BIOCHEMISTRY: Baseless Allegations?

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Science  07 Sep 2001:
Vol. 293, Issue 5536, pp. 1733b
DOI: 10.1126/science.293.5536.1733b

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. Luptk 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.

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