Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Biocatalytic cyclization of small macrolactams by a penicillin-binding protein-type thioesterase

Nature Chemical Biology volume 20, pages 120–128 (2024)Cite this article

Subjects

Abstract

Macrocyclic peptides represent promising scaffolds for chemical tools and potential therapeutics. Synthetic methods for peptide macrocyclization are often hampered by C-terminal epimerization and oligomerization, leading to difficult scalability. While chemical strategies to circumvent this issue exist, they often require specific amino acids to be present in the peptide sequence. Herein, we report the characterization of Ulm16, a peptide cyclase belonging to the penicillin-binding protein-type class of thioesterases that catalyze head-to-tail macrolactamization of nonribosmal peptides. Ulm16 efficiently cyclizes various nonnative peptides ranging from 4 to 6 amino acids with catalytic efficiencies of up to 3 × 106 M−1 s−1. Unlike many previously described homologs, Ulm16 tolerates a variety of C- and N-terminal amino acids. The crystal structure of Ulm16, along with modeling of its substrates and site-directed mutagenesis, allows for rationalization of this wide substrate scope. Overall, Ulm16 represents a promising tool for the biocatalytic production of macrocyclic peptides.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Cyclic peptide natural products biosynthesized by PBP-type TEs.
Fig. 2: Substrate scope of Ulm16 and SurE.
Fig. 3: Crystal structure of Ulm16.
Fig. 4: Covalent docking of peptide substrates.
Fig. 5: Results from site-directed mutagenesis experiments.

Similar content being viewed by others

Data availability

Ulm16 12–440 coordinates and processed diffraction data have been deposited into the PDB under the accession code 8FEK. Other structures used in this paper are available at the PDB (6KSU and 6KSV). Protein sequences used in this study are from the NCBI database: Ulm16 (accession ATU31793.1), CppA (QQY97180.1), PenA (WP_158102277), SurE (BBZ90014.1), MppK (AAU34204.1), Lon18 (QUJ09165.1), FlkO (AGI87381.1), WolJ (UNO41476.1) and DsaJ (AJW76712.1). PDB files of AlphaFold models generated this for this study are publicly available and can be accessed using the following DOI: https://doi.org/10.6084/m9.figshare.24467026. The data that support the findings of this study are available within the main text and its Supplementary Information files. Data are also available from the corresponding author upon request.

References

  1. Driggers, E. M., Hale, S. P., Lee, J. & Terrett, N. K. The exploration of macrocycles for drug discovery—an underexploited structural class. Nat. Rev. Drug Discov. 7, 608–624 (2008).

    Article  CAS  PubMed  Google Scholar 

  2. Huang, Y., Wiedmann, M. M. & Suga, H. RNA display methods for the discovery of bioactive macrocycles. Chem. Rev. 119, 10360–10391 (2019).

    Article  CAS  PubMed  Google Scholar 

  3. Tsomaia, N. Peptide therapeutics: targeting the undruggable space. Eur. J. Med. Chem. 94, 459–470 (2015).

    Article  CAS  PubMed  Google Scholar 

  4. Malde, A. K., Hill, T. A., Iyer, A. & Fairlie, D. P. Crystal structures of protein-bound cyclic peptides. Chem. Rev. 119, 9861–9914 (2019).

    Article  CAS  PubMed  Google Scholar 

  5. White, C. J. & Yudin, A. K. Contemporary strategies for peptide macrocyclization. Nat. Chem. 3, 509–524 (2011).

    Article  CAS  PubMed  Google Scholar 

  6. Sarojini, V., Cameron, A. J., Varnava, K. G., Denny, W. A. & Sanjayan, G. Cyclic tetrapeptides from nature and design: a review of synthetic methodologies, structure, and function. Chem. Rev. 119, 10318–10359 (2019).

    Article  CAS  PubMed  Google Scholar 

  7. Du, L., Risinger, A. L., King, J. B., Powell, D. R. & Cichewicz, R. H. A potent HDAC inhibitor, 1-Alaninechlamydocin, from a Tolypocladium sp. induces G2/M cell cycle arrest and apoptosis in MIA PaCa-2 cells. J. Nat. Prod. 77, 1753–1757 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Pérez-Victoria, I. et al. Isolation and structural elucidation of cyclic tetrapeptides from Onychocola sclerotica. J. Nat. Prod. 75, 1210–1214 (2012).

  9. Steele, J. A., Uchytil, T. F., Durbin, R. D. & Rich, D. H. Chloroplast coupling factor 1: a species-specific receptor for tentoxin. Proc. Natl Acad. Sci. USA 73, 2245–2248 (1976).

  10. Saito, T. et al. CJ-15, 208, a novel kappa opioid receptor antagonist from a fungus, Ctenomyces serratus ATCC15502. J.Antibiotics 55, 847–854 (2002).

    Article  CAS  Google Scholar 

  11. Chung, B. K. W., White, C. J., Scully, C. C. G. & Yudin, A. K. The reactivity and conformational control of cyclic tetrapeptides derived from aziridine-containing amino acids. Chem. Sci. 7, 6662–6668 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Skropeta, D., Jolliffe, K. A. & Turner, P. Pseudoprolines as removable turn inducers: tools for the cyclization of small peptides. J. Org. Chem. 69, 8804–8809 (2004).

    Article  CAS  PubMed  Google Scholar 

  13. Alcaro, M. C. et al. On-resin head-to-tail cyclization of cyclotetrapeptides: optimization of crucial parameters. J. Pept. Sci. 10, 218–228 (2004).

    Article  CAS  PubMed  Google Scholar 

  14. Meutermans, W. D. F. et al. Difficult macrocyclizations: new strategies for synthesizing highly strained cyclic tetrapeptides. Org. Lett. 5, 2711–2714 (2003).

    Article  CAS  PubMed  Google Scholar 

  15. Vidović, N. et al. Chloride-assisted peptide macrocyclization. Org. Lett. 22, 2129–2134 (2020).

    Article  PubMed  Google Scholar 

  16. Jing, X. & Jin, K. A gold mine for drug discovery: strategies to develop cyclic peptides into therapies. Med. Res. Rev. 40, 753–810 (2020).

    Article  CAS  PubMed  Google Scholar 

  17. Abdalla, M. A. Medicinal significance of naturally occurring cyclotetrapeptides. J. Nat. Med. 70, 708–720 (2016).

    Article  CAS  PubMed  Google Scholar 

  18. Li, Y.-H. et al. Putative nonribosomal peptide synthetase and cytochrome P450 genes responsible for tentoxin biosynthesis in Alternaria alternata ZJ33. Toxins 8, 234 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Witte, T. E., Villeneuve, N., Boddy, C. N. & Overy, D. P. Accessory chromosome-acquired secondary metabolism in plant pathogenic fungi: the evolution of biotrophs into host-specific pathogens. Front. Microbiol. 12, 664276 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  20. Xu, H.-M. et al. Tataricins A and B, two novel cyclotetrapeptides from Aster tataricus, and their absolute configuration assignment. Tetrahedron Lett. 54, 1380–1383 (2013).

    Article  CAS  Google Scholar 

  21. Ma, G.-L. et al. Biosynthesis of tasikamides via pathway coupling and diazonium-mediated hydrazone formation. J. Am. Chem. Soc. 144, 1622–1633 (2022).

    Article  CAS  PubMed  Google Scholar 

  22. Kohli, R. M., Walsh, C. T. & Burkart, M. D. Biomimetic synthesis and optimization of cyclic peptide antibiotics. Nature 418, 658–661 (2002).

    Article  CAS  PubMed  Google Scholar 

  23. 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).

    Article  CAS  PubMed  Google Scholar 

  24. Horsman, M. E., Hari, T. P. A. & Boddy, C. N. Polyketide synthase and non-ribosomal peptide synthetase thioesterase selectivity: logic gate or a victim of fate? Nat. Prod. Rep. 33, 183–202 (2016).

    Article  CAS  PubMed  Google Scholar 

  25. Gao, X. et al. Cyclization of fungal nonribosomal peptides by a terminal condensation-like domain. Nat. Chem. Biol. 8, 823–830 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Hoyer, K. M., Mahlert, C. & Marahiel, M. A. The iterative gramicidin S thioesterase catalyzes peptide ligation and cyclization. Chem. Biol. 14, 13–22 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Kuranaga, T. et al. Total synthesis of the nonribosomal peptide surugamide B and identification of a new offloading cyclase family. Angew. Chem. 130, 9591–9595 (2018).

    Article  Google Scholar 

  28. 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.e4 (2019).

    Article  CAS  PubMed  Google Scholar 

  29. Thankachan, D. et al. A trans-acting cyclase offloading strategy for nonribosomal peptide synthetases. ACS Chem. Biol. 14, 845–849 (2019).

    Article  CAS  PubMed  Google Scholar 

  30. Matsuda, K. et al. SurE is a trans -acting thioesterase cyclizing two distinct non-ribosomal peptides. Org. Biomol. Chem. 17, 1058–1061 (2019).

    Article  CAS  PubMed  Google Scholar 

  31. Matsuda, K. et al. Heterochiral coupling in non-ribosomal peptide macrolactamization. Nat. Catal. 3, 507–515 (2020).

    Article  CAS  Google Scholar 

  32. Matsuda, K., Fujita, K. & Wakimoto, T. PenA, a penicillin-binding protein-type thioesterase specialized for small peptide cyclization. J. Ind. Microbiol. Biotechnol. 48, kuab023 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Fazal, A., Wheeler, J., Webb, M. E. & Seipke, R. F. The N-terminal substrate specificity of the SurE peptide cyclase. Org. Biomol. Chem. 20, 7232–7235 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Kobayashi, M., Fujita, K., Matsuda, K. & Wakimoto, T. Streamlined chemoenzymatic synthesis of cyclic peptides by non-ribosomal peptide cyclases. J. Am. Chem. Soc. 145, 3270–3275 (2023).

    Article  CAS  PubMed  Google Scholar 

  35. Fazal, A., Webb, M. E. & Seipke, R. F. The desotamide family of antibiotics. Antibiotics 9, 452 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Booth, T. J. et al. Bifurcation drives the evolution of assembly-line biosynthesis. Nat. Commun. 13, 3498 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Mirdita, M. et al. ColabFold: making protein folding accessible to all. Nat. Methods 19, 679–682 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. 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).

    Article  CAS  PubMed  Google Scholar 

  39. Gao, D.-W. et al. A polyketide cyclase that forms medium-ring lactones. J. Am. Chem. Soc. 143, 80–84 (2021).

    Article  CAS  PubMed  Google Scholar 

  40. Bar-Even, A. et al. The moderately efficient enzyme: evolutionary and physicochemical trends shaping enzyme parameters. Biochemistry 50, 4402–4410 (2011).

    Article  CAS  PubMed  Google Scholar 

  41. Hostetler, M. A. et al. Synthetic natural product inspired cyclic peptides. ACS Chem. Biol. 16, 2604–2611 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Walsh, C. & Wencewicz, T. A. Antibiotics: Challenges, Mechanisms, Opportunities (ASM Press, 2016).

  43. Dubus, A., Normark, S., Kania, M. & Page, M. G. P. The role of tyrosine 150 in catalysis of beta-lactam hydrolysis by AmpC beta.-lactamase from Escherichia coli investigated by site-directed mutagenesis. Biochemistry 33, 8577–8586 (1994).

    Article  CAS  PubMed  Google Scholar 

  44. McIntosh, J. A. et al. Circular logic: nonribosomal peptide-like macrocyclization with a ribosomal peptide catalyst. J. Am. Chem. Soc. 132, 15499–15501 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Ludewig, H. et al. Characterization of the fast and promiscuous macrocyclase from plant PCY1 enables the use of simple substrates. ACS Chem. Biol. 13, 801–811 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Nguyen, G. K. T. et al. Butelase-mediated cyclization and ligation of peptides and proteins. Nat. Protoc. 11, 1977–1988 (2016).

    Article  CAS  PubMed  Google Scholar 

  47. Hemu, X., Qiu, Y., Nguyen, G. K. T. & Tam, J. P. Total synthesis of circular bacteriocins by butelase 1. J. Am. Chem. Soc. 138, 6968–6971 (2016).

    Article  CAS  PubMed  Google Scholar 

  48. Nguyen, G. K. T. et al. Butelase 1: a versatile ligase for peptide and protein macrocyclization. J. Am. Chem. Soc. 137, 15398–15401 (2015).

    Article  CAS  PubMed  Google Scholar 

  49. Waterhouse, A. M., Procter, J. B., Martin, D. M. A., Clamp, M. & Barton, G. J. Jalview version 2—a multiple sequence alignment editor and analysis workbench. Bioinformatics 25, 1189–1191 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Terlouw, B. R. et al. MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters. Nucleic Acids Res. 51, D603–D610 (2023).

    Article  CAS  PubMed  Google Scholar 

  52. Gilchrist, C. L. M. & Chooi, Y.-H. clinker & clustermap.js: automatic generation of gene cluster comparison figures. Bioinformatics 37, 2473–2475 (2021).

    Article  CAS  PubMed  Google Scholar 

  53. Jones, D. T., Taylor, W. R. & Thornton, J. M. The rapid generation of mutation data matrices from protein sequences. Bioinformatics 8, 275–282 (1992).

    Article  CAS  Google Scholar 

  54. Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35, 1547–1549 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Schmidt, J. J. et al. A versatile chemoenzymatic synthesis for the discovery of potent cryptophycin analogs. ACS Chem. Biol. 15, 524–532 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Minor, W., Cymborowski, M., Otwinowski, Z. & Chruszcz, M. HKL-3000: the integration of data reduction and structure solution–from diffraction images to an initial model in minutes. Acta Crystallogr. D. Biol. Crystallogr. 62, 859–866 (2006).

    Article  PubMed  Google Scholar 

  57. Rossmann, M. G. The molecular replacement method. Acta Crystallogr. A 46, 73–82 (1990).

    Article  PubMed  Google Scholar 

  58. Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D. Biol. Crystallogr. 66, 213–221 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Liebschner, D. et al. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr. Sect. Struct. Biol. 75, 861–877 (2019).

    Article  CAS  Google Scholar 

  60. Waterhouse, A. et al. Swiss-model: Homology modelling of protein structures and complexes. Nucleic Acids Res. 46, W296–W303 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D. Biol. Crystallogr. 66, 486–501 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D. Biol. Crystallogr. 66, 12–21 (2010).

    Article  CAS  PubMed  Google Scholar 

  63. Blanco-Canosa, J. B., Nardone, B., Albericio, F. & Dawson, P. E. Chemical protein synthesis using a second-generation n-acylurea linker for the preparation of peptide-thioester precursors. J. Am. Chem. Soc. 137, 7197–7209 (2015).

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We thank A. Alwali and L. Wilbanks for their helpful discussions and aid with UPLC–MS and protein expression, respectively, C. Martinez-Brokaw and M. Hostetler for their advice on chemical synthesis and G. Buechel for her initial work on peptide synthesis. This work was funded by the National Institutes of Health (grant nos. 1R35GM138002 to E.I.P. and 1F31CA275390 to R.S.P.). Z.L.B. acknowledges the National Science Foundation for support under the Graduate Research Fellowship Program under grant no. DGE-1842166. We acknowledge the support from the Purdue Center for Cancer Research, NIH grant no. P30 CA023168.

Author information

Authors and Affiliations

  1. Department of Chemistry, Purdue University, West Lafayette, IN, USA

    Zachary L. Budimir, Rishi S. Patel, Alyssa Eggly, Claudia N. Evans, Hannah M. Rondon-Cordero, Jessica J. Adams, Chittaranjan Das & Elizabeth I. Parkinson

  2. Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA

    Elizabeth I. Parkinson

Authors
  1. Zachary L. Budimir
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Rishi S. Patel
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Alyssa Eggly
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Claudia N. Evans
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Hannah M. Rondon-Cordero
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Jessica J. Adams
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Chittaranjan Das
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Elizabeth I. Parkinson
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Z.L.B., C.N.E. and J.J.A. synthesized all the peptides used in this study. A.E. and C.N.E. performed nuclear magnetic resonance analyses of the peptides. Z.L.B., R.S.P. and H.M.R.-C. expressed the proteins. Z.L.B. performed the protein assays. R.S.P. performed the crystallography studies. Z.L.B. and R.S.P. performed the docking studies. Z.L.B., R.S.P., C.D. and E.I.P. conceived of the ideas and wrote the paper, with input from all authors. Project management and funding was the responsibility of C.D. and E.I.P.

Corresponding author

Correspondence to Elizabeth I. Parkinson.

Ethics declarations

Competing interests

The authors declare no competing interests.

Peer review

Peer review information

Nature Chemical Biology thanks Hai Deng, Akimasa Miyanaga and Ryan Seipke for their contribution to the peer review of this work.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Extended Data Fig. 1 Alpha fold models of predicted and validated PBP-TEs.

compared to the SurE Crystal structure (RMSD). The alpha fold model of SurE was used as a control and was compared to its known crystal structure. Highlighted in red is the loop region, which is shorter in the Ulm16 sequence, in yellow is the lipocalin loop previously hypothesized to play a role in substrate selectivity, and in orange is the sequence insertion only found in Ulm16 (residues 106-122).

Extended Data Fig. 2 Biosynthetic gene clusters of PBP-TEs that lack the loop region.

These biosynthetic gene clusters all share high homology to the ulleungmycin biosynthetic gene cluster and are predicted to produce natural products identical or very similar to the ulleungmycins.

Extended Data Fig. 3 Ulm peptide structure.

The Ulleungmycin A sequence was modified to incorporate only commercially available amino acids, resulting in a new sequence referred to as 'Ulm'. The changed amino acids are highlighted in grey, while the C-Terminal amino acid is highlighted in red and the N-Terminal amino acid is highlighted in blue.

Extended Data Fig. 4 Michaelis-Menten plots of Ulm16 kinetics for three peptide thioesters and alanine scans of the 'Ulm' peptide.

The names of the substrates used are indicated above each plot, and the enzyme concentrations employed are provided in the methods section. The data is summarized in of the main text. The plots represent the mean of triplicate experiments, and the error bars indicate the standard error of the mean (S.E.M).

Extended Data Fig. 5 Michaelis-Menten plots of Ulm16 and SurE kinetics for a common substrate (13).

The names of the substrates used are indicated above each plot, and the enzyme concentrations employed are provided in the methods section. The plots represent the mean of triplicate experiments, and the error bars indicate the standard error of the mean (S.E.M).

Extended Data Fig. 6 Michaelis-Menten plot of Ulm16 incubated with tetrapeptide 16.

The names of the substrates used are indicated above each plot, and the enzyme concentrations employed are provided in the methods section. The data is summarized in Table 1 of the main text. The plots represent the mean of triplicate experiments, and the error bars indicate the standard error of the mean (S.E.M).

Extended Data Fig. 7 Covalent docking of tetrapeptide 16 with SurE and comparison with Ulm16.

(a, b) Side-by-side of lowest MMGBSA score poses for SurE-16 (orange, A) and Ulm16-16 (blue, B). Peptide 16 is noticeably farther away from the hydrophobic pocket of the lipocalin domain in SurE due to differing angle of the lipocalin domain. (c) Overlay of Ulm16-16 (Sky blue-Light blue) and SurE-16 (Orange-Light Orange) highlights residues that we believe are key for binding and cyclization. Residues L284/L300 and D306/D297 are in the alpha beta hydrolase domain, and we hypothesize are key in binding the C-terminal D-amino acid. Residues R446/R431 and Y443/Y428 are in the lipocalin domain. We hypothesize that they help in cyclization of the peptide. The alpha beta hydrolase domain has been hidden for clarity. (d) Overlay of the C-terminal SNAC-D-Leu (orange) from the SurE substrate bound crystal structure (6SKV) and C-terminal covalently docked D-Tyr from peptide 16 (light orange). (e) Overlay of the C-Terminal SNAC-D-Leu (orange) from the SurE substrate bound crystal structure (6SKV) and C-terminal covalently docked D-Tyr from peptide 16 with Ulm16 (blue) showing they are occupying the same pocket.

Extended Data Fig. 8 Side-by-side comparison of top 5 lowest MMGBSA scoring peptides from covalent docking of 16 with SurE (light orange, A) and Ulm16 (light blue, B).

Peptide 16 exhibits limited access to the hydrophobic pocket within the lipocalin domain of SurE, resulting in a notable diversity of poses generated. Conversely, in the case of Ulm16, distinct conformations of the lipocalin domain facilitate a more proximal interaction with the hydrophobic pocket, leading to a predominant binding orientation consistently observed across outputs. Residues L286/L300 and D306/D297 are in the alpha-beta-hydrolase domain while Y443/Y428 is in the lipocalin domain.

Supplementary information

Supplementary Information

Supplementary Schemes 1 and 2, Tables 1–4, Notes 1 and 2, Figs. 1–106 and references.

Reporting Summary

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Budimir, Z.L., Patel, R.S., Eggly, A. et al. Biocatalytic cyclization of small macrolactams by a penicillin-binding protein-type thioesterase. Nat Chem Biol 20, 120–128 (2024). https://doi.org/10.1038/s41589-023-01495-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41589-023-01495-z

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing