The hairpin ribozyme is one of four known natural catalytic RNAs that carry out sequence-specific cleavage of RNA. It is of particular biochemical interest because, unlike ‘classic’ ribozymes, such as the group I intron, it appears not to employ metal ions as catalytic cofactors. We have determined the crystal structure of a hairpin-ribozyme-inhibitor complex at a resolution of 2.4 Å. The active site of the ribozyme results from docking of two irregular double helices. Docking results in major structural rearrangements of the helices, including a distortion of the substrate strand that brings it into a reactive conformation. It remains to be established whether this RNA enzyme relies exclusively on binding energy to carry out catalysis, or whether some other mechanism, such as general acid-base catalysis, is being employed.

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