Fig. 3: SufB2 uses a triplet anticodon-codon pairing scheme at the A site.
From: Insights into genome recoding from the mechanism of a classic +1-frameshifting tRNA
a GTP hydrolysis by EF-Tu as a function of time for delivery of G37- or native-state SufB2- or ProL-TC to the A site of a 70S IC. Although the concentration of TCs was limiting, which would limit the rate of binding of TCs to the 70S IC, the observed differences in the yield of GTPase activity indicated that binding was not the sole determinant, but that other factors, such as the identity and the methylation state of the tRNA, affected the GTPase activity. b Dipeptide fMP formation as a function of time for delivery of G37- or native-state SufB2- or ProL-TC to the A site of a 70S IC. Due to the limiting concentration of the 70S IC, which did not include the tRNA substrate, the yield of di- or tri-peptide formation assays was constant even with different tRNAs in TCs. c The yield of fMP and fMR in dipeptide formation assays in which equimolar mixtures of native-state SufB2-TC, carrying Pro and/or Arg, and/or native-state ProL-TC, carrying Pro and/or Arg, are delivered to 70S ICs. The mRNA in 70S ICs in (A–C) is AUG-CCC-CGU-U. d Dipeptide formation rate kfMP,obs for delivery of G37-state SufB2-TC to 70S ICs containing sequence variants of the CCC-C motif in the A site. In a, b the bars in the graphs are SD of 3 independent (n = 3) experiments, in c the bars in the graphs are SD of 4 independent (n = 4) experiments, and in d the bars in the graphs are SD of 3 or 4 independent (n = 3 or 4) experiments. All data are presented as mean values ± SD. ∆t: a time interval, ND: not detected.
