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Structural analysis of leader peptide binding enables leader-free cyanobactin processing

Abstract

Regioselective modification of amino acids within the context of a peptide is common to a number of biosynthetic pathways, and many of the resulting products have potential as therapeutics. The ATP-dependent enzyme LynD heterocyclizes multiple cysteine residues to thiazolines within a peptide substrate. The enzyme requires the substrate to have a conserved N-terminal leader for full activity. Catalysis is almost insensitive to immediately flanking residues in the substrate, suggesting that recognition occurs distant from the active site. Nucleotide and peptide substrate co-complex structures of LynD reveal that the substrate leader peptide binds to and extends the β-sheet of a conserved domain of LynD, whereas catalysis is accomplished in another conserved domain. The spatial segregation of catalysis from recognition combines seemingly contradictory properties of regioselectivity and promiscuity, and it appears to be a conserved strategy in other peptide-modifying enzymes. A variant of LynD that efficiently processes substrates without a leader peptide has been engineered.

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Figure 1: The heterocyclase reaction.
Figure 2: Crystal structures of LynD complexes.
Figure 3: The role of the substrate leader in promoting catalysis.
Figure 4: An engineered heterocyclase enzyme.

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Acknowledgements

This work was supported by grants from the European Research Council (no. 339367, J.H.N. and M.J.), the UK Biotechnology and Biological Sciences Research Council (no. BB/K015508/1, J.H.N. and M.J.) and the Wellcome Trust, which funded the purchase of the TripleTOF 5600 mass spectrometer at the Biomedical Sciences Research Complex Mass Spectrometry and Proteomics Facility, University of St. Andrews (grant no. 094476/Z/10/Z), and the MALDI TOF-TOF Analyser (grant no. WT079272AIA). We acknowledge use of the Diamond (beamlines I02 and I24) and ESRF (beamline ID29) synchrotrons. J.H.N. is a Royal Society Wolfson Merit Award Holder and a 1000 talent scholar of the Chinese Government at Sichuan University.

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Contributions

J.K. carried out crystallization and X-ray crystallography experiments, interpreted data and wrote the paper. G.M. carried out protein expression and purification, heterocyclization reactions, ITC measurements and selective 18O labeling experiments; interpreted data; and wrote the paper. A.F.B. carried out site-directed mutagenesis, protein expression and purification, heterocyclization reactions and MALDI-TOF/MS data acquisition experiments; interpreted data; and wrote the paper. H.L. carried out protein expression and purification, crystallization and X-ray crystallography experiments, and interpreted data. S.S. carried out MALDI-TOF/MS, LC/MS and MS/MS data acquisition experiments and interpreted data. C.B. carried out MALDI-TOF/MS, LC/MS and MS/MS data acquisition experiments and interpreted data. T.L. carried out 31P NMR experiments and interpreted data. W.E.H. interpreted data and wrote the paper. M.J. interpreted data and wrote the paper. J.H.N. carried out X-ray crystallography experiments, interpreted data and wrote the paper.

Corresponding author

Correspondence to James H Naismith.

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Competing interests

The Universities of St. Andrews and Aberdeen have filed a patent application with the UK Patent Office on the use of modified LynD enzyme. J.K., A.F.B., G.M., W.E.H., M.J. and J.H.N. are among those listed as inventors.

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Koehnke, J., Mann, G., Bent, A. et al. Structural analysis of leader peptide binding enables leader-free cyanobactin processing. Nat Chem Biol 11, 558–563 (2015). https://doi.org/10.1038/nchembio.1841

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