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Simultaneous binding of two proteins to opposite sides of a single transfer RNA

Abstract

Transfer RNA (tRNA) is a small nucleic acid (typically 76 nucleotides) that forms binary complexes with proteins, such as aminoacyl tRNA synthetases (RS) and Trbp111. The latter is a widely distributed structure-specific tRNA-binding protein that is incorporated into cell signaling molecules. The structure of Trbp111 was modeled onto to the outer, convex side of the L-shaped tRNA. Here we present RNA footprints that are consistent with this model. This binding mode is in contrast to that of tRNA synthetases, which bind to the inside, or concave side, of tRNA. These opposite locations of binding for these two proteins suggest the possibility of a ternary complex. The formation of a tRNA synthetase–tRNA–Trbp111 ternary complex was detected by two independent methods. The results indicate that the tRNA is sandwiched between the two protein molecules. A thermodynamic and functional analysis is consistent with the tRNA retaining its native structure in the ternary complex. These results may have implications for how the translation apparatus is linked to other cellular machinery.

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Figure 1: Trbp111 binding to tRNA.
Figure 2: Synthetase–tRNA–Trbp111 ternary complex detected by gel electrophoresis.
Figure 3: Changes in sNBD fluorescence of sNBD-tRNAIle upon binding IleRS or Trbp111.
Figure 4: Simultaneous binding of IleRS and Trbp111 to sNBD-tRNAIle.
Figure 5

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Acknowledgements

This work was supported by the National Institutes of Health, and by a fellowship from the National Foundation of Cancer Research. A.T.A. is an NIH postdoctoral fellow. We thank B. Nordin for providing tRNAIle for the PACE analysis.

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Correspondence to Paul Schimmel.

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Nomanbhoy, T., Morales, A., Abraham, A. et al. Simultaneous binding of two proteins to opposite sides of a single transfer RNA. Nat Struct Mol Biol 8, 344–348 (2001). https://doi.org/10.1038/86228

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