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Structure of the N6-adenine DNA methyltransferase M•TaqI in complex with DNA and a cofactor analog

Nature Structural Biology volume 8, pages 121–125 (2001)Cite this article

Abstract

The 2.0 Å crystal structure of the N6-adenine DNA methyltransferase M•TaqI in complex with specific DNA and a nonreactive cofactor analog reveals a previously unrecognized stabilization of the extrahelical target base. To catalyze the transfer of the methyl group from the cofactor S-adenosyl-l-methionine to the 6-amino group of adenine within the double-stranded DNA sequence 5′-TCGA-3′, the target nucleoside is rotated out of the DNA helix. Stabilization of the extrahelical conformation is achieved by DNA compression perpendicular to the DNA helix axis at the target base pair position and relocation of the partner base thymine in an interstrand π-stacked position, where it would sterically overlap with an innerhelical target adenine. The extrahelical target adenine is specifically recognized in the active site, and the 6-amino group of adenine donates two hydrogen bonds to Asn 105 and Pro 106, which both belong to the conserved catalytic motif IV of N6-adenine DNA methyltransferases. These hydrogen bonds appear to increase the partial negative charge of the N6 atom of adenine and activate it for direct nucleophilic attack on the methyl group of the cofactor.

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Figure 1: Three-dimensional structure of the ternary complex of M•TaqI.
Figure 2: Schematic representation of hydrogen bonds and salt bridges between M•TaqI and the DNA substrate.
Figure 3: Stereo view of the active site of M•TaqI.
Figure 4: Structural comparison between the presented ternary complex and the binary complex of M•TaqI15 within the active site.

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Acknowledgements

We would like to thank N. Bleimling for producing M•TaqI, S. Milardovic′ for help during initial crystallization experiments and M. Weyand for help with the refinement and graphical presentation. This work was supported in part by a grant from the Deutsche Forschungsgemeinschaft.

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Author notes

  1. Marc Pignot

    Present address: Aventis Research & Technologies GmbH & Co KG, Bioorganic Systems & Synthesis, Industriepark Höchst G 830, D-65926, Frankfurt am Main, Germany

  2. Elmar Weinhold

    Present address: Institut für Organische Chemie der RWTH Aachen, Professor-Pirlet-Str. 1, D-52056, Aachen, Germany

Authors and Affiliations

  1. Abteilung Physikalische Biochemie, Max-Planck-Institut für molekulare Physiologie, Otto-Hahn-Str. 11, Dortmund, D-44227, Germany

    Karsten Goedecke, Marc Pignot, Roger S. Goody, Axel J. Scheidig & Elmar Weinhold

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Correspondence to Elmar Weinhold.

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Goedecke, K., Pignot, M., Goody, R. et al. Structure of the N6-adenine DNA methyltransferase M•TaqI in complex with DNA and a cofactor analog. Nat Struct Mol Biol 8, 121–125 (2001). https://doi.org/10.1038/84104

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