title: Peptide bond formation does not involve acid-base catalysis by ribosomal residues.
abstract: 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)-tRNA(fMet) with a modified A-site tRNA substrate, Phelac-tRNA(Phe), 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-tRNA(Phe) is estimated to be >300 s(-1).
authors.affiliation: Institute of Physical Biochemistry, University of Witten/Herdecke, Stockumer Strasse 10, 58448 Witten, Germany.
authors.forename: Peter
authors.initials: P
authors.lastname: Bieling
authors.forename: Malte
authors.initials: M
authors.lastname: Beringer
authors.forename: Sarah
authors.initials: S
authors.lastname: Adio
authors.forename: Marina V
authors.initials: MV
authors.lastname: Rodnina
mesh_terms: D000143:Acids / Q000737:chemistry; D000468:Alkalies / Q000737:chemistry; D002384:Catalysis; D006863:Hydrogen-Ion Concentration; D007700:Kinetics; D010455:Peptides / Q000737:chemistry* / Q000378:metabolism*; D010458:Peptidyl Transferases / Q000378:metabolism; D014176:Protein Biosynthesis; D012343:RNA, Transfer / Q000378:metabolism; D012270:Ribosomes / Q000235:genetics* / Q000378:metabolism*; D013379:Substrate Specificity; D046249:Transfer RNA Aminoacylation
chemical_list: D000143:Acids; D000468:Alkalies; D010455:Peptides; D012343:RNA, Transfer; D010458:Peptidyl Transferases