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NMR structure of the Tn916 integrase–DNA complex

Nature Structural Biology volume 6, pages 366–373 (1999)Cite this article

Abstract

The integrase protein catalyzes the excision and integration of the Tn 916 conjugative transposon, a promiscuous genetic element that spreads antibiotic resistance in pathogenic bacteria. The solution structure of the N-terminal domain of the Tn916 integrase protein bound to its DNA-binding site within the transposon arm has been determined. The structure reveals an interesting mode of DNA recognition, in which the face of a three-stranded antiparallel β-sheet is positioned within the major groove. A comparison to the structure of the homing endonuclease I-PpoI–DNA complex suggests that the three-stranded sheet may represent a new DNA-binding motif whose residue composition and position within the major groove are varied to alter specificity. The structure also provides insights into the mechanism of conjugative transposition. The DNA in the complex is bent ˜35° and may, together with potential interactions between bound integrase proteins at directly repeated sites, significantly bend the arms of the transposon.

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Figure 1: a, Schematic of the Tn916 transposon.
Figure 2: The NMR solution structure of the complex between the N-terminal domain of integrase and its DNA-binding site (INT-DBD–DNA).
Figure 3: a, Schematic plot of the protein–DNA contacts seen in the structure of the INT-DBD–DNA complex.
Figure 4: a, Comparison of the free (colored blue) and bound (colored green) forms of the INT-DBD.
Figure 5: Comparison of the INT-DBD with the only other known proteins that bind the major groove of DNA through β-sheet secondary structural elements.

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Acknowledgements

This work was supported by grants from the U.S. Department of Energy and the National Institutes of Health. We thank F. Delaglio and D. Garrett for software support; T. Dieckmann, M. Grzeskowiak and M. Phillips for technical support; F. Allain, J. Bowie, D. Eisenberg, and C. Kim for useful discussions. We also thank B. Stoddard for the coordinates of the I-PpoI DNA complex.

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  1. Department of Chemistry and Biochemistry and UCLA–DOE Laboratory of Structural Biology and Genetics, University of California, Los Angeles, 405 Hilgard Ave, Los Angeles, 90095, California, USA

    Jonathan M. Wojciak, Kevin M. Connolly & Robert T. Clubb

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Correspondence to Robert T. Clubb.

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Wojciak, J., Connolly, K. & Clubb, R. NMR structure of the Tn916 integrase–DNA complex. Nat Struct Mol Biol 6, 366–373 (1999). https://doi.org/10.1038/7603

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