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.

Molecular basis for interactions between an acyl carrier protein and a ketosynthase

Abstract

Fatty acid synthases are dynamic ensembles of enzymes that can biosynthesize long hydrocarbon chains efficiently. Here we visualize the interaction between the Escherichia coli acyl carrier protein (AcpP) and β-ketoacyl-ACP-synthase I (FabB) using X-ray crystallography, NMR, and molecular dynamics simulations. We leveraged this structural information to alter lipid profiles in vivo and provide a molecular basis for how protein–protein interactions can regulate the fatty acid profile in E. coli.

Fig. 1: Crystal structure of E. coli AcpP–FabB complex.
Fig. 2: Protein–protein interactions and the fatty acid profile.

Data availability

The AcpP–FabB crystal structure coordinates are available through the Protein Data Bank website using the accession code 5KOF. The NMR assignments have been deposited with the Biological Magnetic Resonance Bank (BMRB), IDs 27872 and 27874, and are available in Supplementary Table 2.

References

  1. 1.

    Finzel, K., Lee, D. J. & Burkart, M. D. Chembiochem 16, 528–547 (2015)..

  2. 2.

    Feng, Y. & Cronan, J. E. J. Biol. Chem. 284, 29526–29535 (2009).

  3. 3.

    Wright, H. T. & Reynolds, K. A. Curr. Opin. Microbiol. 10, 447–453 (2007).

  4. 4.

    Yu, X., Liu, T., Zhu, F. & Khosla, C. Proc. Natl Acad. Sci. USA 108, 18643–18648 (2011).

  5. 5.

    Gajewski, J. et al. Nat. Chem. Biol. 13, 363–365 (2017).

  6. 6.

    Rock, C. & Cronan, J. E. Methods Enzymol. 71, 341–351 (1981).

  7. 7.

    Kim, Y. & Prestegard, J. H. Biochemistry 28, 8792–8797 (1989).

  8. 8.

    Roujeinikova, A. et al. J. Mol. Biol. 365, 135–145 (2007).

  9. 9.

    Majerus, P. W., Alberts, A. W. & Vagelos, P. R. Proc. Natl Acad. Sci. USA 53, 410–417 (1965).

  10. 10.

    Chan, D. I., Stockner, T., Tieleman, D. P. & Vogel, H. J. J. Biol. Chem. 283, 33620–33629 (2008).

  11. 11.

    Crosby, J. & Crump, M. P. Nat. Prod. Rep. 29, 1111 (2012).

  12. 12.

    Thiele, G. A. R. et al. Biochemistry 56, 2533–2536 (2017).

  13. 13.

    Nguyen, C. et al. Nature 505, 427–431 (2014).

  14. 14.

    Cronan, J. E. Biochem. J. 460, 157–163 (2014).

  15. 15.

    Beld, J., Cang, H. & Burkart, M. D. Angew. Chem. Int. Ed. Engl. 53, 14456–14461 (2014).

  16. 16.

    Worthington, A. S., Rivera, H., Torpey, J. W., Alexander, M. D. & Burkart, M. D. ACS Chem. Biol. 1, 687–691 (2006).

  17. 17.

    Worthington, A. S. & Burkart, M. D. Org. Biomol. Chem. 4, 44–46 (2006).

  18. 18.

    Byers, D. M. & Gong, H. Biochem. Cell Biol. 85, 649–662 (2007).

  19. 19.

    Zhang, L. et al. Cell Res. 26, 1330–1344 (2016).

  20. 20.

    De Lay, N. R. & Cronan, J. E. J. Bacteriol. 188, 287–296 (2006).

  21. 21.

    Garwin, J. L. & Cronan, J. E. Jr. J. Bacteriol. 141, 1457–1459 (1980).

  22. 22.

    Magnuson, K., Jackowski, S., Rock, C. O. & Cronan, J. E. Jr. Microbiol. Rev. 57, 522–542 (1993).

  23. 23.

    Garwin, J. L., Klages, A. L. & Cronan, J. E. Jr. J. Biol. Chem. 255, 3263–3265 (1980).

  24. 24.

    Rossini, E., Gajewski, J., Klaus, M., Hummer, G. & Grininger, M. Chem. Commun. 54, 11606–11609 (2018).

  25. 25.

    De Lay, N. R. & Cronan, J. E. J. Biol. Chem. 282, 20319–20328 (2007).

  26. 26.

    Kosa, N. M., Haushalter, R. W., Smith, A. R. & Burkart, M. D. Nat. Methods 9, 981–984 (2012).

  27. 27.

    Battye, T. G. G., Kontogiannis, L., Johnson, O., Powell, H. R. & Leslie, A. G. W. Acta Crystallogr. D 67, 271–281 (2011).

  28. 28.

    Adams, P. D. et al. Acta Crystallogr. D 66, 213–221 (2010).

  29. 29.

    Delaglio, F. et al. J. Biomol. NMR 6, 277–293 (1995).

  30. 30.

    Lee, W., Tonelli, M. & Markley, J. L. Bioinformatics 31, 1325–1327 (2015).

  31. 31.

    Williamson, M. P. Prog. Nucl. Magn. Reson. Spectrosc. 73, 1–16 (2013).

  32. 32.

    Pettersen, E. F. et al. J. Comput. Chem. 25, 1605–1612 (2004).

  33. 33.

    Vanquelef, E. et al. R.E.D. Nucleic Acids Res. 39, W511–W517 (2011).

Download references

Acknowledgements

S.C.T. and M.D.B. are supported by NIH GM100305 and GM095970. M.D.B. is also supported by National Science Foundation (NSF) Division of Integrative Organismal Systems (IOS) grant 1516156, and R.L. is also supported by NIH GM093040 and GM079383. This research used resources of the Advanced Light Source, which is a Department of Energy (DOE) Office of Science User Facility under contract no. DE-AC02-05CH11231. The authors thank the staff of beamline 8.2.1 at the Advanced Light Source for support during X-ray diffraction data collection, X. Huang and S. Opella for their guidance and assistance with NMR collection at the UCSD Biomolecular NMR facility, and B. Fuglestad for many helpful discussions on NMR. The authors thank J. E. Cronan for the CY1877 strain. Additional funding from the institutional Chemical and Structural Biology Training Grant (National Institute of General Medical Sciences grant T32GM108561) and the National Science Foundation Graduate Research Fellowship is also acknowledged.

Author information

Affiliations

Authors

Contributions

J.C.M. performed the crystallography and structural analysis, and prepared the manuscript. D.J.L. performed protein NMR, cloning and in vivo complementation, fatty acid analysis, and also prepared the manuscript. D.R.J. performed crystallography and structural analysis. A.J.S. performed MD simulations and analysis. J.B. performed synthesis of the crosslinker and fatty acid analysis. J.F.B. performed structural refinement and validation. J.J.H. performed GCMS and analysis. R.L. provided computational support and supervised MD and dry laboratory work. M.D.B. supervised synthesis, protein NMR, fatty acid complementation, and GCMS analysis. S.C.T. supervised crystallography and wet laboratory work. All authors contributed to editing the manuscript.

Corresponding authors

Correspondence to Michael D. Burkart or Shiou-Chuan Tsai.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

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

Supplementary information

Supplementary Information

Supplementary Tables 1–3, Supplementary Figures 1–20

Reporting Summary

Supplementary Video 1

Principal component analysis of AcpP-FabB molecular dynamics simulations.

Supplementary Video 2

Principal component analysis of AcpP-FabB molecular dynamics simulations.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Milligan, J.C., Lee, D.J., Jackson, D.R. et al. Molecular basis for interactions between an acyl carrier protein and a ketosynthase. Nat Chem Biol 15, 669–671 (2019). https://doi.org/10.1038/s41589-019-0301-y

Download citation

Further reading

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