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Crystal structures of homoserine dehydrogenase suggest a novel catalytic mechanism for oxidoreductases

Nature Structural Biology volume 7, pages 238–244 (2000)Cite this article

Abstract

The structure of the antifungal drug target homoserine dehydrogenase (HSD) was determined from Saccharomyces cerevisiae in apo and holo forms, and as a ternary complex with bound products, by X-ray diffraction. The three forms show that the enzyme is a dimer, with each monomer composed of three regions, the nucleotide-binding region, the dimerization region and the catalytic region. The dimerization and catalytic regions have novel folds, whereas the fold of the nucleotide-binding region is a variation on the Rossmann fold. The novel folds impose a novel composition and arrangement of active site residues when compared to all other currently known oxidoreductases. This observation, in conjunction with site-directed mutagenesis of active site residues and steady-state kinetic measurements, suggest that HSD exhibits a new variation on dehydrogenase chemistry.

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Figure 1: Electron density maps for the two crystal forms of HSD.
Figure 2: The structure of HSD from Saccharomyces cerevisiae.
Figure 3: Stereo diagram of the metal binding site in HSD, located between strand βf and helix α2H.
Figure 4: Stereo diagrams of the active site of HSD in the apo, holo and ternary complex form.
Figure 5: Proposed reaction mechanisms of hydride transfer for HSD.

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References

  1. Andriole, V.T. Current and future therapy of invasive fungal infections. Curr. Clin. Top. Infect. Dis. 18, 19–36 (1998).

    CAS  PubMed  Google Scholar 

  2. Graybill, J.R. Systemic mycoses in the 21st century. Infect. Dis. Clin. North Am. 9, 297–311 (1995).

    CAS  PubMed  Google Scholar 

  3. Sternberg, S. The emerging fungal threat. Science 266, 1632–1634 (1994).

    Article  CAS  Google Scholar 

  4. DeMuri, G.P. & Hostetter, M.K. Resistance to antifungal agents. Pediatr. Clin. North Am. 42, 665–685 (1995).

    Article  CAS  Google Scholar 

  5. Wise, K.A., Speed, B.R., Ellis, D.H. & Andrew, J.H. Two fatal infections in immunocompromised patients caused by Scedosporium inflatum. Pathology 25, 187–189 (1993).

    CAS  PubMed  Google Scholar 

  6. Yamaguchi, H. et al. RI-331, a new antifungal antibiotic. Ann. N.Y. Acad. Sci. 544, 188–190 (1988).

    Article  CAS  Google Scholar 

  7. Yamaki, H. et al. The mechanism of antifungal action of (S)-2-amino-4-oxo-5- hydroxypentanoic acid, RI-331: the inhibition of homoserine dehydrogenase in Saccharomyces cerevisiae. Biochem. Biophys. Res. Commun. 168, 837–843 (1990).

    Article  CAS  Google Scholar 

  8. Yamaki, H., Yamaguchi, M., Tsuruo, T. & Yamaguchi, H. Mechanism of action of an antifungal antibiotic, RI-331 (S)-2-amino-4- oxo-5-hydroxypentanoic acid; kinetics of inactivation of homoserine dehydrogenase from Saccharomyces cerevisiae. J. Antibiot. (Tokyo) 45, 750–755 (1992).

    Article  CAS  Google Scholar 

  9. Hall, M.D., Levitt, D.G. & Banaszak, L.J. Crystal structure of Escherichia coli malate dehydrogenase. A complex of the apoenzyme and citrate at 1.87 Å resolution. J. Mol. Biol. 226, 867–882 (1992).

    Article  CAS  Google Scholar 

  10. White, J.L. et al. A comparison of the structures of apo dogfish M4 lactate dehydrogenase and its ternary complexes. J. Mol. Biol. 102, 759–779 (1976).

    Article  CAS  Google Scholar 

  11. Skarzynski, T., Moody, P.C. & Wonacott, A.J. Structure of holo-glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus at 1.8 Å resolution. J. Mol. Biol. 193, 171–187 (1987).

    Article  CAS  Google Scholar 

  12. Rossmann, M.G. & Argos, P. The taxonomy of binding sites in proteins. Mol. Cell. Biochem. 21, 161–182 (1978).

    Article  CAS  Google Scholar 

  13. Lesk, A.M. NAD-binding domains of dehydrogenases. Curr. Opin. Struct. Biol. 5, 775–783 (1995).

    Article  CAS  Google Scholar 

  14. Black, S. & Wright, N.G. Homoserine dehydrogenase. J. Biol. Chem. 213, 51–60 (1955).

    CAS  PubMed  Google Scholar 

  15. Thoden, J.B. et al. Structural analysis of UDP-sugar binding to UDP-galactose 4-epimerase from Escherichia coli. Biochemistry 36, 6294–6304 (1997).

    CAS  PubMed  Google Scholar 

  16. Gibrat, J.F., Madej, T. & Bryant, S.H. Surprising similarities in structure comparison. Curr. Opin. Struct. Biol. 6, 377–385 (1996).

    Article  CAS  Google Scholar 

  17. DeLaBarre, B. et al. Crystallization and preliminary X-ray diffraction studies of homoserine dehydrogenase from Saccharomyces cerevisiae. Acta Crystallogr. D 54, 413–415 (1998).

    Article  CAS  Google Scholar 

  18. Pavagi, S., Kochhar, S., Kochhar, V.K. & Sane, P.V. Purification and characterization of homoserine dehydrogenase from spinach leaves. Biochem. Mol. Biol. Int. 36, 649–658 (1995).

    CAS  PubMed  Google Scholar 

  19. Wedler, F.C. & Ley, B.W. Homoserine dehydrogenase-I (Escherichia coli): action of monovalent ions on catalysis and substrate association–dissociation. Arch. Biochem. Biophys. 301, 416–423 (1993).

    Article  CAS  Google Scholar 

  20. Yumoto, N., Kawata, Y., Noda, S. & Tokushige, M. Rapid purification and characterization of homoserine dehydrogenase from Saccharomyces cerevisiae. Arch. Biochem. Biophys. 285, 270–275 (1991).

    Article  CAS  Google Scholar 

  21. Jörnvall, H. et al. Short-chain dehydrogenases/reductases (SDR). Biochemistry 34, 6003–6013 (1995).

    Article  Google Scholar 

  22. Jez, J.M., Bennett, M.J., Schlegel, B.P., Lewis, M. & Penning, T.M. Comparative anatomy of the aldo-keto reductase superfamily. Biochem. J. 326, 625–636 (1997).

    Article  CAS  Google Scholar 

  23. Gruen, L.C. & McTgue, P.T. Hydration equilibria of aliphatic aldehydes in H2O and D2O. J. Chem. Soc. V, 5217–5229 (1963).

    Article  Google Scholar 

  24. Bell, R.P. The reversible hydration of carbonyl compounds. In Advances in physical organic chemistry, Vol. 4 (ed. Gold, V.) 1–29 (Academic Press, London and New York; 1966).

    Google Scholar 

  25. Corbier, C., Della Seta, F. & Branlant, G. A new chemical mechanism catalyzed by a mutated aldehyde dehydrogenase. Biochemistry 31, 12532–12535 (1992).

    Article  CAS  Google Scholar 

  26. Winberg, J.O. & McKinley-McKee, J.S. Drosophila melanogaster alcohol dehydrogenase: mechanism of aldehyde oxidation and dismutation. Biochem. J. 329, 561–570 (1998).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  28. Terwilliger, T.C. Multiwavelength anomalous diffraction phasing of macromolecular structures: analysis of MAD data as single isomorphous replacement with anomalous scattering data using the MADMRG Program. Methods Enzymol. 276, 530–537 (1997).

    Article  CAS  Google Scholar 

  29. 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 

  30. Cowtan, K. & Main, P. Miscellaneous algorithms for density modification. Acta Crystallogr. D 54, 487–493 (1998).

    Article  CAS  Google Scholar 

  31. Brünger, A.T. et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905–921 (1998).

    Article  Google Scholar 

  32. Kleywegt, G.J. & Brünger, A.T. Checking your imagination: applications of the free R value. Structure 4, 897–904 (1996).

    Article  CAS  Google Scholar 

  33. Westhead, D.R., Slidel, T.W., Flores, T.P. & Thornton, J.M. Protein structural topology: automated analysis and diagrammatic representation. Protein Sci. 8, 897–904 (1999).

    Article  CAS  Google Scholar 

  34. Kraulis, P.J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946–950 (1991).

    Article  Google Scholar 

  35. Esnouf, R.M. Further additions to MolScript version 1.4, including reading and contouring of electron-density maps. Acta Crystallogr. D 55, 938–940 (1999).

    Article  CAS  Google Scholar 

  36. Merritt, E.A. & Murphy, M.E.P. A program for photorealistic molecular graphics. Acta Crystallogr. D 50, 869–873 (1994).

    Article  CAS  Google Scholar 

  37. Read, R.J. Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Crystallogr. A 42, 140–149 (1986).

    Article  Google Scholar 

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Acknowledgements

We would like to thank past and present members of the Berghuis and Wright laboratories for their assistance and suggestions. Our thanks go also to R. Read and L. Tong for advice regarding the determination of the NCS axis, and D. Yang for helpful hints in establishing useful phasing information. This work was funded by a grant from the Medical Research Council of Canada to A.M.B, and a grant from the Natural Sciences and Engineering Research Council of Canada to G.D.W. B.D. is the recipient of a scholarship from the International Centre for Diffraction Data, A.M.B. is the recipient of an MRC/PMAC-HRF Research Career Award, and G.D.W. is the recipient of an MRC Scholarship.

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  1. Antimicrobial Research Centre and Department of Biochemistry, McMaster University, 1200 Main Street West, Hamilton, L8N 3Z5, Ontario, Canada

    Byron DeLaBarre, Paul R. Thompson, Gerard D. Wright & Albert M. Berghuis

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Correspondence to Albert M. Berghuis.

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DeLaBarre, B., Thompson, P., Wright, G. et al. Crystal structures of homoserine dehydrogenase suggest a novel catalytic mechanism for oxidoreductases. Nat Struct Mol Biol 7, 238–244 (2000). https://doi.org/10.1038/73359

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