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Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA


How DNA repair proteins distinguish between the rare sites of damage and the vast expanse of normal DNA is poorly understood. Recognizing the mutagenic lesion 8-oxoguanine (oxoG) represents an especially formidable challenge, because this oxidized nucleobase differs by only two atoms from its normal counterpart, guanine (G). Here we report the use of a covalent trapping strategy to capture a human oxoG repair protein, 8-oxoguanine DNA glycosylase I (hOGG1), in the act of interrogating normal DNA. The X-ray structure of the trapped complex features a target G nucleobase extruded from the DNA helix but denied insertion into the lesion recognition pocket of the enzyme. Free energy difference calculations show that both attractive and repulsive interactions have an important role in the preferential binding of oxoG compared with G to the active site. The structure reveals a remarkably effective gate-keeping strategy for lesion discrimination and suggests a mechanism for oxoG insertion into the hOGG1 active site.

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Figure 1: Generation of 8-oxoguanine (oxoG), its recognition by human 8-oxoguanine DNA glycosylase (hOGG1) and overview of the structure-based trapping strategy used here to obtain a complex of hOGG1 bound to undamaged DNA.
Figure 2: Comparison of the overall structures of trapped complexes obtained with oxoG-containing (left) or G-containing (right) DNA.
Figure 3: View of the active site region of hOGG1–DNA complexes, showing extra-helical nucleobases bound to either the lesion recognition pocket or the alternative site.
Figure 4: Computational analysis of the binding free energy difference between oxoG and G.
Figure 5: Superposition of the oxoG complex with the G complex in the region around the protein–DNA interface.

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  1. Michaels, M. L. & Miller, J. H. The GO system protects organisms from the mutagenic effect of the spontaneous lesion 8-hydroxyguanine (7,8-dihydro-8-oxoguanine). J. Bacteriol. 174, 6321–6325 (1992)

    Article  CAS  Google Scholar 

  2. Grollman, A. P. & Moriya, M. Mutagenesis by 8-oxoguanine: an enemy within. Trends Genet. 9, 246–249 (1993)

    Article  CAS  Google Scholar 

  3. Cappelli, E. et al. Rates of base excision repair are not solely dependent on levels of initiating enzymes. Carcinogenesis 22, 387–393 (2001)

    Article  CAS  Google Scholar 

  4. Bruner, S. D., Norman, D. P. & Verdine, G. L. Structural basis for recognition and repair of the endogenous mutagen 8-oxoguanine in DNA. Nature 403, 859–866 (2000)

    Article  ADS  CAS  Google Scholar 

  5. Fromme, J. C., Bruner, S. D., Yang, W., Karplus, M. & Verdine, G. L. Product-assisted catalysis in base-excision DNA repair. Nature Struct. Biol. 10, 204–211 (2003)

    Article  CAS  Google Scholar 

  6. Norman, D. P., Chung, S. J. & Verdine, G. L. Structural and biochemical exploration of a critical amino acid in human 8-oxoguanine glycosylase. Biochemistry 42, 1564–1572 (2003)

    Article  CAS  Google Scholar 

  7. Norman, D. P. G., Bruner, S. D. & Verdine, G. L. Coupling of substrate recognition and catalysis by a human base-excision DNA repair protein. J. Am. Chem. Soc. 123, 359–360 (2001)

    Article  CAS  Google Scholar 

  8. Luger, K., Mader, A. W., Richmond, R. K., Sargent, D. F. & Richmond, T. J. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389, 251–260 (1997)

    Article  ADS  CAS  Google Scholar 

  9. Viadiu, H. & Aggarwal, A. K. Structure of BamHI bound to nonspecific DNA: a model for DNA sliding. Mol. Cell 5, 889–895 (2000)

    Article  CAS  Google Scholar 

  10. Robinson, H. et al. The hyperthermophile chromosomal protein Sac7d sharply kinks DNA. Nature 392, 202–205 (1998)

    Article  ADS  CAS  Google Scholar 

  11. Gao, Y. G. et al. The crystal structure of the hyperthermophile chromosomal protein Sso7d bound to DNA. Nature Struct. Biol. 5, 782–786 (1998)

    Article  CAS  Google Scholar 

  12. Huang, H., Harrison, S. C. & Verdine, G. L. Trapping of a catalytic HIV reverse transcriptase•template:primer complex through a disulfide bond. Chem. Biol. 7, 355–364 (2000)

    Article  CAS  Google Scholar 

  13. Huang, H., Chopra, R., Verdine, G. L. & Harrison, S. C. Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance. Science 282, 1669–1675 (1998)

    Article  ADS  CAS  Google Scholar 

  14. Verdine, G. L. & Norman, D. P. Covalent trapping of protein-DNA complexes. Annu. Rev. Biochem. 72, 337–366 (2003)

    Article  CAS  Google Scholar 

  15. Fromme, J. C., Banerjee, A., Huang, S. J. & Verdine, G. L. Structural basis for removal of adenine mispaired with 8-oxoguanine by MutY adenine DNA glycosylase. Nature 427, 652–656 (2004)

    Article  ADS  CAS  Google Scholar 

  16. Simonson, T., Archontis, G. & Karplus, M. Free energy simulations come of age: protein-ligand recognition. Acc. Chem. Res. 35, 430–437 (2002)

    Article  CAS  Google Scholar 

  17. Yang, W., Bitetti-Putzer, R. & Karplus, M. Chaperoned alchemical free energy simulations: A general method for QM, MM, and QM/MM potentials. J. Chem. Phys. 120, 9450–9453 (2004)

    Article  ADS  CAS  Google Scholar 

  18. Brooks, C. L. III, Karplus, M. & Pettitt, B. M. Advances in Chemical Physics Vol. 71 (Wiley & Sons, New York, 1988)

    Book  Google Scholar 

  19. Verdine, G. L. & Bruner, S. D. How do DNA repair proteins locate damaged bases in the genome? Chem. Biol. 4, 329–334 (1997)

    Article  CAS  Google Scholar 

  20. Bjoras, M., Seeberg, E., Luna, L., Pearl, L. H. & Barrett, T. E. Reciprocal “flipping” underlies substrate recognition and catalytic activation by the human 8-oxo-guanine DNA glycosylase. J. Mol. Biol. 317, 171–177 (2002)

    Article  CAS  Google Scholar 

  21. Berdal, K. G., Johansen, R. F. & Seeberg, E. Release of normal bases from intact DNA by a native DNA repair enzyme. EMBO J. 17, 363–367 (1998)

    Article  CAS  Google Scholar 

  22. O'Brien, P. J. & Ellenberger, T. The Escherichia coli 3-methyladenine DNA glycosylase AlkA has a remarkably versatile active site. J. Biol. Chem. 279, 26876–26884 (2004)

    Article  CAS  Google Scholar 

  23. MacMillan, A. M. & Verdine, G. L. Engineering tethered DNA molecules by the convertible nucleoside approach. Tetrahedron 47, 2603–2616 (1991)

    Article  CAS  Google Scholar 

  24. Carson, M. J. Ribbons 2.0. J. Appl. Crystallogr. 24, 379–384 (1991)

    Article  Google Scholar 

  25. Schaefer, M., Sommer, M. & Karplus, M. pH-dependence of protein stability: absolute electrostatic free energy differences between conformations. J. Phys. Chem. B 101, 1663–1683 (1997)

    Article  CAS  Google Scholar 

  26. Cui, Q., Elstner, M., Kaxiras, E., Frauenheim, T. & Karplus, M. A QM/MM implementation of the self-consistent charge density functional tight binding (SCC-DFTB) method. J. Phys. Chem. B 105, 569–585 (2001)

    Article  CAS  Google Scholar 

  27. Dinner, A. R., Blackburn, G. M. & Karplus, M. Uracil-DNA glycosylase acts by substrate autocatalysis. Nature 413, 752–755 (2001)

    Article  ADS  CAS  Google Scholar 

  28. MacKerell, A. D. Jr et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 102, 3586–3616 (1998)

    Article  CAS  Google Scholar 

  29. Simonson, T., Archontis, G. & Karplus, M. Continuum treatment of long-range interactions in free energy calculations. Application to protein-ligand binding. J. Phys. Chem. B 101, 8347–8360 (1997)

    Article  CAS  Google Scholar 

  30. Bash, P. A. et al. Computer simulation and analysis of the reaction pathway of triosephosphate isomerase. Biochemistry 30, 5826–5832 (1991)

    Article  CAS  Google Scholar 

  31. Cervi, A. R., Guy, A., Leonard, G. A., Teoule, R. & Hunter, W. N. The crystal structure of N4-methylcytosine.guanosine base-pairs in the synthetic hexanucleotide d(CGCGm4CG). Nucleic Acids Res. 21, 5623–5629 (1993)

    Article  CAS  Google Scholar 

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We are grateful to Y. Korkhin for help in data collection and processing. We thank Enanta Pharmaceuticals for use of their X-ray instrumentation. We acknowledge the entire staff at MACCHESS, especially C. Heaton and B. Miller, and NSLS X4A for assistance in data collection and processing. We thank D. Jeruzalmi and C. Fromme for valuable discussions. This work was supported by grants from the NIH to G.L.V. and M.K.Author contributions A.B. was responsible for performing the structural and biochemical experiments described herein, whereas W.Y. performed the computational simulations.

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Correspondence to Martin Karplus or Gregory L. Verdine.

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The authors declare that they have no competing financial interests.

Supplementary information

Supplementary Table S1

Data collection and model statistics. (DOC 54 kb)

Supplementary Figure Legends

Figure captions for Supplementary Figures S1-S4. (DOC 35 kb)

Supplementary Methods

Additional details on computational methods and data collection and structure solution. (DOC 56 kb)

Supplementary Figure S1

Structural validation of the trapping strategy and crosslinking biochemistry. (PDF 658 kb)

Supplementary Figure S2

Electron density map around the G in the exo- site and the crosslinked C in the G-complex. (JPG 550 kb)

Supplementary Figure S3

Structural representations of the carbonyl of Gly42 and different nucleobases used in this study. (JPG 149 kb)

Supplementary Figure S4

Electron density maps around the analogs in the crosslinked complexes. (JPG 767 kb)

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Banerjee, A., Yang, W., Karplus, M. et al. Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA. Nature 434, 612–618 (2005).

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