Structural basis of the interaction between cyclodipeptide synthases and aminoacylated tRNA substrates
- Gabrielle Bourgeois1,
- Jérôme Seguin2,
- Morgan Babin2,
- Muriel Gondry2,
- Yves Mechulam1 and
- Emmanuelle Schmitt1,3
- 1 Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France;
- 2 Univ Paris-Saclay, CEA, CNRS, I2BC, 91198, Gif-sur-Yvette, France
- ↵* Corresponding author; email: emmanuelle.schmitt{at}polytechnique.edu
Abstract
Cyclodipeptide synthases (CDPSs) catalyze the synthesis of various cyclodipeptides by using two aminoacyl-tRNA (aa-tRNA) substrates in a sequential mechanism. Here, we studied binding of phenylalanyl-tRNAPhe to the CDPS from Candidatus Glomeribacter gigasporarum (Cglo-CDPS) by gel filtration and electrophoretic mobility shift assay. We determined the crystal structure of the Cglo-CDPS:Phe-tRNAPhe complex to 5 Å resolution and further studied it in solution using small-angle X-ray scattering (SAXS). The data show that the major groove of the acceptor stem of the aa-tRNA interacts with the enzyme through the basic β2 and β7 strands of CDPSs belonging to the XYP subfamily. A bending of the CCA extremity enables the amino acid moiety to be positioned in the P1 pocket while the terminal A76 adenosine occupies the P2 pocket. Such a positioning indicates that the present structure illustrates the binding of the first aa-tRNA. In cells, CDPSs and the elongation factor EF-Tu share aminoacylated tRNAs as substrates. The present study shows that CDPSs and EF-Tu interact with opposite sides of tRNA. This may explain how CDPSs hijack aa-tRNAs from canonical ribosomal protein synthesis.
Keywords
- Rossmann fold
- aminoacyl-tRNA synthetases
- cyclodipeptides
- non-ribosomal peptide synthesis
- transfer RNA
- Received February 26, 2020.
- Accepted July 6, 2020.
- Published by Cold Spring Harbor Laboratory Press for the RNA Society
This article, published in RNA, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
