Direct measurement of a pK_a near neutrality for the catalytic cytosine in the genomic HDV ribozyme using raman crystallography

The hepatitis delta virus (HDV) ribozyme uses a cytosine to facilitate general acid-base catalysis. Biochemical studies suggest that C75 has a pK _a perturbed to near neutrality. To measure this pK_a directly, Raman spectra were recorded on single ribozyme crystals using a Raman microscope. A spectral feature arising from a single neutral cytosine was identified at 1528 cm^-1. At low pH, this mode was replaced with a new spectral feature. Monitoring these features as a function of pH revealed pK_a values for the cytosine that couple anticooperatively with Mg²⁺ binding, with values of 6.15 and 6.40 in the presence of 20 and 2 mM Mg²⁺, respectively. These pK_a values agree well with those obtained from ribozyme activity experiments in solution. To correlate the observed pK_a with a specific nucleotide, crystals of C75U, which is catalytically inactive, were examined. The Raman difference spectra show that this mutation does not affect the conformation of the ribozyme. However, crystals of C75U did not produce a signal from a protonatable cytosine, providing strong evidence that protonation of C75 is being monitored in the wild-type ribozyme. These studies provide the first direct physical measurement of a pK_a near neutrality for a catalytic residue in a ribozyme and show that ribozymes, like their protein enzyme counterparts, can optimize the pK_a of their side chains for proton transfer.