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.
