A Single Adenosine with a Neutral p K a in the Ribosomal Peptidyl Transferase Center

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Abstract
Biochemical and crystallographic evidence suggests that 23 S ribosomal RNA (rRNA) is the catalyst of peptide bond formation. To explore the mechanism of this reaction, we screened for nucleotides in Escherichia coli 23 S rRNA that may have a perturbed p K a (where K a is the acid constant) based on the pH dependence of dimethylsulfate modification. A single universally conserved A (number 2451) within the central loop of domain V has a near neutral p K a of 7.6 ± 0.2, which is about the same as that reported for the peptidyl transferase reaction. In vivo mutational analysis of this nucleotide indicates that it has an essential role in ribosomal function. These results are consistent with a mechanism wherein the nucleotide base of A2451 serves as a general acid base during peptide bond formation.