An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA

Abstract

The large ribosomal subunit catalyses the reaction between the α-amino group of the aminoacyl-tRNA bound to the A site and the ester carbon of the peptidyl-tRNA bound to the P site1, while preventing the nucleophilic attack of water on the ester, which would lead to unprogrammed deacylation of the peptidyl-tRNA. Here we describe three new structures of the large ribosomal subunit of Haloarcula marismortui (Hma) complexed with peptidyl transferase substrate analogues that reveal an induced-fit mechanism in which substrates and active-site residues reposition to allow the peptidyl transferase reaction. Proper binding of an aminoacyl-tRNA analogue to the A site induces specific movements of 23S rRNA nucleotides 2618–2620 (Escherichia coli numbering 2583–2585) and 2541(2506), thereby reorienting the ester group of the peptidyl-tRNA and making it accessible for attack. In the absence of the appropriate A-site substrate, the peptidyl transferase centre positions the ester link of the peptidyl-tRNA in a conformation that precludes the catalysed nucleophilic attack by water. Protein release factors2 may also function, in part, by inducing an active-site rearrangement similar to that produced by the A-site aminoacyl-tRNA, allowing the carbonyl group and water to be positioned for hydrolysis.

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Figure 1: Chemical structures and electron density maps.
Figure 2: Steric exclusion of water results in protection of peptidyl-tRNA from deacylation in the uninduced state.
Figure 3: Movements of rRNA and peptidyl-tRNA induced by proper binding of the A-site substrate.
Figure 4: Pre-attack conformation of the substrates.

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Acknowledgements

We thank E. Youngman and R. Green for allowing us to use their unpublished rates of peptidyl-tRNA hydrolysis; G. Muth, D. Kitchen and S. Scaringe for assistance with synthetic chemistry; J. Kavran for collection of a diffraction data set; A. Innis for reading the text; and P. Moore for experimental advice and critical reading of the manuscript. Financial support for the National Synchrotron Light Source comes from the US DOE and the NIH. The Advanced Light Source is supported by the DOE. K.S.H.. is supported by a NIH postdoctoral fellowship. This work was supported by NIH and ACS Beginning Investigator grants to S.A.S. and an NIH grant to T.A.S. Author Contributions T.M.S. determined and evaluated the structures of the three complexes of the 50S ribosomal subunit with substrate analogues under the supervision of T.A.S., and K.S.H. designed and synthesized the substrate analogues used under the supervision of S.A.S.

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Correspondence to Thomas A. Steitz.

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The atomic coordinates and structure factors have been deposited into the RCSB Protein Data Bank under accession codes 1VQ6, 1VQ7 and 1VQN. Reprints and permissions information is available at npg.nature.com/reprintsandpermissions. The authors declare no competing financial interests.

Supplementary information

Supplementary Table 1

A table summarizing data and refinement statistics for structure determination. (DOC 52 kb)

Supplementary Figure 1

A schematic drawing of the peptidyl transferase reaction. (PDF 488 kb)

Supplementary Figure 2

Superimposition of structures of the large ribosomal subunit of H. marismortui in the uninduced state. (PDF 1857 kb)

Supplementary Figure 3

Superimposition of structures of the large ribosomal subunit of H. marismortui in the uninduced state. (PDF 1625 kb)

Supplementary Figure Legends

Text to accompany the Supplementary Figures. (DOC 20 kb)

Supplementary Video 1

A video clip demonstrating how proper binding of the A-site substrate induces changes to the conformation of the peptidyl transferase center and the P-site substrate. (MOV 3606 kb)

Supplementary Video 2

A close-up view of conformational changes associated with the induced fit mechanism. (MOV 10740 kb)

Supplementary Video Legends

Legends for the Supplementary Videos. (DOC 20 kb)

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Martin Schmeing, T., Huang, K., Strobel, S. et al. An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA. Nature 438, 520–524 (2005). https://doi.org/10.1038/nature04152

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