A single adenosine with a neutral pK(a) in the ribosomal peptidyl transferase center

Biochemical and crystallographic evidence suggests that 23S ribosomal RNA ( rRNA) is the catalyst of peptide bond formation. To explore the mechanism o f this reaction, we screened for nucleotides in Escherichia coli 23S rRNA t hat may have a perturbed pK(a) (where K-a is the acid constant) based on th e pH dependence of dimethylsulfate modification. A single universally conse rved A (number 2451) within the central loop of domain V has a near neutral pK(a) of 7.6 +/- 0.2, which is about the same as that reported for the pep tidyl transferase reaction. In vivo mutational analysis of this nucleotide indicates that it has an essential role in ribosomal function. These result s are consistent with a mechanism wherein the nucleotide base of A2451 serv es as a general acid base during peptide bond formation.