Important Contribution to Catalysis of Peptide Bond Formation by a Single Ionizing Group within the Ribosome

• Published in: Molecular cell 2002-08, Vol.10 (2), p.339-346
• Main Authors: Katunin, Vladimir I, Muth, Gregory W, Strobel, Scott A, Wintermeyer, Wolfgang, Rodnina, Marina V
• Format: Article
• Language: English
• Subjects: Binding Sites; Catalysis - drug effects; Escherichia coli; Hydrogen-Ion Concentration; Ions - metabolism; Kinetics; Mutation; Peptidyl Transferases - metabolism; Protein Biosynthesis - drug effects; Protein Subunits; Puromycin - pharmacology; Ribosomes - chemistry; Ribosomes - drug effects; Ribosomes - genetics; Ribosomes - metabolism; RNA, Ribosomal, 23S - genetics; RNA, Ribosomal, 23S - metabolism; Structure-Activity Relationship; Time Factors
• ISSN: 1097-2765; 1097-4164
• DOI: 10.1016/S1097-2765(02)00566-X

The catalytic mechanism of peptide bond formation on the ribosome is not known. The crystal structure of 50S ribosomal subunits shows that the catalytic center consists of RNA only and suggests potential catalytic residues. Here we report rapid kinetics of the peptidyl transferase reaction with puromycin at rates up to 50 s−1. The rate-pH profile of the reaction reveals that protonation of a single ribosomal residue (pKa = 7.5), in addition to protonation of the nucleophilic amino group, strongly inhibits the reaction (>100-fold). The A2451U mutation within the peptidyl transferase center has about the same inhibitory effect. These results suggest a contribution to overall catalysis of general acid-base and/or conformational catalysis involving an ionizing group at the active site.