Recognition Highlights and Commentaries A tale in molecular recognition : the hammerhead ribozyme

Ribozymes are catalytically active RNA molecules. In the early 1980s, the discovery of catalytic activity in RNA molecules (Grabowski et al., 1981; Guerrier-Takada et al., 1983) led to a change in paradigm in molecular biology that is still ongoing. A couple of years later, small self-cleaving RNAs were discovered in viroids and satellite RNAs of plant viruses (Buzayan et al., 1986; Forster and Symons, 1987). The hammerhead ribozyme belongs to those small nucleolytic ribozymes. The hammerhead ribozyme is characterized by a minimal catalytic core consisting of a three-way junction containing some 15 invariant nucleotides (Haseloff and Gerlach, 1989; Symons, 1997; Figure 1). The basic proton transfer steps (Slim and Gait, 1991; Uhlenbeck, 1987) necessary for chain cleavage were soon established (Figure 2). The small size and the well-identified conserved elements of the hammerhead ribozyme led to a flurry of chemical and biophysical studies that attempted to understand the structure–function relationships of the molecule (Hammann and Lilley, 2002; Wedekind and McKay, 1998). New chemical and biophysical techniques were devised or extended to study RNA molecules. A model of the hammerhead architecture with two co-axially stacked helices and a third helix at an angle was deduced from fluorescence data (Tuschl et al., 1994). Following the first crystal structures (Pley et al., 1994; Scott et al., 1995) which showed the proper orientation of helix I and displayed the non-Watson–Crick base pairs involving the conserved residues (Figure 3 right), further kinetic and chemical studies were performed. However, it was soon realized that it was extremely difficult to reconcile all the data obtained by various laboratories around the world (McKay, 1996; Scott, 1999). Although single molecule studies (Lilley, 2005) and elegant kinetic experiments using modified ribozymes (Wang et al., 1999) underscored the importance of molecular dynamics and the ensuing conformational changes, no definite molecular mechanisms emerged from these studies. In the August issue of Cell, Martick and Scott (2006) reported on the much awaited structure of the hammerhead ribozyme close to the transition state. The structure solves so many riddles and controversies about the catalytic mechanism of the hammerhead ribozyme that this paper is destined to become a classic for many years to come. The main architecture of the hammerhead fold is preserved, but a couple of key changes in torsion angles lead to a pretransition state (Figure 3 left), in complete agreement with all accumulated data and the known chemistry of phosphodiester cleavage. Three years earlier, a major insight had been achieved when it became clear that not much catalytic activity remained when the hammerhead ribozyme was reduced to its core of conserved residues maintained by the helices of the three-way junction (De La Pena et al., 2003; Khvorova et al., 2003; Uhlenbeck, 2003). This showed that the naturally occurring peripheral elements JOURNAL OF MOLECULAR RECOGNITION J. Mol. Recognit. 2007; 20: 1–3 Published online 6 November 2006 in Wiley InterScience (www.interscience.wiley.com) DOI:10.1002/jmr.806