavage.

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Structural Biology

Background:

  • The hammerhead ribozyme is a key model for RNA catalysis.
  • The precise roles of metal ions and water in its cleavage mechanism are debated.

Purpose of the Study:

  • To investigate the catalytic functions of metal ions and water molecules bound to the hammerhead ribozyme.
  • To elucidate the mechanism of RNA cleavage.

Main Methods:

  • X-ray crystallography of a full-length hammerhead ribozyme structure (2 Å resolution).
  • Molecular dynamics simulations.
  • Analysis of metal ion and water molecule interactions within the active site.

Main Results:

  • A single manganese ion (Mn2+) directly binds to the A9 phosphate in the active site.

Related Experiment Videos

  • A well-ordered water molecule forms a hydrogen-bond network connecting G12 (general base) and G8 (general acid).
  • This network is proposed to facilitate proton transfer during RNA cleavage.

    • Conclusions:

    • The identified manganese ion and water molecule play crucial roles in the hammerhead ribozyme's catalytic mechanism.
    • The findings support a proton transfer mechanism facilitated by a specific active site water molecule and metal ion coordination.