6Y4B

Structure of cyclodipeptide synthase from Candidatus Glomeribacter gigasporarum bound to Phe-tRNAPhe

Summary for 6Y4B

• Entry DOI: 10.2210/pdb6y4b/pdb
• Descriptor: RNA (77-MER), Cyclodipeptide synthase, PHENYLALANINE (3 entities in total)
• Functional Keywords: cyclodipeptide synthase, trna, complex, rna binding protein
• Biological source: Escherichia coli; More
• Total number of polymer chains: 2
• Total formula weight: 58804.16

Authors

Bourgeois, G.,Mechulam, Y.,Schmitt, E. (deposition date: 2020-02-20, release date: 2020-12-30, Last modification date: 2024-01-24)

Primary citation

Bourgeois, G.,Seguin, J.,Babin, M.,Gondry, M.,Mechulam, Y.,Schmitt, E.
Structural basis of the interaction between cyclodipeptide synthases and aminoacylated tRNA substrates.
Rna, 26:1589-1602, 2020

PubMed 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-tRNA to the CDPS from (-CDPS) by gel filtration and electrophoretic mobility shift assay. We determined the crystal structure of the -CDPS:Phe-tRNA 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.

PubMed: 32680846
DOI: 10.1261/rna.075184.120

Experimental method

X-RAY DIFFRACTION (5 Å)