Structural basis of the interaction between cyclodipeptide synthases and aminoacylated tRNA substrates

Gabrielle Bourgeois (1) , Jérôme Seguin (2) , Morgan Babin (2) , Muriel Gondry (2, 3) , Yves Mechulam (1) , Emmanuelle Schmitt (1)

1 BIOC - Laboratoire de Biologie Structurale de la Cellule
2 I2BC - Institut de Biologie Intégrative de la Cellule
3 BIOSYN - Enzymologie et Biosynthèse Peptidique Non Ribosomale

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.

Mots clés: aminoacyl-tRNA synthetases; cyclodipeptides; non-ribosomal peptide synthesis; Rossmann fold; transfer RNA; nonribosomal peptide synthesis

Domaines: Sciences du Vivant [q-bio]

Gabrielle Bourgeois, Jérôme Seguin, Morgan Babin, Muriel Gondry, Yves Mechulam, et al.. Structural basis of the interaction between cyclodipeptide synthases and aminoacylated tRNA substrates. RNA (New York, N.Y.), 2020, ⟨10.1261/rna.075184.120⟩. ⟨hal-02907478⟩