The structure of concanavalin A and its bound solvent determined with small-molecule accuracy at 0.94 [Aring ]resolution

Abstract

The structure of concanavalin A, a saccharide-binding metalloprotein of subunit molecular weight 25000 Da§, is reported with precision and accuracy equivalent to those of small-molecule crystal structures. An X-ray data-to-parameter ratio of 6.1:1 has allowed the first unrestrained anisotropic refinement of a protein structure and, indeed, one of large molecular weight. This has been achieved by the combined power of synchrotron radiation, a highly sensitive CCD-based area detector and cryogenic techniques on crystals of exceptional quality. The high precision of the atomic coordinates and the direct observation of many hydrogen atom positions, on both the protein and bound solvent, provide new insights into the protein structure, including precise geometry of the metal-binding sites, the role of water molecules in the extended saccharide-binding site, the structure and dynamics of bound and buried water, and direct evidence that proximal carboxylic acid side chains can exist as carboxyl–carboxylate pairs. The biophysical chemistry of this protein is thereby elucidated in detail in this and the companion paper.

References

1. W. I. Weis and K. Drickamer, Annu. Rev. Biochem., 1996, 65, 441.
2. J. Becker, G. N. Reeke Jr., J. L. Wang, B. A. Cunningham and G. M. Edelman, J. Biol. Chem., 1975, 250, 1513.
3. K. Hardman, R. C. Agarwal and M. J. Freiser, J. Mol. Biol., 1982, 157, 69.
4. C. Emmerich, J. R. Helliwell, M. Redshaw, J. H. Naismith, S. J. Harrop, J. Raftery, A. J. Kalb (Gilboa), J. Yariv, Z. Dauter and K. S. Wilson, Acta Crystallogr., Sect. D, 1994, 50, 749.
5. Z. Derewenda, J. Yariv, J. R. Helliwell, A. J. Kalb (Gilboa), E. J. Dodson, M. Z. Papiz, T. Wan and J. W. Campbell, EMBO J., 1989, 8, 2189.
6. J. H. Naismith, C. Emmerich, J. Habash, S. J. Harrop, J. R. Helliwell, W. N. Hunter, J. Raftery, A. J. Kalb (Gilboa) and J. Yariv, Acta Crystallogr., Sect. D, 1994, 50, 847.
7. S. J. Harrop, J. R. Helliwell, T. Wan, A. J. Kalb (Gilboa), L. Tong and J. Yariv, Acta Crystallogr., Sect. D, 1996, 52, 143.
8. G. Bradbrook, T. Gleichmann, S. J. Harrop, I. H. Hillier, J. Habash, A. J. Kalb (Gilboa), J. Yariv and J. R. Helliwell, J. Chem. Soc., Faraday Trans., submitted.
9. J. H. Naismith and R. A. Field, J. Biol. Chem., 1996, 271, 972.
10. J. R. Helliwell and M. Helliwell, Chem. Commun., 1996, 1595.
11. A. J. Kalb (Gilboa), J. Yariv, J. R. Helliwell and M. Z. Papiz, J. Cryst. Growth, 1988, 88, 537.
12. S. Parkin, B. Rupp and H. Hope, Acta Crystallogr., Sect. D, 1996, 52, 1161.
13. A. Deacon, J. Habash, S. J. Harrop, J. R. Helliwell, W. N. Hunter, G. A. Leonard, M. Peterson, A. Hädener, A. J. Kalb (Gilboa), N. M. Allinson, C. Castelli, K. Moon, S. McSweeney, A. Gonzalez, A. W. Thompson, S. Ealick, D. M. Szebenyi and R. Walter, Rev. Sci. Instrum., 1995, 66, 1287.
14. A. Deacon, T. Gleichmann, S. J. Harrop, J. R. Helliwell, A. J. Kalb (Gilboa) and J. Yariv, Rev. Sci. Instrum., 1996, 67, 1.
15. N. E. Chayen, T. J. Boggon, A. Cassetta, A. Deacon, T. Gleichmann, J. Habash, S. J. Harrop, J. R. Helliwell, Y. P. Nieh, M. R. Peterson, J. Raftery, E. H. Snell, A. Hadener, A. C. Niemann, D. P. Siddons, V. Stojanoff, A. W. Thompson, T. Ursby and M. Wulff, Quart. Rev. Biophys., 1996, 29, 227.
16. M. W. Tate, E. F. Eikenberry, S. L. Barna, M. E. Wall, J. L. Lawrance and S. M. Gruner, J. Appl. Crystallogr., 1995, 28, 196.
17. Z. Otwinowski and W. Minor, DENZO and SCALEPACK, Molecular Structure Corporation, 1996.
18. G. M. Sheldrick, SHELXL93, University of Gottingen, 1993.
19. G. M. Sheldrick, SHELXL96, University of Gottingen, 1996.
20. T. A. Jones, J. Y. Zou, S. W. Cowan and M. Kjeldgaard, Acta Crystallogr., Sect. A, 1991, 47, 110.
21. A. J. Kalb and I. Pecht, Biochim. Biophys. Acta, 1973, 303, 264.
22. E. Meirovitch, Z. Luz and A. J. Kalb (Gilboa), J. Am. Chem. Soc., 1974, 96, 7538.
23. E. Meirovitch, Z. Luz and A. J. Kalb (Gilboa), J. Am. Chem. Soc., 1974, 96, 7542.
24. D. C. Phillips, Sci. Am., 1966, 215, 78.
25. J. Bouckaert, R. Loris, F. Pootmans and L. Wyns, Proteins, Struct., Funct. Genet., 1995, 23, 510.
26. M. C. Vaney, S. Maignon, M. Ries-Kautt and A. Ducruix, Acta Crystallogr., Sect. D, 1996, 52, 505.
27. K. Kurachi, L. C. Sieker and L. H. Jensen, J. Biol. Chem., 1971, 250, 7663.
28. M. M. Flocco and S. L. Mowbray, J. Mol. Biol., 1995, 254, 96.
29. J. Habash, J. Raftery, M. S. Lehmann, C. Wilkinson, J. W. Campbell and J. R. Helliwell, J. Chem. Soc., Faraday Trans., 1997, 93, 4313.
30. J. R. Helliwell and C. Wilkinson, in Neutron and Synchrotron Radiation for Condensed Matter studies: Applications to Soft Condensed Matter and Biology, ed. J. Baruchel, J. L. Hodeau, M. S. Lehmann, J. R. Regnard and C. Schlenker, Springer-Verlag, 1994, vol. III, ch. XII.
31. International Tables for Crystallography Volume C, ed. A. J. C. Wilson, Kluwer Academic Publisher, Dordrecht, 1995, section 9.5.1.1, p. 700.
32. J. R. Helliwell, Nat. Struct. Biol., 1977, 4, 874.
33. Z. Dauter, V. S. Lamzin and K. S. Wilson, Curr. Opin. Struct. Biol., 1997, 7, 681.