Structural basis for DNA recognition and processing by UvrB (original) (raw)

References

  1. Friedberg, E.C., Walker, G.C. & Siede, W. DNA repair and mutagenesis. (ASM Press, Washington, D.C., 1995).
  2. Sancar, A. DNA excision repair. Annu. Rev. Biochem. 65, 43–81 (1996).
    Article CAS Google Scholar
  3. Lloyd, R.S. & Van Houten, B . DNA damage recognition. in DNA Repair Mechanisms: Impact on Human Diseases and Cancer (ed. Vos, J.-M.) 25–66 (R.G. Landes Company, Biomedical Publishers, Austin, Texas, 1995).
    Google Scholar
  4. Goosen, N. & Moolenaar, G.F. Role of ATP hydrolysis by UvrA and UvrB during nucleotide excision repair. Res. Microbiol. 152, 401–409 (2001).
    Article CAS Google Scholar
  5. Van Houten, B. Nucleotide excision repair in Escherichia coli. Microbiol. Rev. 54, 18–51 (1990).
    CAS PubMed PubMed Central Google Scholar
  6. Theis, K. et al. The nucleotide excision repair protein UvrB, a helicase-like enzyme with a catch. Mutat. Res. 460, 277–300 (2000).
    Article CAS Google Scholar
  7. Verhoeven, E.E., Wyman, C., Moolenaar, G.F. & Goosen, N. The presence of two UvrB subunits in the UvrAB complex ensures damage detection in both DNA strands. EMBO J. 21, 4196–4205 (2002).
    Article CAS Google Scholar
  8. Orren, D.K. & Sancar, A. Formation and enzymatic properties of the UvrB-DNA complex. J. Biol. Chem. 265, 15796–15803 (1990).
    CAS PubMed Google Scholar
  9. Skorvaga, M., Theis, K., Mandavilli, B.S., Kisker, C. & Van Houten, B. The beta-hairpin motif of UvrB is essential for DNA binding, damage processing, and UvrC-mediated incisions. J. Biol. Chem. 277, 1553–1559 (2002).
    Article CAS Google Scholar
  10. Lin, J.-J. & Sancar, A. Active site of (A)BC excinuclease: I. Evidence for 5′ incision by UvrC through a catalytic site involving Asp399, Asp438, and His538 residues. J. Biol. Chem. 267, 17688–17692 (1992).
    CAS PubMed Google Scholar
  11. Sancar, A. & Rupp, W.D. A novel repair enzyme: UvrABC excision nuclease of Escherichia coli cuts a DNA strand on both sides of the damaged region. Cell 33, 249–260 (1983).
    Article CAS Google Scholar
  12. Verhoeven, E.E., van Kesteren, M., Moolenaar, G.F., Visse, R. & Goosen, N. Catalytic sites for 3′ and 5′ incision of Escherichia coli nucleotide excision repair are both located in UvrC. J. Biol. Chem. 275, 5120–5123 (2000).
    Article CAS Google Scholar
  13. Caron, P.R., Kushner, S.R. & Grossman, L. Involvement of helicase-II (UvrD gene product) and DNA Polymerase-I in excision mediated by the UvrABC protein complex. Proc. Natl. Acad. Sci. USA 82, 4925–4929 (1985).
    Article CAS Google Scholar
  14. Husain, I., Houten, B.V., Thomas, D.C., Abdel-Monem, M. & Sancar, A. Effect of DNA polymerase I and DNA helicase II on the turnover rate of UvrABC excision nuclease. Proc. Natl. Acad. Sci. USA 82, 6774–6778 (1985).
    Article CAS Google Scholar
  15. Machius, M., Henry, L., Palnitkar, M. & Deisenhofer, J. Crystal structure of the DNA nucleotide excision repair enzyme UvrB from Thermus thermophilus. Proc. Natl. Acad. Sci. USA 96, 11717–11722 (1999).
    Article CAS Google Scholar
  16. Nakagawa, N. et al. Crystal structure of Thermus thermophilus HB8 UvrB protein, a key enzyme of nucleotide excision repair. J. Biochem. 126, 986–990 (1999).
    Article CAS Google Scholar
  17. Theis, K., Chen, P.J., Skorvaga, M., Houten, B.V. & Kisker, C. Crystal structure of UvrB, a DNA helicase adapted for nucleotide excision repair. EMBO J. 18, 6899–6907 (1999).
    Article CAS Google Scholar
  18. Truglio, J.J. et al. Interactions between UvrA and UvrB: the role of UvrB's domain 2 in nucleotide excision repair. EMBO J. 23, 2498–2509 (2004).
    Article CAS Google Scholar
  19. Hsu, D.S., Kim, S.T., Sun, Q. & Sancar, A. Structure and function of the UvrB protein. J. Biol. Chem. 270, 8319–8327 (1995).
    Article CAS Google Scholar
  20. Gordienko, I. & Rupp, W.D. The limited strand-separating activity of the UvrAB protein complex and its role in the recognition of DNA damage. EMBO J. 16, 889–895 (1997).
    Article CAS Google Scholar
  21. Visse, R., King, A., Moolenaar, G.F., Goosen, N. & van de Putte, P. Protein-DNA interactions and alterations in the DNA structure upon UvrB-DNA preincision complex formation during nucleotide excision repair in Escherichia coli. Biochemistry 33, 9881–9888 (1994).
    Article CAS Google Scholar
  22. Zou, Y. & Van Houten, B. Strand opening by the UvrA2B complex allows dynamic recognition of DNA damage. EMBO J. 18, 4889–4901 (1999).
    Article CAS Google Scholar
  23. Skorvaga, M. et al. Identification of residues within UvrB that are important for efficient DNA binding and damage processing. J. Biol. Chem. 279, 51574–51580 (2004).
    Article CAS Google Scholar
  24. DellaVecchia, M.J. et al. Analyzing the handoff of DNA from UvrA to UvrB utilizing DNA-protein photoaffinity labeling. J. Biol. Chem. 279, 45245–45256 (2004).
    Article CAS Google Scholar
  25. Moolenaar, G.F., Hoglund, L. & Goosen, N. Clue to damage recognition by UvrB: residues in the beta-hairpin structure prevent binding to non-damaged DNA. EMBO J. 20, 6140–6149 (2001).
    Article CAS Google Scholar
  26. Moolenaar, G.F., Schut, M. & Goosen, N. Binding of the UvrB dimer to non-damaged and damaged DNA: residues Y92 and Y93 influence the stability of both subunits. DNA Repair (Amst.) 4, 699–713 (2005).
    Article CAS Google Scholar
  27. Zou, Y. et al. DNA damage recognition of mutated forms of UvrB proteins in nucleotide excision repair. Biochemistry 43, 4196–4205 (2004).
    Article CAS Google Scholar
  28. Sancar, A., Franklin, K.A. & Sancar, G.B. Escherichia coli DNA photolyase stimulates uvrABC excision nuclease in vitro. Proc. Natl. Acad. Sci. USA 81, 7397–7401 (1984).
    Article CAS Google Scholar
  29. Mees, A. et al. Crystal structure of a photolyase bound to a CPD-like DNA lesion after in situ repair. Science 306, 1789–1793 (2004).
    Article CAS Google Scholar
  30. Malta, E., Moolenaar, G.F. & Goosen, N. Base flipping in nucleotide excision repair. J. Biol. Chem. 281, 2184–2194 (2006).
    Article CAS Google Scholar
  31. Zou, Y., Walker, R., Bassett, H., Geacintov, N.E. & Houten, B.V. Formation of DNA repair intermediates and incision by the ATP-dependent UvrB-UvrC endonuclease. J. Biol. Chem. 272, 4820–4827 (1997).
    Article CAS Google Scholar
  32. Moolenaar, G.F. et al. The effect of the DNA flanking the lesion on formation of the UvrB-DNA preincision complex. J. Biol. Chem. 275, 8038–8043 (2000).
    Article CAS Google Scholar
  33. Shi, Q., Thresher, R., Sancar, A. & Griffith, J. Electron microscopic study of (A)BC excinuclease—DNA is sharply bent in the UvrB-DNA complex. J. Mol. Biol. 226, 425–432 (1992).
    Article CAS Google Scholar
  34. Lin, J.J., Phillips, A.M., Hearst, J.E. & Sancar, A. Active site of (A)BC excinuclease: II. Binding, bending and catalysis mutants of UvrB reveal a direct role in 3′ and an indirect role in 5′ incision. J. Biol. Chem. 267, 17693–17700 (1992).
    CAS PubMed Google Scholar
  35. Verhoeven, E.E., Wyman, C., Moolenaar, G.F., Hoeijmakers, J.H. & Goosen, N. Architecture of nucleotide excision repair complexes: DNA is wrapped by UvrB before and after damage recognition. EMBO J. 20, 601–611 (2001).
    Article CAS Google Scholar
  36. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997).
    Article CAS Google Scholar
  37. Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50, 760–763 (1994).
  38. Jones, T.A., Zou, J.Y., Cowan, S.W. & Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110–119 (1991).
    Article Google Scholar
  39. Laskowski, R.A., McArthur, M.W., Moss, D.S. & Thornton, J.M. PROCHECK—a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283–291 (1993).
    Article CAS Google Scholar

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