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. 1989 Aug;8(8):2189–2193. doi: 10.1002/j.1460-2075.1989.tb08341.x

The structure of the saccharide-binding site of concanavalin A.

Z Derewenda 1, J Yariv 1, J R Helliwell 1, A J Kalb 1, E J Dodson 1, M Z Papiz 1, T Wan 1, J Campbell 1
PMCID: PMC401146  PMID: 2792084

Abstract

A complex of concanavalin A with methyl alpha-D-mannopyranoside has been crystallized in space group P212121 with a = 123.9 A, b = 129.1 A and c = 67.5 A. X-ray diffraction intensities to 2.9 A resolution have been collected on a Xentronics/Nicolet area detector. The structure has been solved by molecular replacement where the starting model was based on refined coordinates of an I222 crystal of saccharide-free concanavalin A. The structure of the saccharide complex was refined by restrained least-squares methods to an R-factor value of 0.19. In this crystal form, the asymmetric unit contains four protein subunits, to each of which a molecule of mannoside is bound in a shallow crevice near the surface of the protein. The methyl alpha-D-mannopyranoside molecule is bound in the C1 chair conformation 8.7 A from the calcium-binding site and 12.8 A from the transition metal-binding site. A network of seven hydrogen bonds connects oxygen atoms O-3, O-4, O-5 and O-6 of the mannoside to residues Asn14, Leu99, Tyr100, Asp208 and Arg228. O-2 and O-1 of the mannoside extend into the solvent. O-2 is hydrogen-bonded through a water molecule to an adjacent asymmetric unit. O-1 is not involved in any hydrogen bond and there is no fixed position for its methyl substituent.

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Selected References

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  1. Bernstein F. C., Koetzle T. F., Williams G. J., Meyer E. F., Jr, Brice M. D., Rodgers J. R., Kennard O., Shimanouchi T., Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol. 1977 May 25;112(3):535–542. doi: 10.1016/s0022-2836(77)80200-3. [DOI] [PubMed] [Google Scholar]
  2. Brewer C. F., Sternlicht H., Marcus D. M., Grollman A. P. Interactions of saccharides with concanavalin A. Mechanism of binding of alpha- and beta-methyl D-glucopyranoside to concanavalin A as determined by 13C nuclear magnetic resonance. Biochemistry. 1973 Oct 23;12(22):4448–4457. doi: 10.1021/bi00746a023. [DOI] [PubMed] [Google Scholar]
  3. Cunningham B. A., Wang J. L., Waxdal M. J., Edelman G. M. The covalent and three-dimensional structure of concanavalin A. II. Amino acid sequence of cyanogen bromide fragment F3. J Biol Chem. 1975 Feb 25;250(4):1503–1512. [PubMed] [Google Scholar]
  4. Dani M., Manca F., Rialdi G. Calorimetric study of concanavalin A binding to saccharides. Biochim Biophys Acta. 1981 Jan 30;667(1):108–117. doi: 10.1016/0005-2795(81)90071-4. [DOI] [PubMed] [Google Scholar]
  5. Edelman G. M., Cunningham B. A., Reeke G. N., Jr, Becker J. W., Waxdal M. J., Wang J. L. The covalent and three-dimensional structure of concanavalin A. Proc Natl Acad Sci U S A. 1972 Sep;69(9):2580–2584. doi: 10.1073/pnas.69.9.2580. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Greer J., Kaufman H. W., Kalb A. J. An x-ray crystallographic study of concanavalin A. J Mol Biol. 1970 Mar 14;48(2):365–366. doi: 10.1016/0022-2836(70)90169-5. [DOI] [PubMed] [Google Scholar]
  7. Hardman K. D., Agarwal R. C., Freiser M. J. Manganese and calcium binding sites of concanavalin A. J Mol Biol. 1982 May 5;157(1):69–86. doi: 10.1016/0022-2836(82)90513-7. [DOI] [PubMed] [Google Scholar]
  8. Hardman K. D., Ainsworth C. F. Structure of concanavalin A at 2.4-A resolution. Biochemistry. 1972 Dec 19;11(26):4910–4919. doi: 10.1021/bi00776a006. [DOI] [PubMed] [Google Scholar]
  9. Hardman K. D., Ainsworth C. F. Structure of the concanavalin A-methyl alpha-D-mannopyranoside complex at 6-A resolution. Biochemistry. 1976 Mar 9;15(5):1120–1128. doi: 10.1021/bi00650a026. [DOI] [PubMed] [Google Scholar]
  10. Jacrot B., Cusack S., Dianoux A. J., Engelman D. M. Inelastic neutron scattering analysis of hexokinase dynamics and its modification on binding of glucose. Nature. 1982 Nov 4;300(5887):84–86. doi: 10.1038/300084a0. [DOI] [PubMed] [Google Scholar]
  11. Kalb A. J., Levitzki A. Metal-binding sites of concanavalin A and their role in the binding of alpha-methyl d-glucopyranoside. Biochem J. 1968 Oct;109(4):669–672. doi: 10.1042/bj1090669. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Kalb A. J., Lustig A. The molecular weight of concanavalin A. Biochim Biophys Acta. 1968 Oct 21;168(2):366–367. doi: 10.1016/0005-2795(68)90161-x. [DOI] [PubMed] [Google Scholar]
  13. Quiocho F. A. Carbohydrate-binding proteins: tertiary structures and protein-sugar interactions. Annu Rev Biochem. 1986;55:287–315. doi: 10.1146/annurev.bi.55.070186.001443. [DOI] [PubMed] [Google Scholar]
  14. Reeke G. N., Jr, Becker J. W., Edelman G. M. The covalent and three-dimensional structure of concanavalin A. IV. Atomic coordinates, hydrogen bonding, and quaternary structure. J Biol Chem. 1975 Feb 25;250(4):1525–1547. [PubMed] [Google Scholar]
  15. Shoham M., Yonath A., Sussman J. L., Moult J., Traub W., Kalb A. J. Crystal structure of demetallized concanavalin A: the metal-binding region. J Mol Biol. 1979 Jun 25;131(2):137–155. doi: 10.1016/0022-2836(79)90070-6. [DOI] [PubMed] [Google Scholar]
  16. Sturtevant J. M. Heat capacity and entropy changes in processes involving proteins. Proc Natl Acad Sci U S A. 1977 Jun;74(6):2236–2240. doi: 10.1073/pnas.74.6.2236. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Villafranca J. J., Viola R. E. The use of 13C spin lattice relaxation times to study the interaction of alpha-methyl-D-glucopyranoside with concanavalin A. Arch Biochem Biophys. 1974 Feb;160(2):465–468. doi: 10.1016/0003-9861(74)90422-6. [DOI] [PubMed] [Google Scholar]
  18. Yariv J., Kalb A. J., Levitzki A. The interaction of concanavalin A with methyl alpha-D-glucopyranoside. Biochim Biophys Acta. 1968 Sep 3;165(2):303–305. doi: 10.1016/0304-4165(68)90063-9. [DOI] [PubMed] [Google Scholar]
  19. Yariv J., Kalb A. J., Papiz M. Z., Helliwell J. R., Andrews S. J., Habash J. Properties of a new crystal form of the complex of concanavalin A with methyl alpha-D-glucopyranoside. J Mol Biol. 1987 Jun 5;195(3):759–760. doi: 10.1016/0022-2836(87)90198-7. [DOI] [PubMed] [Google Scholar]

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