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Structures of Hha I methyltransferase complexed with substrates containing mismatches at the target base

Nature Structural Biology volume 5, pages 872–877 (1998)Cite this article

Abstract

Three structures have been determined for complexes between Hha I methyltransferase (M. Hha I) and oligonucleotides containing a G:A, G:U or G:AP (AP = abasic or apurinic/apyrimidinic) mismatch at the target base pair. The mismatched adenine, uracil and abasic site are all flipped out of the DNA helix and located in the enzyme's active-site pocket, adopting the same conformation as in the flipped-out normal substrate. These results, particularly the flipped-out abasic deoxyribose sugar, provide insight into the mechanism of base flipping. If the process involves the protein pushing the base out of the helix, then the push must take place not on the base, but rather on the sugar-phosphate backbone. Thus rotation of the DNA backbone is probably the key to base flipping.

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Figure 1: a, Close up of the 5'-GCGC-3'/5'-GXGC-3' sequence, where X = A (top), U (middle), and AP (bottom).
Figure 2: M.HhaI-AdoHcy-G:A mismatch.
Figure 3: M.HhaI-AdoHcy-G:U mismatch.
Figure 4: M.HhaI-AdoHcy-G:AP mismatch.

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Acknowledgements

We thank K. McCloy for protein purification and crystallization, and S. Kumar and X. Zhang for discussion and comments on the manuscript. M.O'G. was supported in part by a National Institutes of Health fellowship (GM17052). Work was supported in part by National Institutes of Health Grants to R.J.R. and X.C.

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  1. Margaret O'Gara

    Present address: Pfizer Central Research, Discovery Biology, Ramsgate Road, Sandwich, Kent, CT13 3NJ, England

Authors and Affiliations

  1. Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, 30322, Georgia, USA

    John R. Horton & Xiaodong Cheng

  2. New England Biolabs, 32 Tozer Road, Beverly, 01915, Massachusetts, USA

    Richard J. Roberts

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  4. Xiaodong Cheng
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O'Gara, M., Horton, J., Roberts, R. et al. Structures of Hha I methyltransferase complexed with substrates containing mismatches at the target base . Nat Struct Mol Biol 5, 872–877 (1998). https://doi.org/10.1038/2312

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