Skip to main content
SpringerLink
Log in

Copper coordination in formylglycine generating enzymes

  • Regular Article
  • Published:
The European Physical Journal Special Topics Aims and scope Submit manuscript

Abstract

Formylglycine generating enzyme is a copper and oxygen-dependent protein, which catalyzes C–H activation, namely the transformation of peptidyl cysteine to formylglycine. No crystal structures of the enzyme containing copper were published so far. Here, we show by combinations of density functional theory with force fields in the QM/MM approach how copper can be incorporated in the enzyme based on two crystal structures containing Ag(I) and Cd(II) in place of Cu(I) and Cu(II). While we find a linear coordination for Cu(I) and a distorted octahedral environment for Cu(II) we also find the possibility of tetrahedral coordinations in both cases. This structural flexibility may allow the enzyme to catalyze the redox process and accommodate copper in both oxidation states.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. T. Dierks, A. Dickmanns, A. Preusser-Kunze, B. Schmidt, M. Mariappan, K. von Figura, R. Ficner, M.G. Rudolph, Cell 121, 541 (2005)

    Article  Google Scholar 

  2. M. Knop, P. Engi, R. Lemnaru, F.P. Seebeck, ChemBioChem 16, 2147 (2015)

    Article  Google Scholar 

  3. M. Meury, M. Knop, F.P. Seebeck, Angew. Chem. Int. Ed. 56, 8115 (2017)

    Article  Google Scholar 

  4. A. Changela, K. Chen, Y. Xue, J. Holschen, C.E. Outten, T.V. O’Halloran, A. Mondragon, Science 301, 1383 (2003)

    Article  ADS  Google Scholar 

  5. R. Wimmer, T. Herrmann, M. Solioz, K. Wuthrich, J. Biol. Chem. 274, 22597 (1999)

    Article  Google Scholar 

  6. D. Roeser, A. Preusser-Kunze, B. Schmidt, K. Gasow, J.G. Wittmann, T. Dierks, K. von Figura, M.G. Rudolph, Proc. Natl. Acad. Sci. USA 103, 81 (2006)

    Article  ADS  Google Scholar 

  7. L. Carlson, E.R. Ballister, E. Skordalakes, D.S. King, M.A. Breidenbach, S.A. Gilmore, J.M. Berger, C.R. Bertozzi, J. Biol. Chem. 283, 20117 (2008)

    Article  Google Scholar 

  8. A.D. MacKerell, D. Bashford, M. Bellott, R.L. Dunbrack, J.D. Evanseck, M.J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, J. Phys. Chem. B 102, 3586 (1998)

    Article  Google Scholar 

  9. A.D. MacKerell, N.K. Banavali, J. Comput. Chem. 21, 105 (2000)

    Article  Google Scholar 

  10. A.D. Mackerell, M. Feig, C.L. Brooks, J. Comput. Chem. 25, 1400 (2004)

    Article  Google Scholar 

  11. S.E. Feller, A.D. MacKerell, J. Phys. Chem. B 104, 7510 (2000)

    Article  Google Scholar 

  12. S.E. Feller, K. Gawrisch, A.D. MacKerell, J. Am. Chem. Soc. 124, 318 (2002)

    Article  Google Scholar 

  13. N. Foloppe, A.D. MacKerell, J. Comput. Chem. 21, 86 (2000)

    Article  Google Scholar 

  14. J.C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R.D. Skeel, L. Kalé, K. Schulten, J. Comput. Chem. 26, 1781 (2005)

    Article  Google Scholar 

  15. J.M. Word, S.C. Lovell, J.S. Richardson, D.C. Richardson, J. Mol. Biol. 285, 1735 (1999)

    Article  Google Scholar 

  16. W.L. Jorgensen, J. Chandrasekhar, J.D. Madura, R.W. Impey, M.L. Klein, J. Chem. Phys. 79, 926 (1983)

    Article  ADS  Google Scholar 

  17. W. Humphrey, A. Dalke, K. Schulten, J. Mol. Graphics 14, 27 (1996)

    Article  Google Scholar 

  18. P. Sherwood, A. de Vries, M. Guest, G. Schreckenbach, C. Catlow, S. French, A. Sokol, S. Bromley, W. Thiel, A. Turner, et al., Comp. Theor. Chem. 632, 1 (2003)

    Google Scholar 

  19. S. Metz, J. Kästner, A.A. Sokol, T.W. Keal, P. Sherwood, WIREs Comput. Mol. Sci. 4, 101 (2014)

    Article  Google Scholar 

  20. ChemShell, a Computational Chemistry Shell, Accessed May 8 (2017) see http://www.chemshell.org

  21. W. Smith, C. Yong, P. Rodger, Mol. Simul. 28, 385 (2002)

    Article  Google Scholar 

  22. TURBOMOLE V7.0, 2015 a development of University of Karlsruhe and Forschungszentrum Karlsruhe GmbH, 1989–2007, TURBOMOLE GmbH, since 2007, Accessed May 8 2017, available from http://www.turbomole.com

  23. A.D. Becke, J. Chem. Phys. 98, 5648 (1993)

    Article  ADS  Google Scholar 

  24. F. Weigend, R. Ahlrichs, Phys. Chem. Chem. Phys. 7, 3297 (2005)

    Article  Google Scholar 

  25. F. Weigend, Phys. Chem. Chem. Phys. 8, 1057 (2006)

    Article  Google Scholar 

  26. J. Kästner, J.M. Carr, T.W. Keal, W. Thiel, A. Wander, P. Sherwood, J. Phys. Chem. A 113, 11856 (2009)

    Article  Google Scholar 

  27. J.J. Warren, K.M. Lancaster, J.H. Richards, H.B. Gray, J. Inorg. Biochem. 115, 119 (2012)

    Article  Google Scholar 

  28. I. Shimizu, Y. Morimoto, D. Faltermeier, M. Kerscher, S. Paria, T. Abe, H. Sugimoto, N. Fujieda, K. Asano, T. Suzuki, P. Comba, S. Itoh, Inorg. Chem. 56, 9634 (2017)

    Article  Google Scholar 

  29. S. Itoh, N. Kishikawa, T. Suzuki, H.D. Takagi, Dalton Trans. 6, 1066 (2005)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany

    Sonia Álvarez-Barcia & Johannes Kästner

Authors
  1. Sonia Álvarez-Barcia
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Johannes Kästner
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Álvarez-Barcia, S., Kästner, J. Copper coordination in formylglycine generating enzymes. Eur. Phys. J. Spec. Top. 227, 1657–1664 (2019). https://doi.org/10.1140/epjst/e2019-800149-7

Download citation

  • Received:

  • Revised:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1140/epjst/e2019-800149-7

Search

Navigation