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Structural insights into cognate versus near-cognate discrimination during decoding.

Agirrezabala X, Schreiner E, Trabuco LG, Lei J, Ortiz-Meoz RF, Schulten K, Green R, Frank J
EMBO J 30 1497-507 (2011)
Cited: 36 times
EuropePMC logo PMID: 21378755

Abstract

The structural basis of the tRNA selection process is investigated by cryo-electron microscopy of ribosomes programmed with UGA codons and incubated with ternary complex (TC) containing the near-cognate Trp-tRNA(Trp) in the presence of kirromycin. Going through more than 350 000 images and employing image classification procedures, we find ∼8% in which the TC is bound to the ribosome. The reconstructed 3D map provides a means to characterize the arrangement of the near-cognate aa-tRNA with respect to elongation factor Tu (EF-Tu) and the ribosome, as well as the domain movements of the ribosome. One of the interesting findings is that near-cognate tRNA's acceptor stem region is flexible and CCA end becomes disordered. The data bring direct structural insights into the induced-fit mechanism of decoding by the ribosome, as the analysis of the interactions between small and large ribosomal subunit, aa-tRNA and EF-Tu and comparison with the cognate case (UGG codon) offers clues on how the conformational signals conveyed to the GTPase differ in the two cases.

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  1. ADMET profiling and molecular docking of potential antimicrobial peptides previously isolated from African catfish, Clarias gariepinus. Okella H, Okello E, Mtewa AG, Ikiriza H, Kaggwa B, Aber J, Ndekezi C, Nkamwesiga J, Ajayi CO, Mugeni IM, Ssentamu G, Ochwo S, Odongo S, Tolo CU, Kato CD, Engeu PO. Front Mol Biosci 9 1039286 (2022)


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  9. EF-G catalyzes tRNA translocation by disrupting interactions between decoding center and codon-anticodon duplex. Liu G, Song G, Zhang D, Zhang D, Li Z, Lyu Z, Dong J, Achenbach J, Gong W, Zhao XS, Nierhaus KH, Qin Y. Nat Struct Mol Biol 21 817-824 (2014)
  10. How EF-Tu can contribute to efficient proofreading of aa-tRNA by the ribosome. Noel JK, Whitford PC. Nat Commun 7 13314 (2016)
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  12. Deducing the kinetics of protein synthesis in vivo from the transition rates measured in vitro. Rudorf S, Thommen M, Rodnina MV, Lipowsky R. PLoS Comput Biol 10 e1003909 (2014)
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  16. Cotranslational protein assembly imposes evolutionary constraints on homomeric proteins. Natan E, Endoh T, Haim-Vilmovsky L, Flock T, Chalancon G, Hopper JTS, Kintses B, Horvath P, Daruka L, Fekete G, Pál C, Papp B, Oszi E, Magyar Z, Marsh JA, Elcock AH, Babu MM, Robinson CV, Sugimoto N, Teichmann SA. Nat Struct Mol Biol 25 279-288 (2018)
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  18. Exploring the balance between folding and functional dynamics in proteins and RNA. Jackson J, Nguyen K, Whitford PC. Int J Mol Sci 16 6868-6889 (2015)
  19. Decoding on the ribosome depends on the structure of the mRNA phosphodiester backbone. Keedy HE, Thomas EN, Zaher HS. Proc Natl Acad Sci U S A 115 E6731-E6740 (2018)
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  21. Flexibility in the insulin receptor ectodomain enables docking of insulin in crystallographic conformation observed in a hormone-bound microreceptor. Vashisth H. Membranes (Basel) 4 730-746 (2014)
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  24. Quantitative Characterization of Domain Motions in Molecular Machines. Maji S, Shahoei R, Schulten K, Frank J. J Phys Chem B 121 3747-3756 (2017)
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