Nature Structural & Molecular Biology 13, 423 - 428 (2006)
Published online: 30 April 2006; | doi:10.1038/nsmb1091
Peptide bond formation does not involve acid-base catalysis by ribosomal residuesPeter Bieling1, 2, 3, Malte Beringer1, 3, Sarah Adio1, 2
& Marina V Rodnina11
Institute of Physical Biochemistry, University of Witten/Herdecke, Stockumer Strasse 10, 58448 Witten, Germany. 2
Present addresses: EMBL Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany (P.B.) and Adolf Butenandt Institute, Ludwig Maximilian University, Schillerstrasse 42, 80336 Munich, Germany (S.A.). 3
These authors contributed equally to this work.
Correspondence should be addressed to Marina V Rodnina rodnina@uni-wh.de Ribosomes catalyze the formation of peptide bonds between aminoacyl esters of transfer RNAs within a catalytic center composed of ribosomal RNA only. Here we show that the reaction of P-site formylmethionine (fMet)-tRNAfMet with a modified A-site tRNA substrate, Phelac-tRNAPhe, in which the nucleophilic amino group is replaced with a hydroxyl group, does not show the pH dependence observed with small substrate analogs such as puromycin and hydroxypuromycin. This indicates that acid-base catalysis by ribosomal residues is not important in the reaction with the full-size substrate. Rather, the ribosome catalyzes peptide bond formation by positioning the tRNAs, or their 3' termini, through interactions with rRNA that induce and/or stabilize a pH-insensitive conformation of the active site and provide a preorganized environment facilitating the reaction. The rate of peptide bond formation with unmodified Phe-tRNAPhe is estimated to be >300 s-1.
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