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Structural snapshots of the minimal PKS system responsible for octaketide biosynthesis


Type II polyketide synthases (PKSs) are multi-enzyme complexes that produce secondary metabolites of medical relevance. Chemical backbones of such polyketides are produced by minimal PKS systems that consist of a malonyl transacylase, an acyl carrier protein and an α/β heterodimeric ketosynthase. Here, we present X-ray structures of all ternary complexes that constitute the minimal PKS system for anthraquinone biosynthesis in Photorhabdus luminescens. In addition, we characterize this invariable core using molecular simulations, mutagenesis experiments and functional assays. We show that malonylation of the acyl carrier protein is accompanied by major structural rearrangements in the transacylase. Principles of an ongoing chain elongation are derived from the ternary complex with a hexaketide covalently linking the heterodimeric ketosynthase with the acyl carrier protein. Our results for the minimal PKS system provide mechanistic understanding of PKSs and a fundamental basis for engineering PKS pathways for future applications.

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Fig. 1: Type II PKS gene cluster of anthraquinone (AQ 256) biosynthesis in P. luminescens.
Fig. 2: Crystal structures of holo-AntF alone and in complex with PlMCAT.
Fig. 3: Proposed reaction mechanism of malonate loading and polyketide chain elongation.
Fig. 4: Crystal structures of AntDE:apo-AntF and AntDE:holo-AntF.
Fig. 5: The AntDE-bound hexaketide is derived from iterative chain elongation steps.
Fig. 6: The minimal PKS system is responsible for octaketide biosynthesis.

Data availability

Crystallographic data have been deposited in the Protein Data Bank ( under the PDB IDs 6SM4, 6SM6, 6SMD, 6SMO and 6SMP. All other data are available in the text, methods, Supplementary Information, or upon request.


  1. 1.

    Hopwood, D. A. Genetic contributions to understanding polyketide synthases. Chem. Rev. 97, 2465–2497 (1997).

    CAS  PubMed  Google Scholar 

  2. 2.

    Hertweck, C. The biosynthetic logic of polyketide diversity. Angew. Chem. Int. Ed. 48, 4688–4716 (2009).

    CAS  Google Scholar 

  3. 3.

    McDaniel, R., Ebert-Khosla, S., Fu, H., Hopwood, D. A. & Khosla, C. Engineered biosynthesis of novel polyketides: influence of a downstream enzyme on the catalytic specificity of a minimal aromatic polyketide synthase. Proc. Natl Acad. Sci. USA 91, 11542–11546 (1994).

    CAS  PubMed  Google Scholar 

  4. 4.

    Carreras, C. W., Gehring, A. M., Walsh, C. T. & Khosla, C. Utilization of enzymatically phosphopantetheinylated acyl carrier proteins and acetyl-acyl carrier proteins by the actinorhodin polyketide synthase. Biochemistry 36, 11757–11761 (1997).

    CAS  PubMed  Google Scholar 

  5. 5.

    Bao, W., Wendt-Pienkowski, E. & Hutchinson, C. R. Reconstitution of the iterative type II polyketide synthase for tetracenomycin F2 biosynthesis. Biochemistry 37, 8132–8138 (1998).

    CAS  PubMed  Google Scholar 

  6. 6.

    Chen, A., Re, R. N. & Burkart, M. D. Type II fatty acid and polyketide synthases: deciphering protein–protein and protein–substrate interactions. Nat. Prod. Rep. 35, 1029–1045 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  7. 7.

    Lambalot, R. H. & Walsh, C. T. Cloning, overproduction, and characterization of the Escherichia coli holo–acyl carrier protein synthase. J. Biol. Chem. 270, 24658–24661 (1995).

    CAS  PubMed  Google Scholar 

  8. 8.

    Serre, L., Verbree, E. C., Dauter, Z., Stuitje, A. R. & Derewenda, Z. S. The Escherichia coli malonyl-CoA:acyl carrier protein transacylase at 1.5 Å resolution. Crystal structure of a fatty acid synthase component. J. Biol. Chem. 270, 12961–12964 (1995).

    CAS  PubMed  Google Scholar 

  9. 9.

    Khosla, C., Gokhale, R. S., Jacobsen, J. R. & Cane, D. E. Tolerance and specificity of polyketide synthases. Annu. Rev. Biochem. 68, 219–253 (1999).

    CAS  PubMed  Google Scholar 

  10. 10.

    Tsai, S.-C. The structural enzymology of iterative aromatic polyketide synthases: a critical comparison with fatty acid synthases. Annu. Rev. Biochem. 87, 503–531 (2018).

    CAS  PubMed  Google Scholar 

  11. 11.

    Sundaram, S. & Hertweck, C. On-line enzymatic tailoring of polyketides and peptides in thiotemplate systems. Curr. Opin. Chem. Biol. 31, 82–94 (2016).

    CAS  PubMed  Google Scholar 

  12. 12.

    Dutta, S. et al. Structure of a modular polyketide synthase. Nature 510, 512–517 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  13. 13.

    Li, X. et al. Structure–function analysis of the extended conformation of a polyketide synthase module. J. Am. Chem. Soc. 140, 6518–6521 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  14. 14.

    Hertweck, C., Luzhetskyy, A., Rebets, Y. & Bechthold, A. Type II polyketide synthases: gaining a deeper insight into enzymatic teamwork. Nat. Prod. Rep. 24, 162–190 (2007).

    CAS  PubMed  Google Scholar 

  15. 15.

    Brachmann, A. O. et al. A type II polyketide synthase is responsible for anthraquinone biosynthesis in Photorhabdus luminescens. ChemBioChem 8, 1721–1728 (2007).

    CAS  PubMed  Google Scholar 

  16. 16.

    Zhou, Q. et al. Molecular mechanism of polyketide shortening in anthraquinone biosynthesis of Photorhabdus luminescens. Chem. Sci. 10, 6341–6349 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  17. 17.

    Cummings, M. et al. Assembling a plug-and-play production line for combinatorial biosynthesis of aromatic polyketides in Escherichia coli. PLoS Biol. 17, e3000347 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  18. 18.

    Walsh, C. T., Gehring, A. M., Weinreb, P. H., Quadri, L. E. & Flugel, R. S. Post-translational modification of polyketide and nonribosomal peptide synthases. Curr. Opin. Chem. Biol. 1, 309–315 (1997).

    CAS  PubMed  Google Scholar 

  19. 19.

    Dreier, J., Shah, A. N. & Khosla, C. Kinetic analysis of the actinorhodin aromatic polyketide synthase. J. Biol. Chem. 274, 25108–25112 (1999).

    CAS  PubMed  Google Scholar 

  20. 20.

    Fu, H., Hopwood, D. A. & Khosla, C. Engineered biosynthesis of novel polyketides: evidence for temporal, but not regiospecific, control of cyclization of an aromatic polyketide precursor. Chem. Biol. 1, 205–210 (1994).

    CAS  PubMed  Google Scholar 

  21. 21.

    Summers, R. G., Ali, A., Shen, B., Wessel, W. A. & Hutchinson, C. R. Malonyl-coenzyme A:acyl carrier protein acyltransferase of Streptomyces glaucescens: a possible link between fatty acid and polyketide biosynthesis. Biochemistry 34, 9389–9402 (1995).

    CAS  PubMed  Google Scholar 

  22. 22.

    Holak, T. A., Kearsley, S. K., Kim, Y. & Prestegard, J. H. Three-dimensional structure of acyl carrier protein determined by NMR pseudoenergy and distance geometry calculations. Biochemistry 27, 6135–6142 (1988).

    CAS  PubMed  Google Scholar 

  23. 23.

    Chan, D. I. & Vogel, H. J. Current understanding of fatty acid biosynthesis and the acyl carrier protein. Biochem. J. 430, 1–19 (2010).

    CAS  PubMed  Google Scholar 

  24. 24.

    Ollis, D. L. et al. The alpha/beta hydrolase fold. Protein Eng. 5, 197–211 (1992).

    CAS  PubMed  Google Scholar 

  25. 25.

    Pastore, A., Saudek, V., Ramponi, G. & Williams, R. J. P. Three-dimensional structure of acylphosphatase: refinement and structure analysis. J. Mol. Biol. 224, 427–440 (1992).

    CAS  PubMed  Google Scholar 

  26. 26.

    Oefner, C., Schulz, H., D’Arcy, A. & Dale, G. E. Mapping the active site of Escherichia coli malonyl-CoA-acyl carrier protein transacylase (FabD) by protein crystallography. Acta Crystallogr. D 62, 613–618 (2006).

    PubMed  Google Scholar 

  27. 27.

    Keatinge-Clay, A. T., Maltby, D. A., Medzihradszky, K. F., Khosla, C. & Stroud, R. M. An antibiotic factory caught in action. Nat. Struct. Mol. Biol. 11, 888–893 (2004).

    CAS  PubMed  Google Scholar 

  28. 28.

    Grammbitter, G. L. C. et al. An uncommon type II PKS catalyzes biosynthesis of aryl polyene pigments. J. Am. Chem. Soc. 141, 16615–16623 (2019).

    CAS  PubMed  Google Scholar 

  29. 29.

    Mathieu, M. et al. The 2.8 Å crystal structure of peroxisomal 3-ketoacyl-CoA thiolase of Saccharomyces cerevisiae: a five-layered αβαβα structure constructed from two core domains of identical topology. Structure. 2, 797–808 (1994).

    CAS  PubMed  Google Scholar 

  30. 30.

    Robbins, T., Kapilivsky, J., Cane, D. E. & Khosla, C. Roles of conserved active site residues in the ketosynthase domain of an assembly line polyketide synthase. Biochemistry 55, 4476–4484 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  31. 31.

    Fu, H., Ebert-Khosla, S., Hopwood, D. A. & Khosla, C. Engineered biosynthesis of novel polyketides: dissection of the catalytic specificity of the act ketoreductase. J. Am. Chem. Soc. 116, 4166–4170 (1994).

    CAS  Google Scholar 

  32. 32.

    Jakobi, K. & Hertweck, C. A gene cluster encoding resistomycin biosynthesis in Streptomyces resistomycificus; exploring polyketide cyclization beyond linear and angucyclic patterns. J. Am. Chem. Soc. 126, 2298–2299 (2004).

    CAS  PubMed  Google Scholar 

  33. 33.

    Sherman, D. H., Kim, E. S., Bibb, M. J. & Hopwood, D. A. Functional replacement of genes for individual polyketide synthase components in Streptomyces coelicolor A3(2) by heterologous genes from a different polyketide pathway. J. Bacteriol. 174, 6184–6190 (1992).

    CAS  PubMed  PubMed Central  Google Scholar 

  34. 34.

    Heath, R. J. & Rock, C. O. The Claisen condensation in biology. Nat. Prod. Rep. 19, 581–596 (2002).

    CAS  PubMed  Google Scholar 

  35. 35.

    Duchaud, E. et al. The genome sequence of the entomopathogenic bacterium Photorhabdus luminescens. Nat. Biotechnol. 21, 1307–1313 (2003).

    CAS  PubMed  Google Scholar 

  36. 36.

    Kulak, N. A., Pichler, G., Paron, I., Nagaraj, N. & Mann, M. Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells. Nat. Methods 11, 319–324 (2014).

    CAS  PubMed  Google Scholar 

  37. 37.

    Kabsch, W. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Cryst. 26, 795–800 (1993).

    CAS  Google Scholar 

  38. 38.

    McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Cryst. 40, 658–674 (2007).

    CAS  Google Scholar 

  39. 39.

    Roujeinikova, A. et al. Structural studies of fatty acyl-(acyl carrier protein) thioesters reveal a hydrophobic binding cavity that can expand to fit longer substrates. J. Mol. Biol. 365, 135–145 (2007).

    CAS  PubMed  Google Scholar 

  40. 40.

    Turk, D. MAIN software for density averaging, model building, structure refinement and validation. Acta Crystallogr. D 69, 1342–1357 (2013).

    CAS  PubMed  Google Scholar 

  41. 41.

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

    CAS  PubMed  Google Scholar 

  42. 42.

    Murshudov, G. N. et al. REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr. D 67, 355–367 (2011).

    CAS  PubMed  Google Scholar 

  43. 43.

    Langer, G., Cohen, S. X., Lamzin, V. S. & Perrakis, A. Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7. Nat. Protoc. 3, 1171–1179 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  44. 44.

    Becke, A. D. Density-functional thermochemistry. III. The role of exact exchange. J. Chem. Phys. 98, 5648–5652 (1993).

    CAS  Google Scholar 

  45. 45.

    Lee, C., Yang, W. & Parr, R. G. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys. Rev. B 37, 785–789 (1988).

    CAS  Google Scholar 

  46. 46.

    Schäfer, A., Huber, C. & Ahlrichs, R. Fully optimized contracted Gaussian basis sets of triple zeta valence quality for atoms Li to Kr. J. Chem. Phys. 100, 5829–5835 (1994).

    Google Scholar 

  47. 47.

    Grimme, S., Antony, J., Ehrlich, S. & Krieg, H. A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H–Pu. J. Chem. Phys. 132, 154104 (2010).

    PubMed  Google Scholar 

  48. 48.

    Klamt, A. & Schüürmann, G. COSMO: a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient. J. Chem. Soc., Perkin Trans. 2, 799–805 (1993).

    Google Scholar 

  49. 49.

    Huang, J. & MacKerell, A. D. CHARMM36 all-atom additive protein force field: validation based on comparison to NMR data. J. Comput. Chem. 34, 2135–2145 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  50. 50.

    Ahlrichs, R., Bär, M., Häser, M., Horn, H. & Kölmel, C. Electronic structure calculations on workstation computers: the program system turbomole. Chem. Phys. Lett. 162, 165–169 (1989).

    CAS  Google Scholar 

  51. 51.

    Brooks, B. R. et al. CHARMM: the biomolecular simulation program. J. Comput. Chem. 30, 1545–1614 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  52. 52.

    Riahi, S. & Rowley, C. N. The CHARMM-TURBOMOLE interface for efficient and accurate QM/MM molecular dynamics, free energies, and excited state properties. J. Comput. Chem. 35, 2076–2086 (2014).

    CAS  PubMed  Google Scholar 

  53. 53.

    Humphrey, W., Dalke, A. & Schulten, K. VMD: visual molecular dynamics. J. Mol. Graph. 14, 33–38 (1996).

    CAS  PubMed  Google Scholar 

  54. 54.

    Fenyö, D. et al. MALDI sample preparation: the ultra thin layer method. J. Vis. Exp. 192, 1–2 (2007).

    Google Scholar 

  55. 55.

    Rühl, M. et al. Elucidation of chemical modifier reactivity towards peptides and proteins and the analysis of specific fragmentation by matrix-assisted laser desorption/ionization collision-induced dissociation tandem mass spectrometry. Rapid Commun. Mass Spectrom. 33, 40–49 (2019).

    PubMed  Google Scholar 

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We acknowledge financial support from the Deutsche Forschungsgemeinschaft (DFG) SPP 1617 (H.B.B.) and SFB 1035 (V.R.I.K.) projects, as well as from the LOEWE program of the state of Hesse as part of the MegaSyn research cluster (H.B.B.). We thank the staff of beamline X06SA at the Paul Scherrer Institute (SLS, Villigen) for assistance during data collection, S. Fuchs for MALDI-MS analysis, and M. Karas for MALDI-MS access. The Swedish National Infrastructure for Computing (SNIC, 2019/2-3) provided computing time.

Author information




H.B.B. and M.G. initiated and supervised the project; Q.Z. generated the expression constructs and established the activity assays to reconstitute the minimal PKS system; G.L.C.G. and M.R. performed mass spectrometry analyses; A.B. cloned mutants, and purified and crystallized proteins; M.G. determined X-ray structures; A.B., M.S., V.R.I.K. and M.G. analysed structures; V.R.I.K. carried out molecular simulations; and M.G. wrote the paper with input from all authors.

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Correspondence to Helge B. Bode or Michael Groll.

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Bräuer, A., Zhou, Q., Grammbitter, G.L.C. et al. Structural snapshots of the minimal PKS system responsible for octaketide biosynthesis. Nat. Chem. 12, 755–763 (2020).

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