Skip to main content
SpringerLink
Log in

Structural Aspects of Interaction of Homeodomains with DNA

  • Published:
Molecular Biology Aims and scope Submit manuscript

Abstract

This review is devoted to the structural aspects of interaction of homeodomains with DNA. Presented are the list of all homeodomains with known spatial structure and the alignment of their amino acid sequences. The structure of homeodomains and contacts of their amino acid residues with DNA bases and sugar-phosphate backbone are described. The role of water molecules in DNA binding is discussed. Structures of multicomponent protein complexes on DNA including homeodomains are characterized.

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. Rubin, G.M., Yandell, M.D., Wortman, J.R., et al., Science, 2000, vol. 287, pp. 2204–2215.

    Google Scholar 

  2. Kissinger, C.R., Liu, B., Martin-Blanco, E., Kornberg, T.B., and Pabo, C.O., Cell, 1990, vol. 63, pp. 579–590.

    Google Scholar 

  3. Pabo, C.O. and Sauer, R.C., Annu. Rev. Biochem., 1992, vol. 61, pp. 1053–1095.

    Google Scholar 

  4. Laughon, A., Biochemistry, 1991, vol. 30, pp. 11357–11367.

    Google Scholar 

  5. Gehring, W.J., Affolter, M., and Burglin, T., Annu. Rev. Biochem., 1994, vol. 63, pp. 487–526.

    Google Scholar 

  6. Gindilis, V., Goltsman, E., and Verlinsky, Y., J. Assisted Reproduction and Genetics, 1998, vol. 15, pp. 348–357.

    Google Scholar 

  7. Guidebook to the Homeobox Genes, Duboule, D., Ed., Oxford: Oxford University Press, 1994.

    Google Scholar 

  8. Berman, H.M., Westbrook, J., Feng Z., et al., Nucleic Acids Res., 2000, vol. 28, pp. 235–242.

    Google Scholar 

  9. Berman, H.M., Olson, W.K., Beveridge, D.L., et al., Biophys. J., 1992, vol. 63, pp. 751–759.

    Google Scholar 

  10. Bürglin T.R., Encyclopedia of Molecular Biology and Molecular Medicine, vol. 3, Meyers, R.A., Ed., Weinhem: VCH Verlagsgesellschaft mbH, 1996, pp. 55–76.

    Google Scholar 

  11. Guex, N. and Peitsch, M.C., Electrophoresis, 1997, vol. 18, pp. 2714–2723.

    Google Scholar 

  12. Schulz, B., Banuett, F., Dahl, M., et al., Cell, 1990, vol. 60, pp. 295–306.

    Google Scholar 

  13. Gillissen, B., Bergemann, J., Sandmann, C., et al., Cell, 1992, vol. 68, pp. 647–657.

    Google Scholar 

  14. Botfield, M.C., Jancso, A., and Weiss, M.A., Biochemistry, 1994, vol. 33, pp. 6177–6185.

    Google Scholar 

  15. Botfield, M.C., Jancso, A., and Weiss, M.A., Biochemistry, 1994, vol. 33, pp. 8133–8121.

    Google Scholar 

  16. Ades, S.E. and Sauer, R.T., Biochemistry, 1995, vol. 34, pp. 14601–14608.

    Google Scholar 

  17. Pomerantz, J.L. and Sharp, P.A., Biochemistry, 1994, vol. 33, pp. 10851–10858

    Google Scholar 

  18. Gruschus, J.M., Tsao, D.H.H., Wang, L.-H., Nirenberg, M., and Ferretti, J.A., Biochemistry, 1997, vol. 36, pp. 5372–5380.

    Google Scholar 

  19. Stepchenko, A.G., Luchina, N.N., and Pankratova, E.V., Nucleic Acids Res., 1997, vol. 25, pp. 2847–2853.

    Google Scholar 

  20. Stepchenko, A.G., Luchina, N.N., and Polanovsky, O.L., FEBS Lett, 1997, vol. 412, pp. 5–8.

    Google Scholar 

  21. Gehring, W.J., Qian, Y.Q., Billeter, M., et al., Cell, 1994, vol. 78, pp. 211–223.

    Google Scholar 

  22. Damante, G., Pellizzari, L., Esposito, G., et al., EMBO J., 1996, vol. 15, pp. 4992–5000.

    Google Scholar 

  23. Wilson, D.S., Sheng, G., Jun, S., and Desplan, C., Proc. Natl. Acad. Sci. USA, 1996, vol. 93, pp. 6886–6891.

    Google Scholar 

  24. Fraenkel, E., Rould, M.A., Chambers, K.A., and Pabo, C.O., J. Mol. Biol., 1998, vol. 284, pp. 351–361.

    Google Scholar 

  25. Herr, W. and Cleary, M.A., Genes Dev., 1995, vol. 9, pp. 1679–1693.

    Google Scholar 

  26. Phillips, K. and Luisi, B., J. Mol. Biol., 2000, vol. 302, pp. 1023–1039.

    Google Scholar 

  27. Herr, W., Sturm, R.A., Clerc, R.G., et al., Genes Dev., 1988, vol. 2, pp. 1513–1516.

    Google Scholar 

  28. Klemm, J.D., Rould, M.A., Aurora, R., Herr, W., and Pabo, C.O., Cell, 1994, vol. 77, pp. 21–32.

    Google Scholar 

  29. Jacobson, E.M., Li, P., Leon-del-Rio, A., Rosenfeld, M.G., and Aggarwal, A.K., Genes Dev., 1997, vol. 11, pp. 198–212.

    Google Scholar 

  30. Chasman, D.I., Cepek, K., Sharp, P.A., and Pabo, C.O., Genes Dev., 1999, vol. 13, pp. 2650–2657.

    Google Scholar 

  31. Verrijzer, C.P., Alkema, M.J., van Weperen, W.W., et al., EMBO J., 1992, vol. 11, pp. 4993–5003.

    Google Scholar 

  32. Klemm, J.B. and Pabo, C.O., Genes Dev., 1996, vol. 10, pp. 27–36.

    Google Scholar 

  33. Tomilin, A., Remenyi, A., and Lins, K., et al., Cell, 2000, vol. 103, pp. 853–864.

    Google Scholar 

  34. Wilson, D.S., Guenther, B., Desplan, C., and Kuriyan, J., Cell, 1995, vol. 82, pp. 709–719.

    Google Scholar 

  35. Xu, H., Rould, M., Xu, W., Epstein, J., Maas, R., and Pabo, C., Genes Dev., 1999, vol. 13, pp. 1263–1275.

    Google Scholar 

  36. Xu, W., Rould, M.A., Jun, S., Desplan, C., and Pabo, C.O., Cell, 1995, vol. 80, pp. 639–650.

    Google Scholar 

  37. Piper, D.E., Batchelor, A.H., Chang, C.P., Cleary, M.L., and Wolberger, C., Cell, 1999, vol. 96, pp. 587–597.

    Google Scholar 

  38. Passner, J.M., Ryoo, H.D., Shen, L., Mann, R.S., and Aggarwal, A.K., Nature, 1999, vol. 397, pp. 714–719.

    Google Scholar 

  39. Chang, C.-P., Shen, W.-F., Rozenfeld, S., Lawrence, H.-J., Largman, C., and Cleary, M.-L., Genes Dev., 1995, vol. 9, pp. 663–674.

    Google Scholar 

  40. Green, N.C., Rambaldi, I., Teakles, J., and Featherstone, M.S., J. Biol. Chem., 1998, vol. 273, pp. 13273–13279.

    Google Scholar 

  41. Lu, Q. and Kamps, M.P., Mol. Cell Biol., 1996, vol. 16, pp. 1632–1640.

    Google Scholar 

  42. Jabet, C, Gitti, R, Summers, M.F., and Wolberger, C., J. Mol. Biol., 1999, vol. 291, pp. 521–530.

    Google Scholar 

  43. Smith, D.L. and Johnson, A.D., Cell, 1992, vol. 68, pp. 133–142.

    Google Scholar 

  44. Tan, S. and Richmond, T.J., Nature, 1998, vol. 391, pp. 660–666.

    Google Scholar 

  45. Li, T., Stark, M.R., Johnson, A.D., and Wolberger, C., Science, 1995, vol. 270, pp. 262–269.

    Google Scholar 

  46. Li, T., Jin, Y., Vershon, A.K., and Wolberger, C., Nucleic Acids Res., 1998, vol. 26, pp. 5707–5718.

    Google Scholar 

  47. Stark, M.R., Escher, D., and Johnson, A.D., EMBO J., 1999, vol. 18, pp. 1621–1629.

    Google Scholar 

  48. Anderson, J.S., Forman, M.D., Modleski, S., Dahlquist, F.W., and Baxter, S.M., Biochemistry, 2000, vol. 39, pp. 10 045–10 054.

    Google Scholar 

  49. Billeter, M., Qian, Y.Q., Otting, G., Muller, M., Gehring, W., and Wuthrich, K., J. Mol. Biol., 1990, vol. 214, pp. 183–197.

    Google Scholar 

  50. Billeter, M., Qian, Y.Q., Otting, G., Muller, M., Gehring, W., and Wuthrich, K., J. Mol. Biol., 1993, vol. 234, pp. 1084–1093.

    Google Scholar 

  51. Fraenkel, E. and Pabo, C.O., Nature Struct. Biol., 1998, vol. 5, pp. 692–697.

    Google Scholar 

  52. Qian, Y.Q., Resendez-Perez, D., Gehring, W.J., and Wuthrich, K., Proc. Natl. Acad. Sci. USA, 1994, vol. 91, pp. 4091–4095.

    Google Scholar 

  53. Guntert, P., Qian, Y.-Q., Otting, G., Muller, M., Gehring, W.J., and Wuthrich, K., J. Mol. Biol., 1991, vol. 217, pp. 531–549.

    Google Scholar 

  54. Qian, Y.-Q., Furukubo-Tokunaga, K., Resendez-Perez, D., Muller, M., Gehring, W.J., and Wuthrich, K., J. Mol. Biol., 1994, vol. 238, pp. 333–345.

    Google Scholar 

  55. Hirsch, J.A. and Aggarwal, A.K., EMBO J., 1995, vol. 14, pp. 6280–6291.

    Google Scholar 

  56. Clarke, N.D., Kissinger, C.R., Desjarlais, J., Gilliland, G.L., and Pabo, C.O., Protein Sci., 1994, vol. 3, pp. 1779–1787.

    Google Scholar 

  57. Tucker-Kellogg, L., Rould, M., Chambers, K., Ades, S., Sauer, R., and Pabo, C., Structure, 1997, vol. 5, pp. 1047–1054.

    Google Scholar 

  58. Grant, R.A., Rould, M.A., Klemm, J.D., and Pabo, C.O., Biochemistry, 2000, vol. 39, pp. 8187–8192.

    Google Scholar 

  59. Gruschus, J.M., Tsao, D.H.H., Wang, L.-H., Nirenberg, M., and Ferretti, J.A., J. Mol. Biol., 1999, vol. 289, pp. 529–545.

    Google Scholar 

  60. Tsao, D.H., Gruschus, J.M., Wang, L.H., Nirenberg, M., and Ferretti, J.A., J. Mol. Biol., 1995, vol. 251, pp. 297–307.

    Google Scholar 

  61. Esposito, G., Fogolari, F., Damante, G., et al., Eur. J. Biochem., 1996, vol. 241, pp. 101–113.

    Google Scholar 

  62. Ippel, H., Larsson, G., Behravan, G., et al., J. Mol. Biol., 1999, vol. 288, pp. 689–703.

    Google Scholar 

  63. Cox, M., van Tilborg, P.J., de Laat, W., et al., J. Biomol. NMR, 1995, vol. 6, pp. 23–32.

    Google Scholar 

  64. Sivaraja, M., Botfield, M.C., Mueller, M., Jancso, A., and Weiss, M.A., Biochemistry, 1994, vol. 33, pp. 9845–9855.

    Google Scholar 

  65. Morita, E.H., Shirakawa, M., Hayashi, F., Imagawa, M., and Kyogoku, Y., Protein Sci., 1995, vol. 4, pp. 729–739.

    Google Scholar 

  66. Anderson, J.S., Forman, M., Modleski, S., Dahlquist, F.W., and Baxter, S.M., Biochemistry, 2000, vol. 33, pp. 10045–10054.

    Google Scholar 

  67. Wolberger, C., Vershon, A.K., Liu, B., Johnson, A.D., and Pabo, C.O., Cell, 1991, vol. 67, pp. 517–528.

    Google Scholar 

  68. Sprules, T., Green, N., Featherstone, M., and Gehring, K., Biochemistry, 2000, vol. 39, pp. 9943–9950.

    Google Scholar 

  69. Ceska, T.A., Lamers, M., Monaci, P., Nicosia, A., Cortese, R., and Suck, D., EMBO J., 1993, vol. 12, pp. 1805–1810.

    Google Scholar 

  70. Schott, O., Billeter, M., Leiting, B., Wider, G., and Wuthrich, K., J. Mol. Biol., 1997, vol. 267, pp. 673–683.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119899, Russia

    R. K. Ledneva, A. V. Alexeevskii & S. A. Spirin

  2. National Institute of Agricultural Biotechnology, Russian Academy of Agricultural Sciences, Moscow, 127550, Russia

    S. A. Vasil'ev & A. S. Karyagina

Authors
  1. R. K. Ledneva
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. A. V. Alexeevskii
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. S. A. Vasil'ev
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. S. A. Spirin
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. A. S. Karyagina
    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

Ledneva, R.K., Alexeevskii, A.V., Vasil'ev, S.A. et al. Structural Aspects of Interaction of Homeodomains with DNA. Molecular Biology 35, 647–659 (2001). https://doi.org/10.1023/A:1012309917322

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1023/A:1012309917322

Search

Navigation