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Product-assisted catalysis in base-excision DNA repair

Nature Structural & Molecular Biology volume 10, pages 204–211 (2003)Cite this article

Abstract

Most spontaneous damage to bases in DNA is corrected through the action of the base-excision DNA repair pathway. Base excision repair is initiated by DNA glycosylases, lesion-specific enzymes that intercept aberrant bases in DNA and catalyze their excision. How such proteins accomplish the feat of catalyzing no fewer than five sequential reaction steps using a single active site has been unknown. To help answer this, we report the structure of a trapped catalytic intermediate in DNA repair by human 8-oxoguanine DNA glycosylase. This structure and supporting biochemical results reveal that the enzyme sequesters the excised lesion base and exploits it as a cofactor to participate in catalysis. To our knowledge, the present example represents the first documented case of product-assisted catalysis in an enzyme-catalyzed reaction.

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Figure 1: Overview of base-excision repair catalyzed by hOGG1.
Figure 2: Close-up view of the hOGG1 active site region.
Figure 3: Interactions of the sequestered oxoG base with other components in the active site of the borohydride-trapped complex.
Figure 4: Purine analogs as cofactors for hOGG1 in the β-lyase cascade that promotes DNA strand scission.
Figure 5: Active site stereo views of the structures of the nucleobase-soaked and abasic-trapped complexes.
Figure 6: Stereochemistry of C2′ proton abstraction.
Figure 7: Detailed stepwise mechanistic proposal for the entire cascade of reactions catalyzed by hOGG1.

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Acknowledgements

Use of the Argonne National Laboratory Structural Biology Center beamlines at the Advanced Photon Source was supported by the U.S. Department of Energy, Office of Biological and Environmental Research. J.C.F. was supported by an NIH BCMB training grant and by a Graduate Research Fellowship from the NSF. S.D.B is an Eli Lilly Fellow. We are grateful to D.P.G. Norman for assistance with data collection and processing and for helpful discussions. We thank C. Heaton and the entire MacCHESS staff for assistance with data collection. R. Sanishvili, S. Korolev, S. Ginell and A. Joachimak of SBC-CAT at the Advanced Photon Source, Argonne National Laboratory provided valuable advice and assistance.

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  1. Steven D. Bruner

    Present address: Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, 02115, USA

Authors and Affiliations

  1. Department of Molecular and Cellular Biology, Harvard University, Cambridge, 02138, Massachusetts, USA

    J. Christopher Fromme & Gregory L. Verdine

  2. Department of Chemistry and Chemical Biology, Harvard University, Cambridge, 02138, Massachusetts, USA

    Steven D. Bruner, Wei Yang, Martin Karplus & Gregory L. Verdine

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Correspondence to Gregory L. Verdine.

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Fromme, J., Bruner, S., Yang, W. et al. Product-assisted catalysis in base-excision DNA repair. Nat Struct Mol Biol 10, 204–211 (2003). https://doi.org/10.1038/nsb902

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