Journal of Bioenergetics and Biomembranes

, Volume 24, Issue 5, pp 453–461 | Cite as

A model for the catalytic site of F1-ATPase based on analogies to nucleotide-binding domains of known structure

  • Thomas M. Duncan
  • Richard L. Cross
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Abstract

An updated topological model is constructed for the catalytic nucleotide-binding site of the F1-ATPase. The model is based on analogies to the known structures of the MgATP site on adenylate kinase and the guanine nucleotide sites on elongation factor Tu (Ef-Tu) and theras p21 protein. Recent studies of these known nucleotide-binding domains have revealed several common functional features and similar alignment of nucleotide in their binding folds, and these are used as a framework for evaluating results of affinity labeling and mutagenesis studies of the β subunit of F1. Several potentially important residues on β are noted that have not yet been studied by mutagenesis or affinity labeling.

Key words

F1-ATPase nucleotide binding sites protein folding structure prediction 

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References

  1. Admon, A., and Hammes, G. G. (1987).Biochemistry 26, 3193–3197.Google Scholar
  2. Al-Shawi, M. K., and Senior, A. E. (1988).J. Biol. Chem. 263, 19640–19648.Google Scholar
  3. Al-Shawi, M. K., Parsonage, D., and Senior, A. E. (1988).J. Biol. Chem. 263, 19633–19639.Google Scholar
  4. Al-Shawi, M. K., Parsonage, D., and Senior, A. E. (1989).J. Biol. Chem. 264, 15376–15383.Google Scholar
  5. Al-Shawi, M. K., Parsonage, D., and Senior, A. E. (1990).J. Biol. Chem. 265, 4402–4410.Google Scholar
  6. Andrews, W. W., Hill, F. C., and Allison, W. S. (1984).J. Biol. Chem. 259, 14378–14382.Google Scholar
  7. Berden, J. A., Hartog, A. F., and Edel, C. M. (1991).Biochim. Biophys. Acta 1057, 151–156.Google Scholar
  8. Bianchet, M., Ysern, X., Hullihen, J., Pedersen, P. L., and Amzel, L. M. (1991).J. Biol. Chem. 266, 21197–21201.Google Scholar
  9. Bullough, D. A., and Allison, W. S. (1986a).J. Biol. Chem. 261, 5722–5730.Google Scholar
  10. Bullough, D. A., and Allison, W. S. (1986b).J. Biol. Chem. 261, 14171–14177.Google Scholar
  11. Chen, J. M., Lee, G., Brandt-Rauf, G. W., Murphy, R. B., Gibson, K. D., Scheraga, H. A., Rackovsky, S., and Pincus, M. R. (1990).Int. J. Peptide Protein Res. 36, 247–254.Google Scholar
  12. Clark, B. F. C., Kjeldgaard, M., la Cour, T. F. M., Thirup, S., Nyborg, J. (1990).Biochim. Biophys. Acta 1050, 203–208.Google Scholar
  13. Cross, R. L. (1988).J. Bioenerg. Biomembr. 20, 395–405.Google Scholar
  14. Cross, R. L., and Nalin, C. M. (1982).J. Biol. Chem. 257, 2874–2881.Google Scholar
  15. Cross, R. L., Grubmeyer, C., and Penefsky, H. S. (1982).J. Biol. Chem. 257, 12101–12105.Google Scholar
  16. Cross, R. L., Cunningham, D., Miller, C. D., Xue, Z., Zhou, J.-M., and Boyer, P. D. (1987).Proc. Natl. Acad. Sci. USA 84, 5715–5719.Google Scholar
  17. Diederichs, K., and Schulz, G. E. (1991).J. Mol. Biol. 217, 541–549.Google Scholar
  18. Dreusicke, D., Karplus, P. A. and Schulz, G. E. (1988).J. Mol. Biol. 199, 359–371.Google Scholar
  19. Duncan, T. M., Parsonage, D., and Senior, A. E. (1986).FEBS Lett. 208, 1–6.Google Scholar
  20. Duncan, T. M., and Senior, A. E. (1985).J. Biol. Chem. 260, 4901–4907.Google Scholar
  21. Dunn, S. D., and Futai, M. (1980).J. Biol. Chem. 255, 113–118.Google Scholar
  22. Egner, U., Tomasselli, A. G., and Schulz, G. E. (1987).J. Mol. Biol. 195, 649–658.Google Scholar
  23. Esch, F. S., and Allison, W. S. (1978).J. Biol. Chem. 253, 6100–6106.Google Scholar
  24. Falson, P., Leterme, S., Capiau, C., and Boutry, M. (1991).Eur. J. Biochem. 200, 61–67.Google Scholar
  25. Foster, D. L., and Fillingame, R. H. (1982).J. Biol. Chem. 257, 2009–2015.Google Scholar
  26. Fry, D. C., Kuby, S. A., and Mildvan, A. S. (1985).Biochemistry 24, 4680–4694.Google Scholar
  27. Fry, D. C., Kuby, S. A., and Mildvan, A. S. (1986).Proc. Natl. Acad. Sci. USA 83, 907–911.Google Scholar
  28. Fry, D. C., Kuby, S. A., and Mildvan, A. S. (1987).Biochemistry 26, 1645–1655.Google Scholar
  29. Garboczi, D. N., Fox, A. H., Gerring, S. L., and Pedersen, P. L. (1988).Biochemistry 27, 553–560.Google Scholar
  30. Garin, J., Boulay, F., Issartel, J. P., Lunardi, J., and Vignais, P. V. (1986).Biochemistry 25, 4431–4437.Google Scholar
  31. Garnier, J., Osguthorpe, D. J., and Robson, B. (1978).J. Mol. Biol. 120, 97–120.Google Scholar
  32. Girault, G., Berger, G., Galmiche, J.-M., and Andre, F. (1988).J. Biol. Chem. 263, 14690–14695.Google Scholar
  33. Hollemans, M., Runswick, M. J., Fearnley, I. M., and Walker, J. E. (1983).J. Biol. Chem. 258, 9307–9313.Google Scholar
  34. Hsu, S. Y., Noumi, T., Takeyama, M., Maeda, M., Ishibashi, S., and Futai, M. (1987).FEBS Lett. 218, 222–226.Google Scholar
  35. Ida, K., Noumi, T., Maeda, M., Fukui, T., and Futai, M. (1991).J. Biol. Chem. 266, 5424–5429.Google Scholar
  36. Iwamoto, A., Omote, H., Hanada, H., Tomioka, N., Itai, A., Maeda, M., and Futai, M. (1991).J. Biol. Chem. 266, 16350–16355.Google Scholar
  37. Jacobson, M. A., and Colman, R. F. (1984).J. Biol. Chem. 259, 1454–1460.Google Scholar
  38. Kanazawa, H., Horiuchi, Y., Takagi, M., Ishino, Y., and Futai, M. (1980).J. Biochem. 88, 695–703.Google Scholar
  39. Kandpal, R. P., Melese, T., Stroop, S. D., and Boyer, P. D. (1985).J. Biol. Chem. 260, 5542–5547.Google Scholar
  40. Kironde, F. A., and Cross, R. L. (1987).J. Biol. Chem. 262, 3488–3495.Google Scholar
  41. Kironde, F. A., Parsonage, D., and Senior, A. E. (1989).Biochem. J. 259, 421–426.Google Scholar
  42. Lee, R. S., Pagan, J., Satre, M., Vignais, P. V., and Senior, A. E. (1989).FEBS Lett. 253, 269–272.Google Scholar
  43. Lee, R. S., Pagan, J., Wilke-Mounts, S., and Senior, A. E. (1991).Biochemistry 30, 6842–6847.Google Scholar
  44. Lunardi, J., Garin, J., Issartel, J.-P., and Vignais, P. V. (1987).Biol. Chem. 262, 15172–15181.Google Scholar
  45. Melese, T., and Boyer, P.D. (1985).J. Biol. Chem. 260, 15398–15401.Google Scholar
  46. Milner-White, E. J., Coggins, J. R., and Anton, I. A. (1991).J. Mol. Biol. 221, 751–754.Google Scholar
  47. Mueller, D. M. (1988).J. Biol. Chem. 263, 5634–5639.Google Scholar
  48. Mueller, D. M. (1989).J. Biol. Chem. 264, 16552–16556.Google Scholar
  49. Noumi, T., Oka, N., Kanazawa, H., and Futai, M. (1986a).J. Biol. Chem. 261, 7070–7075.Google Scholar
  50. Noumi, T., Taniai, M., Kanazawa, H., and Futai, M. (1986b).J. Biol. Chem. 261, 9196–9201.Google Scholar
  51. Noumi, T., Azuma, M., Shimomura, S., Maeda, M., and Futai, M. (1987).J. Biol. Chem. 262, 14978–14982.Google Scholar
  52. Noumi, T., Maeda, M., and Futai, M. (1988).J. Biol. Chem. 263, 8765–8770.Google Scholar
  53. Odaka, M., Kobayashi, H., Muneyuki, E., and Yoshida, M. (1990).Biochem. Biophys. Res. Commun. 168, 372–378.Google Scholar
  54. Parsonage, D., Duncan, T. M., Wilke-Mounts, S., Kironde, F. A., Hatch, L., and Senior, A. E. (1987a).J. Biol. Chem. 262, 6301–6307.Google Scholar
  55. Parsonage, D., Wilke-Mounts, S., and Senior, A. E. (1987b).J. Biol. Chem. 262, 8022–8026.Google Scholar
  56. Parsonage, D., Wilke-Mounts, S., and Senior, A. E. (1988).Arch. Biochem. Biophys. 261, 222–225.Google Scholar
  57. Penefsky, H. S., and Cross, R. L. (1991).Adv. Enzymol. Relat. Areas. Mol. Biol. 64, 173–214.Google Scholar
  58. Rao, R., Al-Shawi, M. K., and Senior, A. E. (1988a).J. Biol. Chem. 263, 5569–5573.Google Scholar
  59. Rao, R., Cunningham, D., Cross, R. L., and Senior, A. E. (1988b).J. Biol. Chem. 263, 5640–5645.Google Scholar
  60. Richardson, J. S. (1981).Adv. Prot. Chem. 34, 167–339.Google Scholar
  61. Saraste, M., Sibbald, P. R., and Wittinghofer, A. (1990).Trends Biochem. Sci. 15, 430–434.Google Scholar
  62. Schulz, G. E., Schlitz, E., Tomasselli, A. G., Frank, R., Brune, M., Wittinghofer, A., and Schirmer, R. H. (1986).Eur. J. Biochem. 161, 127–132.Google Scholar
  63. Senior, A. E. (1988).Physiol. Rev. 68, 177–231.Google Scholar
  64. Senior, A. E., Langman, L., Cox, G. B., and Gibson, F. (1983).Biochem. J. 210, 395–403.Google Scholar
  65. Shapiro, A. B., Huber, A. H., and McCarty, R. E. (1991).J. Biol. Chem. 266, 4194–4200.Google Scholar
  66. Soga, S., Noumi, T., Takeyama, M., Maeda, M., and Futai, M. (1989).Arch. Biochem. Biophys. 268, 643–648.Google Scholar
  67. Stehle, T., and Schulz, G. E. (1990).J. Mol. Biol. 211, 249–254.Google Scholar
  68. Story, R. M., and Steitz, T. A. (1992).Nature 355, 374–376.Google Scholar
  69. Tagaya, M., Noumi, T., Nakano, K., Futai, M., and Fukui, T. (1988).FEBS Lett. 233, 347–351.Google Scholar
  70. Takeyama, M., Ihara, K., Moriyama, Y., Noumi, T., Ida, K., Tomioka, N., Itai, A., Maeda, M., and Futai, M. (1990).J. Biol. Chem. 265, 21279–21284.Google Scholar
  71. Tommasino, M., and Capaldi, R. A. (1985).Biochemistry 24, 3972–3976.Google Scholar
  72. Tozer, R. G., and Dunn, S. D. (1987).J. Biol. Chem. 262, 10706–10711.Google Scholar
  73. Tsai, M.-D., and Yan, H. (1991).Biochemistry 30, 6806–6818.Google Scholar
  74. Verburg, J. G., and Allison, W. S. (1990).J. Biol. Chem. 265, 8065–8074.Google Scholar
  75. Vogel-Claude, P., Schafer, G., and Trommer, W. E. (1988).FEBS Lett. 227, 107–109.Google Scholar
  76. Vogel, P. D., and Cross, R. L. (1991).J. Biol. Chem. 266, 6101–6105.Google Scholar
  77. Vogel, P. D., Nett, J. H., Sauer, H. E., Schmadel, K., Cross, R. L., and Trommer, W. E. (1992).J. Biol. Chem. 267, 11982–11986.Google Scholar
  78. Walker, J. E., Saraste, M., Runswick, M. J., and Gay, N. J. (1982).EMBO J. 1, 945–951.Google Scholar
  79. Walker, J. E., Saraste, M., and Gay, N. J. (1984).Biochim. Biophys. Acta 768, 164–200.Google Scholar
  80. Weber, J., Lee, R. S.-F., Grell, E., Wise, J. G., and Senior, A. E. (1992).J. Biol. Chem. 267, 1712–1718.Google Scholar
  81. Wise, J. G. (1990).J. Biol. Chem. 265, 10403–10409.Google Scholar
  82. Wise, J. G., Duncan, T. M., Latchney, L. R., Cox, D. N., and Senior, A. E. (1983).Biochem. J. 215, 343–350.Google Scholar
  83. Wise, J. G., Hicke, B. J., and Boyer, P. D. (1987).FEBS Lett. 223, 395–401.Google Scholar
  84. Wittinghofer, A., and Pai, E. F. (1991).Trends Biochem. Sci. 16, 382–387.Google Scholar
  85. Xue, Z., Zhou, J.-M., Melese, T., Cross, R. L., and Boyer, P. D. (1987).Biochemistry 26, 3749–3753.Google Scholar
  86. Xue, Z., Melese, T., Stempel, K. E., Reedy, T. J., and Boyer, P. D. (1988).J. Biol. Chem. 263, 16880–16885.Google Scholar
  87. Yohda, M., Ohta, S., Hisabori, T., and Kagawa, Y. (1988).Biochim. Biophys. Acta 933, 156–164.Google Scholar
  88. Yoshida, M., Poser, J. W., and Allison, W. S. (1981).J. Biol. Chem. 256, 148–153.Google Scholar
  89. Yoshida, M., Allison, W. S., Esch, F. S., and Futai, M. (1982).J. Biol. Chem. 257, 10033–10037.Google Scholar
  90. Ysern, X., Amzel, L. M., and Pedersen, P. L. (1988).J. Bioenerg. Biomembr. 20, 423–450.Google Scholar
  91. Zhuo, S., Garrod, S., Miller, P., and Allison, W. S. (1992).J. Biol. Chem. 267, in press.Google Scholar

Copyright information

© Plenum Publishing Corporation 1992

Authors and Affiliations

  • Thomas M. Duncan
    • 1
  • Richard L. Cross
    • 1
  1. 1.Department of Biochemistry and Molecular BiologySUNY Health Science Center at SyracuseSyracuse

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