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Shape-selective RNA recognition by cysteinyl-tRNA synthetase

Nature Structural & Molecular Biology volume 11, pages 1134–1141 (2004)Cite this article

Abstract

The crystal structure of Escherichia coli cysteinyl-tRNA synthetase (CysRS) bound to tRNACys at a resolution of 2.3 Å reveals base-specific and shape-selective interactions across an extensive protein-RNA recognition interface. The complex contains a mixed α/β C-terminal domain, which is disordered in the unliganded enzyme. This domain makes specific hydrogen bonding interactions with all three bases of the GCA anticodon. The tRNA anticodon stem is bent sharply toward the enzyme as compared with its conformation when bound to elongation factor Tu, providing an essential basis for shape-selective recognition. The CysRS structure also reveals interactions of conserved enzyme groups with the sugar-phosphate backbone in the D loop, adjacent to an unusual G15·G48 tertiary base pair previously implicated in tRNA aminoacylation. A combined mutational analysis of enzyme and tRNA groups at G15·G48 supports the notion that contacts between CysRS and the sugar-phosphate backbone contribute to recognition by indirect readout.

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Figure 1: Ribbon representation of the E. coli CysRS–tRNACys structure.
Figure 2: Conformational changes in tRNACys structure.
Figure 3: Recognition of the tRNA anticodon stem by CysRS.
Figure 4: Indirect readout of the tertiary core.
Figure 5: Recognition of the tRNACys anticodon loop by CysRS.
Figure 6: Surface representation of the CysRS active site.

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Acknowledgements

We thank A. Héroux for data collection at the National Synchrotron Light Source, Brookhaven National Laboratory, and T. Christian for assisting with preparation of the T7 transcript of tRNACys. This work was supported by US National Institutes of Health grants GM63713 (to J.J.P.) and GM56662 (to Y.M.H.).

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  1. Department of Chemistry and Biochemistry, University of California at Santa Barbara, Santa Barbara, 93106-9510, California, USA

    Scott Hauenstein & John J Perona

  2. Department of Biochemistry and Molecular Pharmacology, Thomas Jefferson University, Philadelphia, 19107, Pennsylvania, USA

    Chun-Mei Zhang & Ya-Ming Hou

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  1. Scott Hauenstein
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Correspondence to John J Perona.

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Supplementary Fig. 1

Sequence alignment of CysRS enzymes. (PDF 178 kb)

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Hauenstein, S., Zhang, CM., Hou, YM. et al. Shape-selective RNA recognition by cysteinyl-tRNA synthetase. Nat Struct Mol Biol 11, 1134–1141 (2004). https://doi.org/10.1038/nsmb849

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