DNA-bound structures and mutants reveal abasic DNA binding by APE1 DNA repair and coordination (original) (raw)

References

  1. Lindahl,, T. Instability and decay of the primary structure of DNA. Nature 362, 709–715 (1993).
    Article ADS CAS Google Scholar
  2. Wilson, D. M. & Thompson, L. H. Life without DNA repair. Proc. Natl Acad. Sci. USA 94, 12754– 12757 (1997).
    Article ADS CAS Google Scholar
  3. Wilson, D. M., Takeshita, M., Grollman, A. P. & Demple, B. Incision activity of human apurinic endonuclease (Ape) at abasic site analogs in DNA. J. Biol. Chem. 270, 16002– 16007 (1995).
    Article CAS Google Scholar
  4. Izumi, T. & Mitra, S. Deletion analysis of human AP-endonuclease: minimum sequence required for the endonuclease activity. Carcinogenesis 19, 525–527 ( 1998).
    Article CAS Google Scholar
  5. Lindahl, T. & Wood, R. D. Quality control in DNA repair. Science 286, 1897–1905 ( 1999).
    Article CAS Google Scholar
  6. Tsutakawa, S. E., Jingami, H. & Morikawa, K. Recognition of a TG mismatch: the crystal structure of very short patch repair endonuclease in complex with a DNA duplex. Cell 99, 615–623 ( 1999).
    Article CAS Google Scholar
  7. Hosfield, D. J., Guan, Y., Haas, B. J., Cunningham, R. P. & Tainer, J. A. Structure of the DNA repair enzyme endonuclease IV and its DNA complex: double-nucleotide flipping at abasic sites and three-metal-ion catalysis. Cell 98, 397– 408 (1999).
    Article CAS Google Scholar
  8. Gorman, M. A. et al. The crystal structure of the human DNA repair endonuclease HAP1 suggests the recognition of extra-helical deoxyribose at DNA abasic sites. EMBO J. 16, 6548–6558 (1997).
    Article CAS Google Scholar
  9. Wilson, D. M., Takeshita, M. & Demple, B. Abasic site binding by the human apurinic endonuclease, Ape, and determination of the DNA contact sites. Nucleic Acids Res. 25, 933–939 ( 1997).
    Article CAS Google Scholar
  10. Withka, J. M., Wilde, J. A. & Bolton, P. H. Characterization of conformational features of DNA heteroduplexes containing aldehydic abasic sites. Biochemistry 30, 9931–9940 ( 1991).
    Article CAS Google Scholar
  11. Mol, C. D., Kuo, C. –F., Thayer, M. M., Cunningham, R. P. & Tainer, J. A. Structure and function of the multifunctional DNA-repair enzyme exonuclease III. Nature 374, 381– 386 (1995).
    Article ADS CAS Google Scholar
  12. Erzberger, J. P. & Wilson, D. M. The role of Mg2+ and specific amino acid residues in the catalytic reaction of the major human abasic endonuclease: new insights from EDTA-resistant incision of acyclic abasic site analogs and site-directed mutagenesis. J. Mol. Biol. 290, 447–457 (1999).
    Article CAS Google Scholar
  13. Izumi, T. et al. Intragenic suppression of an active site mutation in the human apurinic/apyrimidinic endonuclease. J. Mol. Biol. 287 , 47–57 (1999).
    Article CAS Google Scholar
  14. Kane, C. M. & Linn, S. Purification and characterization of an apurinic/apyrimidinic endonuclease from HeLa cells. J. Biol. Chem. 256, 3405–3414 ( 1981).
    CAS PubMed Google Scholar
  15. Masuda, Y., Bennett, R. A. & Demple, B. Dynamics of the interaction of human apurinic endonuclease (Ape1) with its substrate and product. J. Biol. Chem. 273, 30352–30359 (1998).
    Article CAS Google Scholar
  16. Bennett, R. A. O., Wilson, D. M., Wong, D. & Demple, B. Interaction of human apurinic endonuclease and DNA polymerase β in the base excision repair pathway. Proc. Natl Acad. Sci. USA 94, 7166–7169 (1997).
    Article ADS CAS Google Scholar
  17. Prasad, R. et al. Specific interaction of DNA polymerase β and DNA ligase I in a multiprotein base excision repair complex from bovine testis. J. Biol. Chem. 271, 16000–16007 (1996).
    Article CAS Google Scholar
  18. Parikh, S. S. et al. Base–excision repair initiation revealed by crystal structures and DNA–binding kinetics of human uracil–DNA glycosylase bound to DNA. EMBO J. 17, 5214– 5226 (1998).
    Article CAS Google Scholar
  19. Waters, T. R., Gallinari, P., Jiricny, J. & Swann, P. F. Human thymine DNA glycosylase binds to apurinic sites in DNA but is displaced by human apurinic endonuclease 1. J. Biol. Chem. 274 , 67–74 (1999).
    Article CAS Google Scholar
  20. Chen, D. S., Herman, V. & Demple, B. Two distinct human DNA diesterases that hydrolyze 3′–blocking deoxyribose fragments from oxidized DNA. Nucleic Acids Res. 19, 5907–5914 (1991).
    Article CAS Google Scholar
  21. Horton, J. K., Srivastava, D. K., Zmudzka, B. Z. & Wilson, S. H. Strategic down–regulation of DNA polymerase beta by antisense RNA sensitizes mammalian cells to specific DNA damaging agents. Nucleic Acids Res. 23, 3810–3815 ( 1995).
    Article CAS Google Scholar
  22. Kubota, Y. et al. Reconstitution of DNA base excision–repair with purified human proteins: interaction between DNA polymerase β and the XRCC1 protein. EMBO J. 15, 6662–6670 (1996).
    Article CAS Google Scholar
  23. Caldecott, K. W., McKeown, C. K., Tucker, J. D., Ljungquist, S. & Thompson, L. H. An interaction between the mammalian DNA repair protein XRCC1 and DNA ligase III. Mol. Cell. Biol. 14, 68–76 (1994).
    Article CAS Google Scholar
  24. Takeshita, M., Chang, C. N., Johnson, F., Will, S. & Grollman, A. P. Oligodeoxynucleotides containing synthetic abasic sites. Model substrates for DNA polymerases and apurinic/apyrimidinic endonucleases. J. Biol. Chem. 262, 10171 –10179 (1987).
    CAS PubMed Google Scholar
  25. Erzberger, J. P., Barsky, D., Scharer, O. D., Colvin, M. E. & Wilson, D. M. Elements in abasic site recognition by the major human and Escherichia coli apurinic/apyrimidinic endonucleases. Nucleic Acids Res. 26, 2771– 2778 (1998).
    Article CAS Google Scholar
  26. Otwinowski,, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–325 ( 1997).
    Article CAS Google Scholar
  27. Navaza, J. AMoRe: an automated package for molecular replacement. Acta Crystallogr. A 50, 157–163 ( 1994).
    Article Google Scholar
  28. Brünger, A. T., Kuriyan, J. & Karplus, M. Crystallographic R factor refinement by molecular dynamics. Science 235, 458–460 (1987).
    Article ADS Google Scholar
  29. Read, R. J. Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Crystallogr. A 42, 140 –149 (1986).
    Article Google Scholar
  30. McRee, D. E. XtalView/Xfit—a versatile program for manipulating atomic coordinates and electron density. J. Struct. Biol. 125, 156–165 (1999).
    Article CAS Google Scholar

Download references