Seminar

A proton wire to couple aminoacyl-tRNA accommodation and peptide bond formation on the ribosome

Axel Innis, PhD

During ribosome-catalyzed peptide bond formation, the α-amino group of an aminoacyl-tRNA attacks the ester carbonyl carbon of a peptidyl-tRNA to yield a peptide that is lengthened by one amino acid. Although this requires the net transfer of a proton from the attacking amine to the 3’-oxygen leaving group of the P-site tRNA, the lack of high-resolution structural data for the complete ribosomal active site with bound full-length substrates or products has made it difficult to assess what role the ribosome might play in coordinating proton movement during catalysis. Using different combinations of natural and non-hydrolyzable aminoacyl-tRNAs, we have determined the crystal structures of pre-attack and post-catalysis complexes of the Thermus thermophilus 70S ribosome at a resolution of ~2.6 Å resolution. Our structures reveal a previously unseen network of hydrogen bonds, or "proton wire", along which hydrogen transfer from the attacking amine could take place to ensure the concerted, rate-limiting formation of an intermediate. This allows us to propose an alternate reaction model that differs substantially from the prevailing models in the field and accounts for much of the existing biochemical and kinetic data.