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. 2021 Feb 9;49(5):2684–2699. doi: 10.1093/nar/gkab033

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© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

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Figure 1. — Kinetic scheme for efficiency and accuracy of codon reading by tRNA (A) and release factors (B). (A) Ribosome complex RC₀ has peptidyl-tRNA in P site and A site programmed with native (GAA) or modified (Gm⁶AA) Glu codon, native (GAU) or modified (Gm⁶AU) Asp codon. Glu-tRNA^Glu, with cognate codon GAA, initially is in free ternary complex (T₃) with EF-Tu and GTP. T₃ binds into A/T site of RC₀, leading to ribosome complex RC₁, where the anticodon of T₃ lacks codon contact. Codon-anticodon contact is formed by conformational change of tRNA in T₃ leading to complex RC₂. Subsequent hydrolysis of GTP in EF-Tu induces conformational change of EF-Tu and leads to complex RC₃. Then EF-Tu in the GDP form rapidly dissociates from RC₃, leading to complex RC₄. In RC₄ tRNA may be accommodated into A site and receive a nascent peptide from P-site tRNA, leading to complex RC₅. Alternatively, tRNA is discarded from the ribosome in a proofreading reaction, which brings RC₄ back to complex RC₀. The efficiencies (k_cat/K_m) for GTP hydrolysis on ribosome bound T₃ for peptide bond formation in response to GAA, Gm⁶AA, GAU and Gm⁶AU codons in A site are in M&M defined in terms of rate constants in Figure 1A (Materials and Methods). (B) Ribosomal termination complex RT₀ has peptidyl-tRNA in P site and A site programmed with native (UAA) or modified (Um⁶AA) stop codon in cognate reactions and with UAG or Um⁶AG in near-cognate reactions. Release factor 1 (RF1) or 2 (RF2) binds to RT₀ forming RT₁. Either release factor (RF) undergoes a conformational change and forms complex RT₂ via transition state RT₁₂* or dissociates from the ribosome. We suggest that the modest selectivity of ground state RT₁ is enhanced in the transition state RT₁₂* (37). Hydrolysis of ester bond in peptidyl-tRNA leads to ribosomal complex RT₃ followed by peptide release and, eventually, RF-release. The efficiency (k_cat/K_m) and maximal rate (k_cat) for ester bond hydrolysis on ribosome bound RF in response to UAA, Um⁶AA, UAG and Um⁶AG codons are defined in terms of rate constants in Figure 1B (Materials and Methods).