Skip to main content
SpringerLink
Log in

The taxonomy of binding sites in proteins

  • Review Articles
  • Published:
Molecular and Cellular Biochemistry Aims and scope Submit manuscript

Summary

Conservation of polypeptide fold and mode of ligand binding is frequently found within proteins of related function. Examples illustrating this phenomenon are taken from NAD linked enzymes, nucleotide binding proteins, polysaccharide binding proteins, heme binding proteins and enzymes with essential Fe-S complexes or zinc atoms.

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. Perutz, M. F., Rossmann, M. G., Cullis, A. F., Muirhead, H., Will, G. and North, A. C. T., 1960. Nature (London) 185, 416–422.

    Google Scholar 

  2. Fitch, W. M. and Margoliash, E., 1967. Science 155, 279–284; and many subsequent papers.

    CAS  PubMed  Google Scholar 

  3. Holbrook, J. J., Liljas, A., Steindel, S. J. and Rossmann, M. G., 1975. in The Enzymes (Boyer, P. D., editor) 3rd edition, Vol. XI, pp. 191–292, Academic Press, New York.

  4. Buehner, M., Ford, G. C., Moras, D., Olsen, K. W. and Rossmann, M. G., 1973. Proc. Natl. Acad. Sci. U.S. 70, 3052–3054.

    Google Scholar 

  5. Rao, S. T. and Rossmann, M. G., 1973. J. Mol. Biol. 76, 241–256.

    Google Scholar 

  6. Rossmann, M. G., Moras, D. and Olsen, K. W., 1974. Nature (London) 250, 194–199.

    Google Scholar 

  7. Eventoff, W. and Rossmann, M. G., 1975. in CRC Critical Reviews in Biochemistry (Fasman, G. D., editor) Vol. 3, pp. 111–140, CRC Press, Cleveland.

  8. Richardson, J. S., Thomas, K. A., Rubin, B. H. and Richardson, D. C., 1975. Proc. Natl. Acad. Sci. U.S. 72, 1349–1353.

    Google Scholar 

  9. Richardson, J. S., 1977. Nature (London) 268, 495–500.

    Google Scholar 

  10. Richardson, J. S., 1976. Proc. Natl. Acad. Sci. U.S. 73, 2619–2623.

    Google Scholar 

  11. Sternberg, M. J. E. and Thornton, J. M., 1977. J. Mol. Biol. 110,269–283.

    Google Scholar 

  12. Rossmann, M. G. and Argos, P. (1975) J. Biol. Chem. 250, 7525–7532.

    Google Scholar 

  13. Bergsma, J., Hol. W. G. J., Jansonius, J. N., Kalk, K. H., Ploegman, J. H. and Smit, J. D. G., 1975. J. Mol. Biol. 98, 637–643.

    Google Scholar 

  14. Phillips, D. C., Sternberg, M. J. E., Thornton, J. M. and Wilson, I. A., 1978. J. Mol. Biol. 119, 329–351.

    Google Scholar 

  15. Richardson, J. S., Richardson, D. C., Thomas, K. A., Silverton, E. W. and Davies, D. R., 1976. J. Mol. Biol. 102, 221–235.

    Google Scholar 

  16. Levine, M., Muirhead, H., Stammers, D. K. and Stuart, D. I., 1978. Nature (London) 271, 626–630.

    Google Scholar 

  17. Tang, J., James, M. N. G., Hsu, I. N., Jenkins, J. A. and Blundell, T. L., 1978. Nature (London) 271, 618–621.

    Google Scholar 

  18. Rossmann, M. G. and Argos, P., 1976. J. Mol. Biol. 105, 75–95.

    Google Scholar 

  19. Remington, S. J. and Matthews, B. W., 1978. Proc. Natl. Acad. Sci. U.S., 75, 2180–2184.

    Google Scholar 

  20. Jukes, T. H. and Cantor, C. R., 1969. in Mammalian Protein Metabolism (Munro, H. N., editor) Vol. III, pp. 21–132, Academic Press, New York.

  21. Sokal, R. R. and Sneath, P. H. A., 1963. Principles of Numerical Taxonomy, W. H. Freeman & Co., San Francisco.

    Google Scholar 

  22. Schulz, G. E. and Schirmer, R. H., 1974. Nature (London) 250, 142–144.

    Google Scholar 

  23. Sternberg, M. J. E. and Thornton, J. M., 1977. J. Mol. Biol. 113, 401–418.

    Google Scholar 

  24. Sternberg, M. J. E. and Thornton, J. M., 1976. J. Mol. Biol. 105, 367–382.

    Google Scholar 

  25. Crick, F. H. C., 1952. Nature (London) 170, 882–883.

    Google Scholar 

  26. Crick, F. H. C., 1953. Acta Crystallogr. 6, 689–697.

    Google Scholar 

  27. Chothia, C., Levitt, M. and Richardson, D., 1977. Proc. Natl. Acad. Sci. U.S. 74, 4130–4134.

    Google Scholar 

  28. Levitt, M. and Chothia, C., 1976. Nature (London) 261, 552–558.

    Google Scholar 

  29. Rossmann, M. G. and Argos, P. 1977. J. Mol. Biol. 109, 99–129.

    Google Scholar 

  30. Ohlsson, I., Nordström, B. and Brändén, C. I., 1974. J. Mol. Biol. 89, 339–354.

    Google Scholar 

  31. Rossmann, M. G., Liljas, A., Brändén, C. I. and Banaszak, L. J., 1975. in The Enzymes (Boyer, P. D., editor) 3rd edition, Vol. XI, pp. 61–102, Academic Press, New York.

  32. Matthews, D. A., Alden, R. A., Bolin, J. T., Filman, D. J., Freer, S. T., Hamlin, R., Hot, W. G. J., Kisliuk, R. L., Pastore, E. J., Plant, L. T., Xuong, N. and Kraut, J., 1978. J. Biol. Chem., in press.

  33. Wootton, J. C., 1974. Nature (London) 252, 542–546.

    Google Scholar 

  34. Otto, J., 1970. Ph.D. Thesis, Ludwig-MaximiliansUniversität, München, Germany.

    Google Scholar 

  35. Matthews, D. A., Alden, R. A., Bolin, J. T., Freer, S. T., Hamlin, R., Xuong, N., Kraut, J., Poe, M., Williams, M. and Hoogsteen, K., 1977. Science 197, 452–455.

    Google Scholar 

  36. Stellwagen, E., Cass, R., Thompson, S. T. and Woody, M., 1975. Nature (London) 257, 716–718.

    Google Scholar 

  37. Garavito, R. M., Rossmann, M. G., Argos, P. and Eventoff, W., 1977. Biochemistry 16, 5065–5071.

    Google Scholar 

  38. Matthews, B. W. and Remington, S. J., 1974. Proc. Natl. Acad. Sci. U.S. 71, 4178–4182.

    Google Scholar 

  39. Johnson, L. N. and Phillips, D. C., 1965. Nature (London) 206, 761–763.

    Google Scholar 

  40. Blake, C. C. F., Johnson, L. N., Mair, G. A.; North, A. C. T., Phillips. D. C. and Sarma, V. R.; 1967. Proc. Roy. Soc. B167, 378–388.

    Google Scholar 

  41. Tsugita, A. and Inouye, M., 1968. J. Mol. Biol. 37, 201–212.

    Google Scholar 

  42. Imoto, T., Johnson, L. N., North, A. C. T., Phillips, D. C. and Rupley, J. A., 1972. in The Enzymes (Boyer, P. D., editor) 3rd edition, Vol. VII, pp. 665–868, Academic Press, New York.

  43. Blake, C. C. F., Koenig, D. F., Mair, G. A., North, A. C. T., Phillips, D. C. and Sarma, V. R., 1965. Nature (London) 206, 757–761.

    Google Scholar 

  44. Ford, L. O., Johnson, L. N., Machin, P. A., Phillips, D. C. and Tjian, R., 1974. J. Mol. Biol. 88, 349–371.

    Google Scholar 

  45. Ghuysen, J. M., 1968. Bacteriol. Rev. 32, 425–464.

    Google Scholar 

  46. Tsugita, A., 1971. in The Enzymes (Boyer, P. D., editor) 3rd edition, Vol. V, pp. 343–411, Academic Press, New York.

  47. Browne, W. J., North, A. C. T., Phillips, D. C., Brew, K., Vanaman, T. C. and Hill, R. L., 1969. J. Mol. Biol. 42, 65–86.

    Google Scholar 

  48. Dickerson, R. E. and Timkovich, R.,1975. in The Enzymes (Boyer, P. D., editor) 3rd edition, Vol. XI, pp. 397–547, Academic Press, New York.

  49. Dickerson, R. E., 1978. in Proceedings of the International Symposium on Biomolecular Structure, Conformation, Function and Evolution, Madras, India, in press.

  50. Mathews, F. S., Levine, M. and Argos, P., 1972. J. Mol. Biol. 64, 449–464.

    Google Scholar 

  51. Mathews, F. S., Argos, P. and Levine, M., 1971. Cold Spring Harbor Symp. Quant. Biol. 36, 387–395.

    Google Scholar 

  52. Hagihara, B., Sato, N. and Yamanaka, T., 1975. in The Enzymes (Boyer, P. D., editor) 3rd edition, Vol. XI, pp. 549–593, Academic Press, New York.

  53. Oshino, N., Imai, Y. and Sato, R., 1971. J. Biochem. (Tokyo) 69, 155–167.

    Google Scholar 

  54. Holloway, P. W. and Katz, J. T., 1972. Biochemistry 11, 3689–3696.

    Google Scholar 

  55. Almassy, R. J. and Dickerson, R. E., 1978. Proc. Natl. Acad. Sci. U.S. 75, 2674–2678.

    Google Scholar 

  56. Perutz, M. F., Muirhead, H., Cox, J. M., Goaman, L. C. G., Mathews, F. S., McGandy, E. L. and Webb, L. E., 1968. Nature (London) 219, 29–32.

    Google Scholar 

  57. Padlan, E. A. and Love, W. E., 1974. J. Biol. Chem. 249, 4067–4078.

    Google Scholar 

  58. Dayhoff, M. O., 1972. in Atlass of Protein Sequence and Structure, Vol. 5, pp. D369-D370.

    Google Scholar 

  59. Czerwinski, E. W. and Mathews, F. S., 1974. J. Mol. Biol. 86, 49–57.

    Google Scholar 

  60. Itagaki, E. and Hager, L. P., 1966. J. Biol. Chem. 241, 3687–3695.

    Google Scholar 

  61. Adman, E. T., Sieker, L. C. and Jensen, L. H., 1973. J. Biol. Chem. 248, 3987–3996.

    Google Scholar 

  62. Sicker, L. C., Adman, E. and Jensen, L. H., 1972. Nature (London) 235, 40–42.

    Google Scholar 

  63. Carter, C. W. Jr., Kraut, J., Freer, S. T., Xuong, N., Alden, R. A. and Bartsch, R. G., 1974. J. Biol. Chem. 249, 4212–4225.

    Google Scholar 

  64. Carter, C. W. Jr., 1977. J. Biol. Chem. 252, 7802–7811.

    Google Scholar 

  65. Kraut, J., Robertus, J. D., Birktoft, J. J., Alden, R. A., Wilcox, P. E. and Powers, J. C., 1971. Cold Spring Harbor Symp. Quant. Biol. 36, 117–123.

    Google Scholar 

  66. Kannan, K. K., Petef, M., Fridborg, K., Cid-Dresdner, H. and Lövgren, S., 1977. FEBS Lett. 73, 115–119.

    Google Scholar 

  67. Wolpert, H. R., Strader, C. D. and Khalifah, R. G., 1977. Biochemistry 16, 5717–5721.

    Google Scholar 

  68. Boiwe, T. and Brändén, C. I., 1977. Eur. J. Biochem. 77, 173–179.

    Google Scholar 

  69. Colman, P. M., Jansonius, J. N. and Matthews, B. W., 1972. J. Mol. Biol. 70, 701–724.

    Google Scholar 

  70. Matthews, B. W., Weaver, L. H. and Kester, W. R., 1974. J. Biol. Chem. 249, 8030–8044.

    Google Scholar 

  71. Lipscomb, W. N., 1974. Tetrahedron 30, 1725–1732.

    Google Scholar 

  72. Lipscomb, W. N., Hartsuck, J. A., Reeke, G. N. Jr., Quiocho, F. A., Bethge, P. H., Ludwig, M. L., Steitz, T. A., Muirhead, H. and Coppola, J. C., 1968. Brookhaven Symp. Biol. 21, 24–90.

    Google Scholar 

  73. Lipscomb, W. N., Reeke, G. N. Jr., Hartsuck, J. A., Quiocho, F. A. and Bethge, P. H., 1970. Phil. Trans. Roy. Soc. Lond. B257, 177–214.

    Google Scholar 

  74. Argos, P., Garavito, R. M., Eventoff, W., Rossmann, M. G. and Branden, C. I., 1978. J. Mol. Biol., in press.

  75. Argos, P., Garavito, R. M., Eventoff, W. and Rossmann, M. G., 1978. in Proceedings of the International Symposium on Biomolecular Structure, Conformation, Function and Evolution, Madras, India, in press.

  76. Weaver, L. H., Kester, W. R. and Matthews, B. W. 1977. J. Mol. Biol. 114, 119–132.

    Google Scholar 

  77. Pangburn, M. K. and Walsh, K. A., 1975. Biochemistry 14, 4050–4054.

    Google Scholar 

  78. Brändén, C. I., Jörnvall, H., Eklund, H. and Furugren, B., 1975. in The Enzymes (Boyer, P. D., editor) 3rd edition, Vol. XI, pp. 103–190, Academic Press, New York.

  79. Dworschack, R. T. and Plapp, B. V., 1977. Biochemistry 16, 111–116.

    Google Scholar 

  80. Lindskog, S., Henderson, L. E., Kannan, K. K., Liljas, A., Nyman, P. O. and Strandberg, B., 1971. in The Enzymes (Boyer, P. D., editor) 3rd edition, Vol. V, pp. 587–665, Academic Press, New York.

  81. Navon, G., Shulman, R. G., Wyluda, B. J. and Yamane, T., 1970. J. Mol. Biol. 51, 15–30.

    Google Scholar 

  82. Woolley, P., 1975. Nature (London) 258, 677–682.

    Google Scholar 

  83. Kester, W. R. and Matthews, B. W., 1977. J. Biol. Chem. 252, 7704–7710.

    Google Scholar 

  84. Verpoorte, J. A., Mehta, S. and Edsall, J. T., 1967. J. Biol. Chem. 242, 4221–4229.

    Google Scholar 

  85. Kannan, K. K., Notstrand, B., Fridborg, K., Lövgren, S., Ohlsson, A. and Petef, M., 1975. Proc. Natl. Acad. Sci. U.S. 72, 51–55.

    Google Scholar 

  86. Carlsson, U., Aasa, R., Henderson, L. E., Jonsson, B. H. and Lindskog, S., 1975. Eur. J. Biochem. 52, 25–36.

    Google Scholar 

  87. Sweet, R. M., Wright, H. T., Janin, J., Chothia, C. H. and Blow, D. M., 1974. Biochemistry 13, 4212–4228.

    Google Scholar 

  88. Richmond, T. J. and Richards, F. M., 1978. J. Mol. Biol. 119, 537–555.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Biological Sciences, Purdue University, 47907, West Lafayette, Indiana, USA

    Michael G. Rossmann & Patrick Argos

Authors
  1. Michael G. Rossmann
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Patrick Argos
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and permissions

About this article

Cite this article

Rossmann, M.G., Argos, P. The taxonomy of binding sites in proteins. Mol Cell Biochem 21, 161–182 (1978). https://doi.org/10.1007/BF00240135

Download citation

  • Received:

  • Issue Date:

  • DOI: https://doi.org/10.1007/BF00240135

Keywords

Search

Navigation