Solution structure of the loop B domain from the hairpin ribozyme

Nat Struct Biol. 1999 Mar;6(3):212-6. doi: 10.1038/6651.


The hairpin ribozyme is a small catalytic RNA with a unique two-domain structure. Here we present the solution structure of the loop B domain of the hairpin ribozyme, which contains most of the catalytically essential nucleotides. The 38-nucleotide domain contains a 16-nucleotide internal loop that forms one of the largest non-Watson-Crick segments of base pairing thus far determined by either NMR or crystallography. Since the solution structure of the smaller loop A domain has been previously solved, an NMR structure-based model of the 22,000 Mr hairpin ribozyme-substrate open complex emerges by joining the two domain structures. Strikingly, catalytically essential functional groups for the loop B domain are concentrated within an expanded minor groove, presenting a clear docking surface for the loop A domain.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Base Sequence
  • Crystallography, X-Ray
  • Hydrogen Bonding
  • Magnetic Resonance Spectroscopy
  • Nucleic Acid Conformation*
  • RNA, Catalytic / chemistry*


  • RNA, Catalytic

Associated data

  • PDB/1B36