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Crystal structure of Staphylococcus aureus tRNA adenosine deaminase TadA in complex with RNA

Nature Structural & Molecular Biology volume 13, pages 153–159 (2006)Cite this article

Abstract

Bacterial tRNA adenosine deaminases (TadAs) catalyze the hydrolytic deamination of adenosine to inosine at the wobble position of tRNAArg2, a process that enables this single tRNA to recognize three different arginine codons in mRNA. In addition, inosine is also introduced at the wobble position of multiple eukaryotic tRNAs. The genes encoding these deaminases are essential in bacteria and yeast, demonstrating the importance of their biological activity. Here we report the crystallization and structure determination to 2.0 Å of Staphylococcus aureus TadA bound to the anticodon stem-loop of tRNAArg2 bearing nebularine, a non-hydrolyzable adenosine analog, at the wobble position. The cocrystal structure reveals the basis for both sequence and structure specificity in the interactions of TadA with RNA, and it additionally provides insight into the active site architecture that promotes efficient hydrolytic deamination.

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Figure 1: TadA deaminates adenosine in tRNA to form inosine.
Figure 2: Structure of TadA in complex with RNA.
Figure 3: Interactions between TadA and RNA.
Figure 4: TadA active site with the adenosine analog nebularine inserted.

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Acknowledgements

We are grateful to the entire beamline staff at NSLS X25A, especially M. Becker, for assistance in data collection and processing, and to members of the Verdine research group for valuable help and discussions and for critical reading of the manuscript. H.C.L. was supported by a postdoctoral fellowship from the Irvington Institute for Immunological Research, A.J.R. was supported by a National Science Foundation graduate fellowship and the work was also supported by a grant from the US National Institutes of Health to G.L.V.

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Authors and Affiliations

  1. Department of Chemistry and Chemical Biology, Harvard University, Cambridge, 02138, Massachusetts, USA

    Heather C Losey, Alexander J Ruthenburg & Gregory L Verdine

  2. Department of Molecular and Cellular Biology, Harvard University, Cambridge, 02138, Massachusetts, USA

    Gregory L Verdine

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  1. Heather C Losey
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Correspondence to Gregory L Verdine.

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Supplementary information

Supplementary Fig. 1

Protein sequence alignment of TadA with related deaminases. (PDF 989 kb)

Supplementary Fig. 2

Conformational changes in TadA. (PDF 512 kb)

Supplementary Fig. 3

Comparison of base pairing observed between C32-A38 in the TadA–RNA structure, the tRNAPhe structure, and a normal C-A+ wobble pair. (PDF 104 kb)

Supplementary Fig. 4

Superposition of three anticodon stem-loops. (PDF 607 kb)

Supplementary Fig. 5

Activity of TadA on minimal RNA stem-loop substrates. (PDF 490 kb)

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Losey, H., Ruthenburg, A. & Verdine, G. Crystal structure of Staphylococcus aureus tRNA adenosine deaminase TadA in complex with RNA. Nat Struct Mol Biol 13, 153–159 (2006). https://doi.org/10.1038/nsmb1047

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