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Structure of the RTP–DNA complex and the mechanism of polar replication fork arrest

Nature Structural Biology volume 8, pages 206–210 (2001)Cite this article

Abstract

The coordinated termination of DNA replication is an important step in the life cycle of bacteria with circular chromosomes, but has only been defined at a molecular level in two systems to date. Here we report the structure of an engineered replication terminator protein (RTP) of Bacillus subtilis in complex with a 21 base pair DNA by X-ray crystallography at 2.5 Å resolution. We also use NMR spectroscopic titration techniques. This work reveals a novel DNA interaction involving a dimeric 'winged helix' domain protein that differs from predictions. While the two recognition helices of RTP are in close contact with the B-form DNA major grooves, the 'wings' and N-termini of RTP do not form intimate contacts with the DNA. This structure provides insight into the molecular basis of polar replication fork arrest based on a model of cooperative binding and differential binding affinities of RTP to the two adjacent binding sites in the complete terminator.

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Figure 1: The structure of the RTP.C110S–sRB complex and summary of protein–DNA interactions.
Figure 2: Sites of RTP–DNA contact from crystallographic data
Figure 3: Perturbations to RTP upon binding DNA as shown by NMR.
Figure 4: Model of the complete RTP–DNA terminator complex.

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Acknowledgements

Use of the Advanced Photon Source was supported by the US Department of Energy, Basic Energy Sciences, Office of Science. Use of the BioCARS Sector 14 was supported by the National Institutes of Health, National Center for Research Resources. This research was supported by grants from the Arnold Yeldham and Mary Raine Medical Research Foundation (M.C.J.W.), the Australia Research Council Fellowship (J.A.W.) and Small Grant Schemes (M.C.J.W. and J.A.W.), and the Swedish Natural Science Research Council (G.O.). We would also like to thank G.F. King for valuable scientific discussion.

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Authors and Affiliations

  1. Department of Chemistry/Biochemistry University of Western Australia and the Western Australian Institute for Medical Research, Nedlands, 6907, Western Australia, Australia

    J.A. Wilce

  2. Department of Pharmacology/Crystallography Centre, University of Western Australia, and the Western Australian Institute for Medical Research, Nedlands, 6907, Western Australia, Australia

    J.P. Vivian & M.C.J. Wilce

  3. Department of Biochemistry, University of Sydney, Sydney, 2006, New South Wales, Australia

    A.F. Hastings, I.G. Duggin & R.G. Wake

  4. Department of Medical Biochemistry and Biophysics, Karolinska Institute, 77, Stockholm, S-171, Sweden

    G. Otting

  5. Structural Chemistry Laboratory, AstraZeneca R&D, 83, Mölndal, S-431, Sweden

    R.H.A. Folmer

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Wilce, J., Vivian, J., Hastings, A. et al. Structure of the RTP–DNA complex and the mechanism of polar replication fork arrest. Nat Struct Mol Biol 8, 206–210 (2001). https://doi.org/10.1038/84934

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