The elucidation of high-resolution structures of RNA enzymes has fueled
discussion about the catalytic abilities of ribonucleotides, specifically
of the purine and pyrimidine bases. Because their pKa's lie outside the
physiological pH range, recent work has focused on whether the pKa's have
been shifted to enable the enzymes to function as general acid-base
catalysts. Three recent reports examine these issues.

Bayfield et al. examined the pH dependence of dimethylsulfate modification
of adenosine 2451 (A2451) in the 23S ribosomal RNA of the Escherichia coli
large ribosomal subunit. The differential reactivity of A2451, which had
been interpreted to reflect a shift of the pKa from very acidic values to
almost neutral pH, appears instead to be the result of a conformational
change due to the loss of a critical monovalent cation. Thompson et al.
explored the role of A2451 by making mutations at this position and
assessing protein synthesis activity in vivo and in vitro of ribosomes
containing these ribosomal RNA variants. All three mutated ribosomes (to C,
G, or U) displayed diminished translational fidelity; nevertheless, all
possessed peptidyl transferase activity, suggesting a largely functional
catalytic apparatus. Luptak et al. used ¹³C NMR to probe the active site
cytosine in the hepatitis delta virus ribozyme. Its pKa was about 5.0 in
both product and precursor states, and thus a transient shift toward
neutral pH would need to occur during the enzyme's trigonal bipyramidal
transition state in order to accord with existing kinetic data. -- GJC

Proc. Natl. Acad. Sci. U.S.A. 98, 10096; 9002 (2001); J. Am. Chem. Soc.
10.1021/ja016091x.