Structure and function of the multifunctional DNA-repair enzyme exonuclease III (original) (raw)

Nature volume 374, pages 381–386 (1995)Cite this article

Abstract

THE repair of DNA requires the removal of abasic sites, which are constantly generated in vivo both spontaneously1 and by enzymatic removal of uracil2, and of bases damaged by active oxygen species, alkylating agents and ionizing radiation3,4. The major apurinic/ apyrimidinic (AP) DNA-repair endonuclease in Escherichia coli is the multifunctional enzyme exonuclease III, which also exhibits 3′-repair diesterase, 3′→ 5′ exonuclease, 3′-phosphomonoesterase and ribonuclease activities5. We report here the 1.7 Å resolution crystal structure of exonuclease III which reveals a 2-fold symmetric, four-layered ap fold with similarities to both deoxyribo-nuclease I6 and RNase H7. In the ternary complex determined at 2.6 Å resolution, Mn2+ and dCMP bind to exonuclease III at one end of the αβ-sandwich, in a region dominated by positive electrostatic potential. Residues conserved among AP endonucleases from bacteria to man cluster within this active site and appear to participate in phosphate-bond cleavage at AP sites through a nucleophilic attack facilitated by a single bound metal ion.

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References

  1. Lindahl, T. Nature 362, 709–715 (1993).
    Article ADS CAS Google Scholar
  2. Taylor, A. F. & Weiss, B. J. Bact. 151, 351–357 (1982).
    CAS PubMed Google Scholar
  3. Sakumi, K. & Sekiguchi, M. Mutat. Res. 236, 161–172 (1990).
    Article CAS Google Scholar
  4. Doetsch, P. W. & Cunningham, R. P. Mutat. Res. 236, 173–201 (1990).
    Article CAS Google Scholar
  5. Demple, B. & Harrison, L. A. Rev. Biochem. 63, 915–948 (1994).
    Article CAS Google Scholar
  6. Oefner, C. & Suck, D. J. molec. Biol. 192, 605–632 (1986).
    Article CAS Google Scholar
  7. Katayanagi, K. et al. Nature 347, 306–309 (1990).
    Article ADS CAS Google Scholar
  8. Richardson, J. S. Adv. Prot. Chem. 34, 167–339 (1981).
    CAS Google Scholar
  9. Beese, L. S. & Steitz, T. A. EMBO J. 10, 25–33 (1991).
    Article CAS Google Scholar
  10. Lahm, A. & Suck, D. J. molec. Biol. 221, 645–667 (1991).
    Article Google Scholar
  11. Weston, S. A., Lahm, A. & Suck, D. J. molec. Biol. 226, 1237–1256 (1992).
    Article CAS Google Scholar
  12. Katayanagi, K. et al. Nature 347, 306–309 (1990).
    Article ADS CAS Google Scholar
  13. Kayana, S. et al. Eur. J. Biochem. 198, 437–440 (1991).
    Article Google Scholar
  14. Katayanagi, K., Okumura, M. & Morikawa, K. Prot. Struct. Funct. Genet. 17, 337–346 (1993).
    Article CAS Google Scholar
  15. Cho, Y., Gorina, S., Jeffrey, P. D. & Pavletich, N. P. Science 265, 346–355 (1994).
    Article ADS CAS Google Scholar
  16. Kuo, C.-F., McRee, D. E., Cunningham, R. P. & Tainer, J. A. J. molec. Biol. 229, 239–242 (1993).
    Article CAS Google Scholar
  17. Read, R. J. Acta crystallogr. A42, 140–149 (1986).
    Article Google Scholar
  18. McRee, D. E. J. molec. Graphics 10, 44–46 (1993).
    Article Google Scholar
  19. Brünger, A., Kuriyan, J. & Karplus, M. Science 235, 458–460 (1987).
    Article ADS Google Scholar
  20. Borgstahl, G. E. O., Rogers, P. H. & Arnone, A. J. molec. Biol. 236, 817–830 (1994).
    Article CAS Google Scholar
  21. Saporito, S. M., Smith-White, B. J. & Cunningham, R. P. J. Bact. 170, 4542–4547 (1988).
    Article CAS Google Scholar
  22. Demple, B., Herman, T. & Chen, D. S. Proc. natn. Acad. Sci. U.S.A. 88, 11450–11454 (1991).
    Article ADS CAS Google Scholar
  23. Seki, S. et al. J. biol. Chem. 266, 20797–20802 (1991).
    CAS PubMed Google Scholar
  24. Robson, C. N., Milne, A. M., Pappin, D. J. C. & Hickson, I. D. Nucleic Acids Res. 19, 1087–1092 (1991).
    Article CAS Google Scholar
  25. Lipman, D. J., Altschul, S. F. & Kececioglu, J. D. Proc. natn. Acad. Sci. U.S.A. 86, 4412–4415 (1989).
    Article ADS CAS Google Scholar

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Author notes

  1. Che-Fu Kuo
    Present address: Department of Structural Biology, Department 46Y, Building AP9A, Abbott Laboratories, One Abbott Park Road, Abbott Park, Illinois, 60064, USA

Authors and Affiliations

  1. Department of Molecular Biology, The Scripps Research Institute, 10666 North Torrey Pines Road, La Jolla, California, 92037, USA
    Clifford D. Mol, Che-Fu Kuo, Maria M. Thayer & John A. Tainer
  2. Department of Biological Sciences, Center for Biochemistry and Biophysics, State University of New York-Albany, Albany, New York, 12222, USA
    Richard P. Cunningham

Authors

  1. Clifford D. Mol
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  2. Che-Fu Kuo
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  3. Maria M. Thayer
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  4. Richard P. Cunningham
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  5. John A. Tainer
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Mol, C., Kuo, CF., Thayer, M. et al. Structure and function of the multifunctional DNA-repair enzyme exonuclease III.Nature 374, 381–386 (1995). https://doi.org/10.1038/374381a0

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