6y4b | pdb_00006y4b

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

spinqualitylabelsall models 6y4b, resolution 5.00Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 6y4b is a 2 chain structure with sequence from Candidatus Glomeribacter gigasporarum BEG34 and Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 5Å Ligands: 4SU, 5MU, H2U, PHE, PSU Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function G2JBB2_9BURK Publication Abstract from PubMed 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(Phe) 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-tRNA(Phe) complex to 5 A 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 beta2 and beta7 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. Structural basis of the interaction between cyclodipeptide synthases and aminoacylated tRNA substrates.,Bourgeois G, Seguin J, Babin M, Gondry M, Mechulam Y, Schmitt E RNA. 2020 Nov;26(11):1589-1602. doi: 10.1261/rna.075184.120. Epub 2020 Jul 17. PMID:32680846 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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