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Site-specific DNA binding using a variation of the double stranded RNA binding motif

Abstract

The integrase family of site-specific recombinases catalyze a diverse array of DNA rearrangements in archaebacteria, eubacteria and yeast. The solution structure of the DNA binding domain of the integrase protein from the conjugative transposon Tn 916 has been determined using NMR spectroscopy. The structure provides the first insights into distal site DNA binding by a site-specific integrase and reveals that the N-terminal domain is structurally similar to the double stranded RNA binding domain (dsRBD). The results of chemical shift mapping experiments suggest that the integrase protein interacts with DNA using residues located on the face of its three stranded β-sheet. This surface differs from the proposed RNA binding surface in dsRBDs, suggesting that different surfaces on the same protein fold can be used to bind DNA and RNA.

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Figure 1: The Tn916 transposon.
Figure 2: Superposition of 25 simulated annealing structures of the IntN domain (residues Arg 6–Asp 70).
Figure 3: Chemical shift differences between free and DNA bound forms of the IntN domain.
Figure 4: Comparison of the structures of a, IntN domain (residues Arg 6–Asp 70 ) and b, staufen dsRBD III protein22.

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Acknowledgements

We thank T. Dieckmann and M. Grzeskowiak for technical support; D. Garrett for the program PIPP and F. Delaglio for the program NMRPipe, J. Omichinski for useful discussions and G. Churchward for the Tn916 integrase clone. This work was supported by a grant from the U.S. Department of Energy.

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Correspondence to Robert T. Clubb.

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Connolly, K., Wojciak, J. & Clubb, R. Site-specific DNA binding using a variation of the double stranded RNA binding motif. Nat Struct Mol Biol 5, 546–550 (1998). https://doi.org/10.1038/799

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