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A D-amino acid editing module coupled to the translational apparatus in archaea

Nature Structural & Molecular Biology volume 12, pages 556–557 (2005)Cite this article

Abstract

We report the crystal structure of an archaea-specific editing domain of threonyl-tRNA synthetase that reveals a marked structural similarity to D-amino acid deacylases found in eubacteria and eukaryotes. The domain can bind D-amino acids despite a low sequence identity to other D-amino acid deacylases. These results together indicate the presence of these deacylases in all three kingdoms of life. This underlines an important role they may have played in enforcing homochirality during translation.

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Figure 1: Crystal structure of Pab-NTD and a comparison with DTD.
Figure 2: Amino acid–binding studies using Bis-ANS fluorescence.

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Acknowledgements

S.D. thanks the Council of Scientific and Industrial Research (CSIR), India, for a senior research fellowship. We thank V.M. Shanmugam and Y. Sharma for help during X-ray data collection and fluorescence experiments, respectively. We thank D. Moras and his lab members, particularly A.-C. Dock-Bregeon, from Institut de Génétique et de Biologie Moléculaire et Cellulaire, Strasbourg, for helpful discussions and providing Pyrococcus abyssi genomic DNA. R.S. is an international senior research fellow of The Wellcome Trust, UK, in Biomedical Science in India.

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  1. Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500 007, India

    Shweta Dwivedi, Shobha P Kruparani & Rajan Sankaranarayanan

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  1. Shweta Dwivedi
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  2. Shobha P Kruparani
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  3. Rajan Sankaranarayanan
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Correspondence to Rajan Sankaranarayanan.

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Supplementary information

Supplementary Fig. 1

Structural superposition of Pab-NTD (cyan and yellow) and DTD (pink and blue) dimers as observed in their respective crystal structures. (PDF 538 kb)

Supplementary Fig. 2

Amino acid binding studies using Bis-ANS fluorescence. (PDF 551 kb)

Supplementary Fig. 3

Crystal soaks with different amino acids. (PDF 509 kb)

Supplementary Fig. 4

Structure-based sequence alignment of the editing domain of a few archaeal ThrRSs along with DTD homologs. (PDF 904 kb)

Supplementary Table 1

Summary of crystallographic data and refinement statistics. (PDF 67 kb)

Supplementary Methods (PDF 75 kb)

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Dwivedi, S., Kruparani, S. & Sankaranarayanan, R. A D-amino acid editing module coupled to the translational apparatus in archaea. Nat Struct Mol Biol 12, 556–557 (2005). https://doi.org/10.1038/nsmb943

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