Abstract
Here we present the crystal structure of the Escherichia coli protein RuvA bound to a key DNA intermediate in recombination, the Holliday junction. The structure, solved by isomorphous replacement and density modification at 6 Å resolution, reveals the molecular architecture at the heart of the branch migration and resolution reactions required to process Holliday intermediates into recombinant DNA molecules. It also reveals directly for the first time the structure of the Holliday junction. A single RuvA tetramer is bound to one face of a junction whose four DNA duplex arms are arranged in an open and essentially four-fold symmetric conformation. Protein–DNA contacts are mediated by two copies of a helix-hairpin-helix motif per RuvA subunit that contact the phosphate backbone in a very similar manner. The open structure of the junction stabilized by RuvA binding exposes a DNA surface that could be bound by the RuvC endonuclease to promote resolution.
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References
West, S.C. Annu. Rev. Genet. 31, 213–244 (1997).
Otsuji, N., Iyehara, H. & Hideshima, Y. J. Bacterial. 117, 337–344 (1974).
Lloyd, R.G., Benson, F.E. & Shurvinton, C.E. Mol. Gen. Genet. 194, 303–309 (1984).
Benson, F., Collier, S. & Lloyd, R.G. Mol. Gen. Genet. 225, 266–272 (1991).
Whitby, M.C., Bolt, E.L., Chan, S.N. & Lloyd, R.G. J. Mol. Biol. 264, 878–890 (1996).
Rafferty, J.B. et al. Science 274, 415–421 (1996).
Eggleston, A.K., Mitchell, A.H. & West, S.C. Cell 89, 607–617 (1997).
van Gool, A.J., Shah, R., Mezard, C. & West, S.C. EMBO. J. 17, 1838–1845 (1998).
Thayer, M.M., Ahern, H., Xing, D.X., Cunningham, R.P. & Tainer, J.A. EMBO J. 14, 4108–4120 (1995).
Doherty, A.J., Serpell, L.C. & Ponting, C.P. Nucleic Acids Res. 24, 2488–2497 (1996).
Rice, D.W., Rafferty, J.B., Artymiuk, P.J. & Lloyd, R.G. Curr. Opin. Struct. Biol. 7, 798–803 (1997).
Hargreaves, D. et al. Acta. Crystallogr., in the press.
Richmond, T.J., Finch, J.T., Rushton, B., Rhodes, D. & Klug, A. Nature 311, 532–537 (1984).
Pelletier, H., Sawaya, M.R., Kumar, A., Wilson, S.H. & Kraut, J. Science 264, 1891–1903 (1994).
Pelletier, H., Sawaya, M.R., Wolfle, W., Wilson, S.H. & Kraut, J. Biochemistry 35, 12742–12761 (1996).
Rafferty, J.B. et al. J. Mol. Biol. 278, 105–116 (1998).
Guo, F., Gopaul, D.N. & Van Duyne, G.D. Nature 389, 40–46 (1997).
Parsons, C.A., Tsaneva, I., Lloyd, R.G. & West, S.C. Proc. Nat. Acad. Sci. USA 89, 5452–5456 (1992).
Yu, X., West, S.C. & Egelman, E.H. J Mol. Biol. 266, 217–222 (1997).
Sharples, G.J., Benson, F.E., Illing, G.T. & Lloyd, R.G. Mol. Gen. Genet. 221, 219–226 (1990).
Mandal, T.N., Mahdi, A.A., Sharples, G.J. & Lloyd, R.G. J Bacteriol. 175, 4325–4334 (1993).
Ariyoshi, M. et al. Cell 78, 1063–1072 (1994).
Otwinowski, Z. & Minor, W. Meth. Enz. 276, 307–326 (1997).
CCP4. The CCP4 suite: Programs for protein crystallography. Acta Crystallogr. D50, 760–763 (1994).
Otwinowski, Z. Proceedings of the CCP4 Study Weekend: Isomorphous Replacement and Anomalous Scattering, p80 (SERC Daresbury Laboratory, Warrington, U.K., 1991).
Cowtan, K. Joint CCP4 and ESF-EACBM Newsletter and Protein Crystallography 31, 34–38 (1994).
Kleywegt, G.J. & Jones, T.A. Masks and Bones. Proceedings of the CCP4 Study Weekend: From First Map to Final Model, p59 (EPSRC Daresbury Laboratory, Warrington, UK., 1994).
Bennett, R.J., Dunderdale, H.J. & West, S.C. Cell 74, 1021–1031 (1993).
Jones, T.A. J. Appl. Crystallogr. 11, 268–270 (1978).
Ferrin, T.E., Huang, C.C., Jarvis, L.E. & Langridge, R. J Mol. Graphics 6, 13–27 (1988).
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Hargreaves, D., Rice, D., Sedelnikova, S. et al. Crystal structure of E.coli RuvA with bound DNA Holliday junction at 6 Å resolution. Nat Struct Mol Biol 5, 441–446 (1998). https://doi.org/10.1038/nsb0698-441
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DOI: https://doi.org/10.1038/nsb0698-441
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