The crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage

Cell. 1995 Jun 30;81(7):991-1002. doi: 10.1016/s0092-8674(05)80004-2.


We have solved the crystal structure of an all-RNA hammerhead ribozyme having a single 2'-O-methyl cytosine incorporated at the active site to prevent cleavage. The conditions used differ from those in another recent solution in four significant ways: first, it is an all-RNA ribozyme rather than a DNA-RNA hybrid; second, the connectivity of the ribozyme backbone strands is different; third, the crystals were grown in the presence of a much lower concentration of salt; and fourth, the crystal packing scheme is very different. Nevertheless, the three-dimensional structure of the all-RNA hammerhead ribozyme is similar to the previous structure. Five potential Mg(II)-binding sites are identified, including one positioned near the ribozyme catalytic pocket. Upon this basis, as well as upon comparisons with the metal-binding sites in the structurally homologous uridine turn of tRNAPhe, we propose a mechanism for RNA catalytic cleavage.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Binding Sites
  • Catalysis
  • Crystallography, X-Ray
  • Cytidine / analogs & derivatives
  • DNA / chemistry
  • DNA / metabolism
  • Hydrogen Bonding
  • Magnesium / metabolism
  • Metals
  • Models, Molecular
  • Molecular Sequence Data
  • Nucleic Acid Conformation*
  • RNA / chemistry
  • RNA / metabolism
  • RNA, Catalytic / chemistry*
  • RNA, Catalytic / metabolism*
  • RNA, Transfer, Phe / chemistry
  • RNA, Transfer, Phe / metabolism


  • Metals
  • RNA, Catalytic
  • RNA, Transfer, Phe
  • 2'-O-methylcytidine
  • Cytidine
  • RNA
  • DNA
  • Magnesium