Structural basis of keto acid utilization in nonribosomal depsipeptide synthesis

Abstract

Nonribosomal depsipeptides are natural products composed of amino and hydroxy acid residues. The hydroxy acid residues often derive from α-keto acids, reduced by ketoreductase domains in the depsipeptide synthetases. Biochemistry and structures reveal the mechanism of discrimination for α-keto acids and a remarkable architecture: flanking intact adenylation and ketoreductase domains are sequences separated by >1,100 residues that form a split ‘pseudoAsub’ domain, structurally important for the depsipeptide module’s synthetic cycle.

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Fig. 1: Domain organization and structure of a depsipeptide module.
Fig. 2: The A domain binds the α-keto acid with an antiparallel carbonyl–carbonyl interaction.
Fig. 3: The catalytic activity of the depsipeptide module.

Data availability

Structure coordinates have been deposited in the PDB under accession codes 6ULW, 6ULX, 6ULY and 6ULZ (Supplementary Table 1).

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Acknowledgements

We thank C. Alonso for TEV protease purification and other laboratory assistance, J. Reimer for preparing amino coenzyme A, members of the Schmeing laboratory for helpful advice and discussion, N. Rogerson for proofreading, staff at APS (F. Murphy and S. Banarjee) and CLS for support during X-ray data collection and N. Magarvey for discussions and suggesting structural work on depsipeptide synthetases. This work was supported by a Canada Research Chair and NSERC Discovery Grant no. 418420 to T.M.S.

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T.M.S., D.A.A. and C.C.-L. designed the study and wrote the manuscript. D.A.A., C.C.-L. and M.J.T. performed biochemical experiments. J.W. performed structure determination and refinement of the A–KR structure using NCS averaging and map sharpening. D.A.A. and C.C.-L. performed crystallization, structure determination and refinement.

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Correspondence to T. Martin Schmeing.

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Supplementary Tables 1 and 2 and Figs. 1–8

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Alonzo, D.A., Chiche-Lapierre, C., Tarry, M.J. et al. Structural basis of keto acid utilization in nonribosomal depsipeptide synthesis. Nat Chem Biol 16, 493–496 (2020). https://doi.org/10.1038/s41589-020-0481-5

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