Mechanism of DNA translocation in a replicative hexameric helicase (original) (raw)

References

  1. Messer, W. The bacterial replication initiator DnaA. DnaA and oriC, the bacterial mode to initiate DNA replication. FEMS Microbiol. Rev. 26, 355–374 (2002)
    CAS PubMed Google Scholar
  2. Bell, S. P. & Dutta, A. DNA replication in eukaryotic cells. Annu. Rev. Biochem. 71, 333–374 (2002)
    Article CAS PubMed Google Scholar
  3. Hickman, A. B. & Dyda, F. Binding and unwinding: SF3 viral helicases. Curr. Opin. Struct. Biol. 15, 77–85 (2005)
    Article CAS PubMed Google Scholar
  4. Neuwald, A. F., Aravind, L., Spouge, J. L. & Koonin, E. V. AAA + : A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes. Genome Res. 9, 27–43 (1999)
    CAS PubMed Google Scholar
  5. Seo, Y. S., Muller, F., Lusky, M. & Hurwitz, J. Bovine papillomavirus (BPV) encoded E1 protein contains multiple activities required for BPV DNA replication. Proc. Natl Acad. Sci. USA 90, 702–706 (1993)
    Article ADS CAS PubMed PubMed Central Google Scholar
  6. Yang, L. et al. The E1 protein of the papillomavirus BPV-1 is an ATP dependent DNA helicase. Proc. Natl Acad. Sci. USA 90, 5086–5090 (1993)
    Article ADS CAS PubMed PubMed Central Google Scholar
  7. Sedman, J. & Stenlund, A. The papillomavirus E1 protein forms a DNA-dependent hexameric complex with ATPase and DNA helicase activities. J. Virol. 72, 6893–6897 (1998)
    CAS PubMed PubMed Central Google Scholar
  8. Ahnert, P. & Patel, S. S. Asymmetric interactions of hexameric bacteriophage T7 DNA helicase with the 5′- and 3′-tails of the forked DNA substrate. J. Biol. Chem. 272, 32267–32273 (1997)
    Article CAS PubMed Google Scholar
  9. LeBowitz, J. H. & McMacken, R. The Escherichia coli dnaB replication protein is a DNA helicase. J. Biol. Chem. 261, 4738–4748 (1986)
    CAS PubMed Google Scholar
  10. Egelman, E. H., Yu, X., Wild, R., Hingorani, M. M. & Patel, S. S. Bacteriophage T7 helicase/primase proteins form rings around single-stranded DNA that suggest a general structure for hexameric helicases. Proc. Natl Acad. Sci. USA 92, 3869–3873 (1995)
    Article ADS CAS PubMed PubMed Central Google Scholar
  11. Kaplan, D. L. & O'Donnell, M. DnaB drives DNA branch migration and dislodges proteins while encircling two DNA strands. Mol. Cell 10, 647–657 (2002)
    Article CAS PubMed Google Scholar
  12. Seo, Y. S. & Hurwitz, J. Isolation of helicase alpha, a DNA helicase from HeLa cells stimulated by a fork structure and signal-stranded DNA-binding proteins. J. Biol. Chem. 268, 10282–10295 (1993)
    CAS PubMed Google Scholar
  13. Gai, D., Zhao, R., Li, D., Finkielstein, C. V. & Chen, X. S. Mechanisms of conformational change for a replicative hexameric helicase of SV40 large tumor antigen. Cell 119, 47–60 (2004)
    Article CAS PubMed Google Scholar
  14. Li, D. et al. Structure of the replicative helicase of the oncoprotein SV40 large tumour antigen. Nature 423, 512–518 (2003)
    Article ADS CAS PubMed Google Scholar
  15. Enemark, E. J., Chen, G., Vaughn, D. E., Stenlund, A. & Joshua-Tor, L. Crystal structure of the DNA binding domain of the replication initiation protein E1 from papillomavirus. Mol. Cell 6, 149–158 (2000)
    Article CAS PubMed Google Scholar
  16. Luo, X., Sanford, D. G., Bullock, P. A. & Bachovchin, W. W. Solution structure of the origin DNA-binding domain of SV40 T-antigen. Nature Struct. Biol. 3, 1034–1039 (1996)
    Article CAS PubMed Google Scholar
  17. Davey, M. J. & O'Donnell, M. Replicative helicase loaders: ring breakers and ring makers. Curr. Biol. 13, R594–R596 (2003)
    Article CAS PubMed Google Scholar
  18. Jeruzalmi, D., O'Donnell, M. & Kuriyan, J. Clamp loaders and sliding clamps. Curr. Opin. Struct. Biol. 12, 217–224 (2002)
    Article CAS PubMed Google Scholar
  19. Enemark, E. J., Stenlund, A. & Joshua-Tor, L. Crystal structures of two intermediates in the assembly of the papillomavirus replication initiation complex. EMBO J. 21, 1487–1496 (2002)
    Article CAS PubMed PubMed Central Google Scholar
  20. Gillette, T. G., Lusky, M. & Borowiec, J. A. Induction of structural changes in the bovine papillomavirus type 1 origin of replication by the viral E1 and E2 proteins. Proc. Natl Acad. Sci. USA 91, 8846–8850 (1994)
    Article ADS CAS PubMed PubMed Central Google Scholar
  21. Sanders, C. M. & Stenlund, A. Recruitment and loading of the E1 initiator protein: an ATP-dependent process catalysed by a transcription factor. EMBO J. 17, 7044–7055 (1998)
    Article CAS PubMed PubMed Central Google Scholar
  22. Schuck, S. & Stenlund, A. Assembly of a double hexameric helicase. Mol. Cell 20, 377–389 (2005)
    Article CAS PubMed Google Scholar
  23. Chen, G. & Stenlund, A. Sequential and ordered assembly of E1 initiator complexes on the papillomavirus origin of DNA replication generates progressive structural changes related to melting. Mol. Cell. Biol. 22, 7712–7720 (2002)
    Article CAS PubMed PubMed Central Google Scholar
  24. Abbate, E. A., Berger, J. M. & Botchan, M. R. The X-ray structure of the papillomavirus helicase in complex with its molecular matchmaker E2. Genes Dev. 18, 1981–1996 (2004)
    Article CAS PubMed PubMed Central Google Scholar
  25. Singleton, M. R., Sawaya, M. R., Ellenberger, T. & Wigley, D. B. Crystal structure of T7 gene 4 ring helicase indicates a mechanism for sequential hydrolysis of nucleotides. Cell 101, 589–600 (2000)
    Article CAS PubMed Google Scholar
  26. Crampton, D. J., Mukherjee, S. & Richardson, C. C. DNA-induced switch from independent to sequential dTTP hydrolysis in the bacteriophage T7 DNA helicase. Mol. Cell 21, 165–174 (2006)
    Article CAS PubMed Google Scholar
  27. Hingorani, M. M. & Patel, S. S. Interactions of bacteriophage T7 primase/helicase protein with single-stranded and double-stranded DNAs. Biochemistry 32, 12478–12487 (1993)
    Article CAS PubMed Google Scholar
  28. Liao, J. C., Jeong, Y. J., Kim, D. E., Patel, S. S. & Oster, G. Mechanochemistry of t7 DNA helicase. J. Mol. Biol. 350, 452–475 (2005)
    Article CAS PubMed Google Scholar
  29. Fouts, E. T., Yu, X., Egelman, E. H. & Botchan, M. R. Biochemical and electron microscopic image analysis of the hexameric E1 helicase. J. Biol. Chem. 274, 4447–4458 (1999)
    Article CAS PubMed Google Scholar
  30. Kawaoka, J., Jankowsky, E. & Pyle, A. M. Backbone tracking by the SF2 helicase NPH-II. Nature Struct. Mol. Biol. 11, 526–530 (2004)
    Article CAS Google Scholar
  31. Wessel, R., Schweizer, J. & Stahl, H. Simian virus 40 T-antigen DNA helicase is a hexamer which forms a binary complex during bidirectional unwinding from the viral origin of DNA replication. J. Virol. 66, 804–815 (1992)
    CAS PubMed PubMed Central Google Scholar
  32. Lin, B. Y., Makhov, A. M., Griffith, J. D., Broker, T. R. & Chow, L. T. Chaperone proteins abrogate inhibition of the human papillomavirus (HPV) E1 replicative helicase by the HPV E2 protein. Mol. Cell. Biol. 22, 6592–6604 (2002)
    Article CAS PubMed PubMed Central Google Scholar
  33. McCoy, A. J., Grosse-Kunstleve, R. W., Storoni, L. C. & Read, R. J. Likelihood-enhanced fast translation functions. Acta Crystallogr. D 61, 458–464 (2005)
    Article PubMed Google Scholar
  34. Esnouf, R. M. An extensively modified version of MolScript that includes greatly enhanced coloring capabilities. J. Mol. Graph. 15, 132–134 (1997)
    Article CAS Google Scholar
  35. Bacon, D. J. & Anderson, W. F. A fast algorithm for rendering space-filling molecule pictures. J. Mol. Graph. 6, 219–220 (1988)
    Article Google Scholar
  36. Merritt, E. A. & Murphy, M. E. P. Raster3D version 2.0 - A program for photorealistic molecular graphics. Acta Crystallogr. D 50, 869–873 (1994)
    Article CAS PubMed Google Scholar

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