Heterochiral coupling is favoured in abiotic peptide bond formation, whereas biotic peptide bond formation is dominated by homochiral coupling. Here, we report that heterochiral coupling is a rather general paradigm in the head-to-tail macrolactamization of non-ribosomal peptide biosynthesis. The canonical cis-acting offloading cyclases, such as type I thioesterase (TE) and terminal condensation-like domains, catalyse head-to-tail macrolactamization between N- and C-terminal residues with d- and l-configurations, respectively. In contrast, the penicillin-binding protein-type TEs, a recently identified family of trans-acting cyclases, couple heterochiral residues with complementary stereoselectivity to the canonical one. Thus, a suite of cis- and trans-TE non-ribosomal peptide synthetases could overcome the stereochemical constraints present in heterochiral head-to-tail macrolactam formation in bacterial non-ribosomal peptide biosynthesis. Furthermore, we provide the structural rationale for the C-terminal stereoselectivity of non-canonical offloading cyclases. Penicillin-binding protein-type TEs with broad substrate specificity are potentially applicable as biocatalysts and genetic tools for synthetic biology.
This is a preview of subscription content
Subscribe to Journal
Get full journal access for 1 year
only $9.92 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Tax calculation will be finalised during checkout.
Rent or Buy article
Get time limited or full article access on ReadCube.
All prices are NET prices.
The crystallographic data that support the findings of this study are available from the Protein Data Bank (http://www.rcsb.org). The coordinates and the structure factor amplitudes for the structures of SurE apo and SurE complexed with 4 have been deposited under accession codes 6KSU and 6KSV, respectively. All other data supporting the plots within this paper and other findings of this study are available from the corresponding author upon reasonable request.
Hill, R. R., Birch, D., Jeff, G. E. & North, M. Enantioselection in peptide bond formation. Org. Biomol. Chem. 1, 965–972 (2003).
Brady, S. F. et al. Practical synthesis of cyclic peptides, with an example of dependence of cyclization yield upon linear sequence. J. Org. Chem. 44, 3101–3105 (1979).
Rich, D. H., Bhatnagar, P., Mathiaparanam, P., Grant, J. A. & Tam, J. P. Synthesis of tentoxin and related dehydro cyclic tetrapeptides. J. Org. Chem. 43, 296–302 (1978).
Sieber, S. A. & Marahiel, M. A. Molecular mechanisms underlying nonribosomal peptide synthesis: approaches to new antibiotics. Chem. Rev. 105, 715–738 (2005).
Trauger, J. W., Kohli, R. M., Mootz, H. D., Marahiel, M. A. & Walsh, C. T. Peptide cyclization catalysed by the thioesterase domain of tyrocidine synthetase. Nature 407, 215–218 (2000).
Gao, X. et al. Cyclization of fungal nonribosomal peptides by a terminal condensation-like domain. Nat. Chem. Biol. 8, 823–830 (2012).
Tsomaia, N. Peptide therapeutics: targeting the undruggable space. Eur. J. Med. Chem. 94, 459–470 (2015).
Kuranaga, T. et al. Total synthesis of the nonribosomal peptide surugamide B and identification of a new offloading cyclase family. Angew. Chem. Int. Ed. 57, 9447–9451 (2018).
Takada, K. et al. Surugamides A–E, cyclic octapeptides with four d-amino acid residues, from a marine Streptomyces sp.: LC-MS-aided inspection of partial hydrolysates for the distinction of d- and l-amino acid residues in the sequence. J. Org. Chem. 78, 6746–6750 (2013).
Mohiman, H. et al. Dereplication of peptidic natural products through database search of mass spectra. Nat. Chem. Biol. 13, 30–37 (2016).
Xu, F., Nazari, B., Moon, K., Bushin, L. B. & Seyedsayamdost, M. R. Discovery of a cryptic antifungal compound from Streptomyces albus J1074 using high-throughput elicitor screens. J. Am. Chem. Soc. 139, 9203–9212 (2017).
Ninomiya, A. et al. Biosynthetic gene cluster for surugamide A encompasses an unrelated decapeptide, surugamide F. ChemBioChem 17, 1709–1712 (2016).
Matsuda, K. et al. SurE is a trans-acting thioesterase cyclizing two distinct non-ribosomal peptides. Org. Biomol. Chem. 17, 1058–1061 (2019).
Magarvey, N. A., Haltli, B., He, M., Greenstein, M. & Hucul, J. A. Biosynthetic pathway for mannopeptimycins, lipoglycopeptide antibiotics active against drug-resistant gram-positive pathogens. Antimicrob. Agents Chemother. 50, 2167–2177 (2006).
Li, Q. et al. Identification of the biosynthetic gene cluster for the anti-infective desotamides and production of a new analogue in a heterologous host. J. Nat. Prod. 78, 944–948 (2015).
Son, S. et al. Genomics-driven discovery of chlorinated cyclic hexapeptides ulleungmycins A and B from a Streptomyces species. J. Nat. Prod. 80, 3025–3031 (2017).
Zhou, Y. et al. Investigation of penicillin binding protein (PBP)-like peptide cyclase and hydrolase in surugamide non-ribosomal peptide biosynthesis. Cell Chem. Biol. 26, 737–744 (2019).
Thankachan, D. et al. A trans-acting cyclase offloading strategy for nonribosomal peptide synthetases. ACS Chem. Biol. 14, 845–849 (2019).
White, C. J. & Yudin, A. K. Contemporary strategies for peptide macrocyclization. Nat. Chem. 3, 509–524 (2011).
Yu, X. & Sun, D. Macrocyclic drugs and synthetic methodologies toward macrocycles. Molecules 18, 6230–6268 (2013).
Medema, M. H. et al. Minimum information about a biosynthetic gene cluster. Nat. Chem. Biol. 11, 625–631 (2015).
Schultz, A. W. et al. Biosynthesis and structures of cyclomarins and cyclomarazines, prenylated cyclic peptides of marine actinobacterial origin. J. Am. Chem. Soc. 130, 4507–4516 (2008).
Ma, J. et al. Biosynthesis of ilamycins featuring unusual building blocks and engineered production of enhanced anti-tuberculosis agents. Nat. Commun. 8, 391 (2017).
Holm, L. & Rosenstrom, P. Dali server: conservation mapping in 3D. Nucleic Acids Res. 38, W545–W549 (2010).
Lahiri, S. D. et al. Structural insight into potent broad-spectrum inhibition with reversible recyclization mechanism: avibactam in complex with CTX-M-15 and Pseudomonas aeruginosa AmpC β-lactamases. Antimicrob. Agents Chemother. 57, 2496–2505 (2013).
Nakano, S. et al. Structural and computational analysis of peptide recognition mechanism of class-C type penicillin binding protein, alkaline d-peptidase from Bacillus cereus DF4-B. Sci. Rep. 5, 13836–13836 (2015).
Delfosse, V. et al. Structure of the archaeal Pab87 peptidase reveals a novel self-compartmentalizing protease family. PLoS ONE 4, e4712–e4712 (2009).
Calcott, M. J. & Ackerley, D. F. Genetic manipulation of non-ribosomal peptide synthetases to generate novel bioactive peptide products. Biotechnol. Lett. 36, 2407–2416 (2014).
Bozhüyük, K. A. J. et al. De novo design and engineering of non-ribosomal peptide synthetases. Nat. Chem. 10, 275–281 (2017).
Niquille, D. L. et al. Nonribosomal biosynthesis of backbone-modified peptides. Nat. Chem. 10, 282–287 (2018).
Bozhüyük, K. A. J. et al. Modification and de novo design of non-ribosomal peptide synthetases using specific assembly points within condensation domains. Nat. Chem. 11, 653–661 (2019).
Pace, C. N., Vajdos, F., Fee, L., Grimsley, G. & Gray, T. How to measure and predict the molar absorption coefficient of a protein. Protein Sci. 4, 2411–2423 (1995).
Rice, L. M., Earnest, T. N. & Brunger, A. T. Single-wavelength anomalous diffraction phasing revisited. Acta Crystallogr. D 56, 1413–1420 (2000).
Kabsch, W. XDS. Acta Crystallogr. D 66, 125–132 (2010).
Evans, P. R. An introduction to data reduction: space-group determination, scaling and intensity statistic. Acta Crystallogr. D 67, 282–292 (2011).
Skubak, P. & Pannu, N. S. Automatic protein structure solution from weak X-ray data. Nat. Commun. 4, 2777 (2013).
McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007).
Terwilliger, T. C. et al. Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard. Acta Crystallogr. D 64, 61–69 (2007).
Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004).
Afonine, P. V. et al. Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallogr. D 68, 352–367 (2012).
Schüttelkopf, A. W. & van Aalten, D. M. PRODRG: a tool for high-throughput crystallography of protein–ligand complexes. Acta Crystallogr. D 60, 1355–1363 (2004).
Bachmann, B. O. & Ravel, J. Methods for in silico prediction of microbial polyketide and nonribosomal peptide biosynthetic pathways from DNA sequence data. Methods Enzymol. 458, 181–217 (2009).
Kim, J. H., Komatsu, M., Shin-ya, K., Omura, S. & Ikeda, H. Distribution and functional analysis of the phosphopantetheinyl transferase superfamily in Actinomycetales microorganisms. Proc. Natl Acad. Sci. USA 115, 6828–6833 (2018).
Komatsu, M., Uchiyama, T., Omura, S., Cane, D. E. & Ikeda, H. Genome-minimized Streptomyces host for the heterologous expression of secondary metabolism. Proc. Natl Acad. Sci. USA 107, 2646–2651 (2010).
We thank H. Ikeda (Kitazato University) for providing vectors and the E. coli strain used for genetic manipulation of S. albidoflavus NBRC12854, and A. Katsuyama (Hokkaido University) for technical assistance in the conformational energy calculation. The synchrotron radiation experiments were performed at beamline BL-1A of the Photon Factory. We also thank the beamline staff of the Photon Factory for their help in collecting X-ray diffraction data. This work was partly supported by the Takeda Science Foundation, the Asahi Glass Foundation, the Naito Foundation, the Uehara Memorial Foundation, the Japan Agency for Medical Research and Development (AMED grant no. JP19ae0101045) and Grants-in-Aid from the Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan (JSPS KAKENHI grant nos. JP16703511, JP16H06443, JP18056499, JP19178402 and JP20H00490).
The authors declare no competing interests.
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Methods, Tables 1 and 2 and Figs. 1–41.
Model of N-formyl-d-Leu tethered on Ser63 of SurE apo structure.
Model of N-formyl-l-Leu tethered on Ser63 of SurE apo structure.
Model of I1P tethered on Ser63 of SurE holo structure.
About this article
Cite this article
Matsuda, K., Zhai, R., Mori, T. et al. Heterochiral coupling in non-ribosomal peptide macrolactamization. Nat Catal 3, 507–515 (2020). https://doi.org/10.1038/s41929-020-0456-7
Nature Catalysis (2020)