Ribozyme's Kick Is In Its Fold

Folding a ribozyme into a three-dimensional structure can adjust the reactivity of the RNA catalyst's nucleotide bases, a study shows (J. Am. Chem. Soc., DOI: 10.1021/ja9060883). Protein enzymes commonly employ contacts within a folded structure to control reactivity. But how RNA nucleobases contribute to ribozyme catalysis remains a point of contention. Paul R. Carey of Case Western Reserve University and Joseph E. Wedekind of the University of Rochester led an international team that examined this issue in the hairpin ribozyme. An adenosine is critical for the ribozyme's RNA-cleaving activity, although the exact role the base plays has been unclear. By applying the vibrational spectroscopy technique Raman crystallography to individual ribozyme crystals of known structure, the team distinguished between two possible situations. The researchers found that the crucial adenosine's acid dissociation constant is elevated by nearly two units in the folded ribozyme compared with adenosine monophosphate as a control molecule. This observation implies that the ribozyme's adenosine is protonated at physiological pH and acts as an acid during the cleavage, ruling out an alternative mechanism in which a coordinated water molecule serves as the acid.