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:

Structure of 4-diphosphocytidyl-2-C- methylerythritol synthetase involved in mevalonate- independent isoprenoid biosynthesis

Nature Structural Biology volume 8, pages 641–648 (2001)Cite this article

Abstract

The YgbP protein of Escherichia coli encodes the enzyme 4-diphosphocytidyl-2-C-methylerythritol (CDP-ME) synthetase, a member of the cytidyltransferase family of enzymes. CDP-ME is an intermediate in the mevalonate-independent pathway for isoprenoid biosynthesis in a number of prokaryotic organisms, algae, the plant plastids and the malaria parasite. Because vertebrates synthesize isoprenoid precursors using a mevalonate pathway, CDP-ME synthetase and other enzymes of the mevalonate-independent pathway for isoprenoid production represent attractive targets for the structure-based design of selective antibacterial, herbicidal and antimalarial drugs. The high-resolution structures of E. coli CDP-ME synthetase in the apo form and complexed with both CTP–Mg2+ and CDP-ME–Mg2+ reveal the stereochemical principles underlying both substrate and product recognition as well as catalysis in CDP-ME synthetase. Moreover, these complexes represent the first experimental structures for any cytidyltransferase with both substrates and products bound.

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

Figure 1: Biosynthesis of the isoprenoid precursor isopentenyl diphosphate (IPP, 8) via the alternative, mevalonate-independent DXP/MEP pathway.
Figure 2: Overall architecture of E. coli CDP-ME synthetase.
Figure 3: Schematic and structural view of the CDP-ME synthetase active site.
Figure 4: Catalytic mechanism of CDP-ME synthetase.

Similar content being viewed by others

Accession codes

Accessions

GenBank/EMBL/DDBJ

Protein Data Bank

References

  1. Sacchettini, J.C. & Poulter, C.D. Creating isoprenoid diversity. Science 277 1788–1789 (1997).

    Article  CAS  Google Scholar 

  2. Rohmer, M. The discovery of a mevalonate-independent pathway for isoprenoid biosynthesis in bacteria, algae and higher plants. Nat. Prod. Rep. 16, 565–574 (1999).

    Article  CAS  Google Scholar 

  3. Jomaa, H. et al. Inhibitors of the nonmevalonate pathway of isoprenoid biosynthesis as antimalarial drugs. Science 285, 1573–1576 (1999).

    Article  CAS  Google Scholar 

  4. Kuzuyama, T., Shimizu, T., Takahashi, S. & Seto, H. Fosmidomycin, a specific inhibitor of 1-deoxy-D-xylulose 5-phosphate reductoisomerase in the non-mevalonate pathway for terpenoid biosynthesis. Tetrahedron Lett. 39, 7913–7916 (1998).

    Article  CAS  Google Scholar 

  5. Lichtenthaler, H.K., Zeidler, J., Schwender, J. & Muller, C. The non-mevalonate isoprenoid biosynthesis of plants as a test system for new herbicides and drugs against pathogenic bacteria and the malaria parasite. Z. Naturforsch. 55, 305–313 (2000).

    Article  CAS  Google Scholar 

  6. Rohdich, F. et al. Cytidine 5′-triphosphate-dependent biosynthesis of isoprenoids: YgbP protein of Escherichia coli catalyzes the formation of 4-diphosphocytidyl-2-C-methylerythritol. Proc. Natl. Acad. Sci. USA 96, 11758–11763 (1999).

    Article  CAS  Google Scholar 

  7. Kuzuyama, T., Takagi, M., Kaneda, K., Dairi, T. & Seto, H. Formation of 4-(cytidine 5′-diphospho)-2-C-methyl-erythritol from 2-C-methyl-erythritol 4-phosphate by 2-C-methyl-erythritol 4-phosphate cytidylyltransferase, a new enzyme in the nonmevalonate pathway. Tetrahedron Lett. 41, 703–706 (2000).

    Article  CAS  Google Scholar 

  8. Rossmann, M.G., Liljas, A., Branden, C.-I. & Banaszak, L.J. The enzymes (Academic Press, New York; 1975).

    Google Scholar 

  9. Berman, H.M. et al. The Protein Data Bank. Nucleic Acids Res. 28, 235–242 (2000).

    Article  CAS  Google Scholar 

  10. Holm, L. & Sander, C. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233, 123–138 (1993).

    Article  CAS  Google Scholar 

  11. Jelakovic, S., Jann, K. & Schulz G.E. The three-dimensional structure of capsule-specific CMP:2-keto-3-deoxy-manno-octonic acid synthetase from Escherichia coli. FEBS Lett. 391, 157–161 (1996).

    Article  CAS  Google Scholar 

  12. Weber, C.H., Park, Y.S., Sanker, S., Kent, C. & Ludwig, M.L. A prototypical cytidylyltransferase: CTP:glycerol-3-phosphate cytidylyltransferase from Bacillus subtilis. Structure Fold. Des. 7, 1113–1124 (1999).

    Article  CAS  Google Scholar 

  13. Mosimann, S.C. et al. Structure of a sialic acid activating synthetase, CMP acylneuraminate synthetase in the presence and absence of CDP. J. Biol. Chem. 276, 8190–8196 (2001).

    Article  CAS  Google Scholar 

  14. Bork, P., Holm, L., Koonin, E.V. & Sander, C. The cytidylyltransferase superfamily: identification of the nucleotide-binding site and fold prediction. Proteins 22, 259–266 (1995).

    Article  CAS  Google Scholar 

  15. Veitch, D.P., Gilham, D. & Cornell, R.B. The role of histidine residues in the HXGH site of CTP:phosphocholine cytidylyltransferase in CTP binding and catalysis. Eur. J. Biochem. 255, 227–234 (1998).

    Article  CAS  Google Scholar 

  16. Cane, D.E., Chow, C., Lillo, A. & Kang, I. Molecular cloning, expression and characterisation of the first three genes in the mevalonate independant isoprenoid pathway in Streptomyces coelicolor. Bioorg. Med. Chem. 9, 1467–1477 (2001).

    Article  CAS  Google Scholar 

  17. Herz, S. et al. Biosynthesis of terpenoids: YgbB protein converts 4-diphosphocytidyl-2C-methyl-D-erythritol 2-phosphate to 2C-methyl-D-erythritol 2,4-cyclodiphosphate. Proc. Natl. Acad. Sci. USA 97, 2486–2490 (1999).

    Article  Google Scholar 

  18. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol . 276, 307–326 (1997).

    Article  CAS  Google Scholar 

  19. French, G.S. & Wilson, K.S. On the treatment of negative intensity observations. Acta Crystallog. A 34, 517–525 (1978).

    Article  Google Scholar 

  20. Collaborative Computational Project Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallog. D 50, 760–763 (1994).

  21. de La Fortelle E., & Bricogne G. Maximum-likelihood heavy-atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods. Methods Enzymol. 276, 472–494 (1997).

    Article  CAS  Google Scholar 

  22. McRee, D.E. A visual protein crystallographic software system for X11/Xview. J. Mol. Graph. 10, 44–46 (1992).

    Article  Google Scholar 

  23. Otwinowski, Z. in Proceedings of the CCP4 study weekend 307–326 (Daresbury Laboratories, Warrington, UK; 1991).

    Google Scholar 

  24. Perrakis, A., Sixma, T.K., Wilson K.S. & Lamzin, V.S. wARP: improvement and extension of crystallographic phases by weighted averaging of multiple refined dummy atomic models. Acta Crystallogr. D 53, 448–455 (1997).

    Article  CAS  Google Scholar 

  25. Jones, T.A. & Kjeldgaard, M.O. Electron-density map interpretation. Methods Enzymol. 277, 173–208 (1997).

    Article  CAS  Google Scholar 

  26. Brunger, A.T. et al. Crystallography and NMR System (CNS): a new software system for macromolecular structure determination. Acta Crystallog. D 54, 905–921 (1998).

    Article  CAS  Google Scholar 

  27. Laskowski, R.A., MacArthur, M.W., Moss, D.S. & Thornton, J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallog. 26, 283–291 (1993).

    Article  CAS  Google Scholar 

  28. Kraulis, P.J. MOLSCRIPT: a program to produce both detailled and schematic plots of structures. J. Appl. Crystallog. 24, 946–950 (1991).

    Article  Google Scholar 

  29. Esnouf, R. An extensively modified version of Molscript that includes greatly enhanced coloring capabilities. J. Mol. Graph. 15, 133–138 (1997).

    Google Scholar 

  30. Amundsen, S. X-POV-Team POV-Ray: persistence of vision ray-tracer. http://www.povray.org (1997).

  31. Nicholls, A. & Honig, B. GRASP. J. Comput. Chem. 12, 435–445 (1991).

    Article  CAS  Google Scholar 

  32. Sprenger G.A. et al. Identification of a thiamin-dependent synthase in Escherichia coli required for the formation of the 1-deoxy-D-xylulose 5-phosphate precursor to isoprenoids, thiamin, and pyridoxol. Proc. Natl. Acad. Sci. USA 94, 12857–12862 (1997).

    Article  CAS  Google Scholar 

  33. Lois, L.M. et al. Cloning and characterization of a gene from Escherichia coli encoding a transketolase-like enzyme that catalyzes the synthesis of D-1-deoxyxylulose 5-phosphate, a common precursor for isoprenoid, thiamin, and pyridoxol biosynthesis. Proc. Natl. Acad. Sci. USA 95, 2105–2110 (1997).

    Article  Google Scholar 

  34. Takahashi, S., Kuzuyama, T., Watanabe, H. & Seto, H. A 1-deoxy-D-xylulose 5-phosphate reductoisomerase catalyzing the formation of 2-C-methyl-D-erythritol 4-phosphate in an alternative nonmevalonate pathway for terpenoid biosynthesis. Proc. Natl. Acad. Sci. USA 95, 9879–9884 (1998).

    Article  CAS  Google Scholar 

  35. Kuzuyama, T., Takahashi, S., Takagi, M. & Seto, H. Characterization of 1-deoxy-D-xylulose 5-phosphate reductoisomerase, an enzyme involved in isopentenyl diphosphate biosynthesis, and identification of its catalytic amino acid residues. J. Biol. Chem. 275, 19928–19932 (2000).

    Article  CAS  Google Scholar 

  36. Luttgen, H. et al. Biosynthesis of terpenoids: YchB protein of Escherichia coli phosphorylates the 2-hydroxy group of 4-diphosphocytidyl-2C-methyl-D-erythritol. Proc. Natl. Acad. Sci. USA 97, 1062–1067 (2000).

    Article  CAS  Google Scholar 

  37. Kuzuyama, T. et al. Studies on the nonmevalonate pathway: conversion of 4-(cytidine 5′-diphospho)-2-C-methyl-erythritol to its 2-phospho derivative by 4-(cytidine 5′-diphospho)-2-C-methyl-erythritol kinase. Tetrahedron Lett. 41, 2925–2928 (2000).

    Article  CAS  Google Scholar 

  38. Takagi, M. et al. Studies on the nonmevalonate pathway: formation of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate from 2-phospho-4-(cytidine 5′-diphospho)-2-C-methyl-D-erythritol. Tetrahedron Lett. 41, 3395–3398 (2000).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work is based in part on research conducted at the Stanford Synchrotron Radiation Laboratory (SSRL), which is funded by the Department of Energy (BES, BER) and the National Institutes of Health (NCRR, NIGMS). We thank the staffs of the SSRL crystallographic beam lines (7-1, 7-2 and 9-2) and members of the Noel laboratory for technical assistance. This work was supported by grants from the Philippe Foundation Inc. to S.B.R. and the NIH (NIGMS) to J.P.N. and to D.E.C.

Author information

Authors and Affiliations

  1. Structural Biology Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, 92037, California, USA

    Stéphane B. Richard, Marianne E. Bowman, Witek Kwiatkowski & Joseph P. Noel

  2. Department of Chemistry, Brown University, Providence, 02912, Rhode Island, USA

    Ilgu Kang, Cathy Chow, Antonietta M. Lillo & David E. Cane

Authors
  1. Stéphane B. Richard
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Marianne E. Bowman
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Witek Kwiatkowski
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Ilgu Kang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Cathy Chow
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Antonietta M. Lillo
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. David E. Cane
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Joseph P. Noel
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Joseph P. Noel.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Richard, S., Bowman, M., Kwiatkowski, W. et al. Structure of 4-diphosphocytidyl-2-C- methylerythritol synthetase involved in mevalonate- independent isoprenoid biosynthesis. Nat Struct Mol Biol 8, 641–648 (2001). https://doi.org/10.1038/89691

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/89691

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