An uncharged amine in the transition state of the ribosomal peptidyl transfer reaction |
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Authors: | Kingery David A Pfund Emmanuel Voorhees Rebecca M Okuda Kensuke Wohlgemuth Ingo Kitchen David E Rodnina Marina V Strobel Scott A |
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Affiliation: | Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA. |
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Abstract: | The ribosome has an active site comprised of RNA that catalyzes peptide bond formation. To understand how RNA promotes this reaction requires a detailed understanding of the chemical transition state. Here, we report the Br?nsted coefficient of the alpha-amino nucleophile with a series of puromycin derivatives. Both 50S subunit- and 70S ribosome-catalyzed reactions displayed linear free-energy relationships with slopes close to zero under conditions where chemistry is rate limiting. These results indicate that, at the transition state, the nucleophile is neutral in the ribosome-catalyzed reaction, in contrast to the substantial positive charge reported for typical uncatalyzed aminolysis reactions. This suggests that the ribosomal transition state involves deprotonation to a degree commensurate with nitrogen-carbon bond formation. Such a transition state is significantly different from that of uncatalyzed aminolysis reactions in solution. |
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