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MutY catalytic core, mutant and bound adenine structures define specificity for DNA repair enzyme superfamily

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Abstract

The DNA glycosylase MutY, which is a member of the Helix-hairpin-Helix (HhH) DNA glycosylase superfamily, excises adenine from mispairs with 8-oxoguanine and guanine. High-resolution crystal structures of the MutY catalytic core (cMutY), the complex with bound adenine, and designed mutants reveal the basis for adenine specificity and glycosyl bond cleavage chemistry. The two cMutY helical domains form a positively-charged groove with the adenine-specific pocket at their interface. The Watson-Crick hydrogen bond partners of the bound adenine are substituted by protein atoms, confirming a nucleotide flipping mechanism, and supporting a specific DNA binding orientation by MutY and structurally related DNA glycosylases.

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Figure 1: Biochemical characterization of wild type and mutant cMutY enzymes.
Figure 2: MutY fold, domain structure, adenine binding and molecular surface in stereo view.
Figure 3: MutY active site, adenine binding, and proposed catalytic mechanism.
Figure 4: MutY adenine specificity and DNA binding with implications for the HhH glycosylase superfamily.

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Acknowledgements

We thank C.D. Putnam for aid with data collection, T.P. Lo, K.E. Morgan, P. Frosst, M. Nelson, and M.L. Dodson for helpful discussions, and M. Pique for help with figures. This work was supported by grants from the National Institutes of Health to J.A.T., R.S.L. and J.H.M., a Distinguished Chair in Environmental Toxicology from The Houston Endowment to R.S.L., a Robert Welch Foundation grant to R.S.L., an NIH Postdoctoral Fellowship grant and an American Cancer Society fellowship to Y.G., a Special Fellowship from the Leukemia Society of America to C.D.M., and a National Science Foundation Graduate Research fellowship to S.S.P.

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  1. Yue Guan, Raymond C. Manuel, Andrew S. Arvai, Sudip S. Parikh and Jeffrey H. Miller: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Molecular Biology, Skaggs Institute for Chemical Biology, The Scripps Research Institute, MB4, 10550 North Torrey Pines Rd., La Jolla, 92037, California, USA

    Yue Guan, Andrew S. Arvai, Sudip S. Parikh, Clifford D. Mol & John A. Tainer

  2. Sealy Center for Molecular Science, University of Texas Medical Branch, 301 University Blvd., Galveston, 77555, Texas, USA

    Raymond C. Manuel & R. Stephen Lloyd

  3. Department of Microbiology and Molecular Genetics, Molecular Biology Institute, UCLA, Los Angeles, 90095, California, USA

    Jeffrey H. Miller

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  1. Yue Guan
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Correspondence to John A. Tainer.

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Guan, Y., Manuel, R., Arvai, A. et al. MutY catalytic core, mutant and bound adenine structures define specificity for DNA repair enzyme superfamily. Nat Struct Mol Biol 5, 1058–1064 (1998). https://doi.org/10.1038/4168

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