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  • Review Article
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Motors and switches: AAA+ machines within the replisome

Nature Reviews Molecular Cell Biology volume 3, pages 826–835 (2002)Cite this article

Key Points

  • The Escherichia coli clamp loader, γ-complex, loads the ring-shaped β-clamp onto DNA in an ATP driven reaction in which the clamp is cracked open, brought to a primed site and closed around the DNA.

  • AAA+ (ATPases associated with a variety of cellular activities) proteins are involved in many different aspects of DNA metabolism.

  • The γ- and δ′-subunits of the γ-complex are AAA+ proteins and so are clamp-loader subunits from eukaryotes, archaea and T4 bacteriophage.

  • The recent crystal structure of the γ3δδ′-assembly, an active clamp loader, indicates that the clamp loader is a pentameric ring. A striking feature of this assembly is the location of ATP sites at the interfaces of the subunits.

  • Clamp loaders from eukaryotes, archaea and T4 bacteriophage share similarities to the E. coli γ-complex and models similar to that of of the E. coli γ-complex can be made for each of these clamp loaders.

  • Many other replication proteins are AAA+ proteins, including the replication initiation proteins, DnaA, the origin recognition complex (ORC), Mcm2–7, Cdc6 and DnaC.

  • The similarities between the γ-complex subunits and other AAA+ proteins that are involved in replication initiation, lead to a model for the function of the replication-initiation proteins based on γ-complex structural and biochemical data.

Abstract

Clamp loaders are required to load the ring-shaped clamps that tether replicative DNA polymerases onto DNA. Recently solved crystal structures, along with a series of biochemical studies, have provided a detailed understanding of the clamp loading reaction. In particular, studies of the Escherichia coli clamp loader — an AAA+ machine — have provided insights into the architecture of clamp loaders from eukaryotes, bacteriophage T4 and archaea. Other AAA+ proteins are also involved in the initiation of DNA replication, and studies of the E. coli clamp loader indicate mechanisms by which these proteins might function.

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Figure 1: Mechanism of clamp-loader action.
Figure 2: The β-dimer is under spring tension.
Figure 3: The crystal structure of γ3δδ′.
Figure 4: Arrangement of clamp-loader subunits in the different branches of life.
Figure 5: A model of replication initiation in E. coli.
Figure 6: Models for replication-initiation proteins.

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References

  1. Stukenberg, P. T., Studwell-Vaughan, P. S. & O'Donnell, M. Mechanism of the sliding β-clamp of DNA polymerase III holoenzyme. J. Biol. Chem. 266, 11328–11334 (1991).Reveals that β binds DNA topologically, and indicates that it encircles DNA like a doughnut.

    CAS  PubMed  Google Scholar 

  2. Kong, X. P., Onrust, R., O'Donnell, M. & Kuriyan, J. Three-dimensional structure of the β-subunit of E. coli DNA polymerase III holoenzyme: a sliding DNA clamp. Cell 69, 425–437 (1992).The crystal structure of the β-sliding clamp confirmed the biochemical prediction of a ring shape for the β-dimer. It also revealed the unexpected three-domain architecture of β, giving the dimer a sixfold appearance.

    CAS  PubMed  Google Scholar 

  3. Baker, T. A. & Bell, S. P. Polymerases and the replisome: machines within machines. Cell 92, 295–305 (1998).

    CAS  PubMed  Google Scholar 

  4. Davey, M. J. & O'Donnell, M. Mechanisms of DNA replication. Curr. Opin. Chem. Biol. 4, 581–586 (2000).

    CAS  PubMed  Google Scholar 

  5. Jeruzalmi, D., O'Donnell, M. & Kuriyan, J. Clamp loaders and sliding clamps. Curr. Opin. Struct. Biol. 12, 217–224 (2002).

    CAS  PubMed  Google Scholar 

  6. O'Donnell, M., Jeruzalmi, D. & Kuriyan, J. Clamp loader structure predicts the architecture of DNA polymerase III holoenzyme and RFC. Curr. Biol. 11, R935–R946 (2001).

    CAS  PubMed  Google Scholar 

  7. Krishna, T. S., Kong, X. P., Gary, S., Burgers, P. M. & Kuriyan, J. Crystal structure of the eukaryotic DNA polymerase processivity factor PCNA. Cell 79, 1233–1243 (1994).The structure of the eukaryotic sliding clamp, PCNA, is essentially superimposable on the β-sliding clamp. Both clamps contain six copies of the same structural domain, except PCNA is a trimer in which each protomer consists of two domains.

    CAS  PubMed  Google Scholar 

  8. Gulbis, J. M., Kelman, Z., Hurwitz, J., O'Donnell, M. & Kuriyan, J. Structure of the C-terminal region of p21(WAF1/CIP1) complexed with human PCNA. Cell 87, 297–306 (1996).

    CAS  PubMed  Google Scholar 

  9. Moarefi, I., Jeruzalmi, D., Turner, J., O'Donnell, M. & Kuriyan, J. Crystal structure of the DNA polymerase processivity factor of T4 bacteriophage. J. Mol. Biol. 296, 1215–1223 (2000).

    CAS  PubMed  Google Scholar 

  10. Matsumiya, S., Ishino, Y. & Morikawa, K. Crystal structure of an archaeal DNA sliding clamp: proliferating cell nuclear antigen from Pyrococcus furiosus. Protein Sci. 10, 17–23 (2001). The structure of the sliding clamp of this archaeal species is shown here to share the same chain fold as the β-sliding clamp and PCNA from eukaryotes.| Article | PubMed |

  11. O'Donnell, M., Onrust, R., Dean, F. B., Chen, M. & Hurwitz, J. Homology in accessory proteins of replicative polymerases — E. coli to humans. Nucleic Acids Res. 21, 1–3 (1993).

    CAS  PubMed  PubMed Central  Google Scholar 

  12. Cullmann, G., Fien, K., Kobayashi, R. & Stillman, B. Characterization of the five replication factor C genes of Saccharomyces cerevisiae. Mol. Cell. Biol. 15, 4661–4671 (1995).

    CAS  PubMed  PubMed Central  Google Scholar 

  13. 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).Describes the AAA+ family and contains not only the alignment of the various sequences but also a discussion of their structure and function.

    CAS  PubMed  Google Scholar 

  14. Cann, I. K. & Ishino, Y. Archaeal DNA replication: identifying the pieces to solve a puzzle. Genetics 152, 1249–1267 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  15. Pritchard, A. E., Dallmann, H. G., Glover, B. P. & McHenry, C. S. A novel assembly mechanism for the DNA polymerase III holoenzyme DnaX complex: association of deltadelta' with DnaX(4) forms DnaX(3)deltadelta'. EMBO J. 19, 6536–6545 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  16. Jeruzalmi, D., O'Donnell, M. & Kuriyan, J. Crystal structure of the processivity clamp loader γ (gamma) complex of E. coli DNA polymerase III. Cell 106, 429–441 (2001).Presents the crystal structure of a functional clamp opener, γ 3 δδ′, as a pentameric ring and discusses how the clamp loader might function with ATP to bind and open the β ring.

    CAS  PubMed  Google Scholar 

  17. Onrust, R. & O'Donnell, M. DNA polymerase III accessory proteins. II. Characterization of δ and δ′. J. Biol. Chem. 268, 11766–11772 (1993).

    CAS  PubMed  Google Scholar 

  18. Cann, I. K. et al. Biochemical analysis of replication factor C from the hyperthermophilic archaeon Pyrococcus furiosus. J. Bacteriol. 183, 2614–2623 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  19. Pisani, F. M., De Felice, M., Carpentieri, F. & Rossi, M. Biochemical characterization of a clamp-loader complex homologous to eukaryotic replication factor C from the hyperthermophilic archaeon Sulfolobus solfataricus. J. Mol. Biol. 301, 61–73 (2000).

    CAS  PubMed  Google Scholar 

  20. Kelman, Z. & Hurwitz, J. A unique organization of the protein subunits of the DNA polymerase clamp loader in the archaeon Methanobacterium thermoautotrophicum ΔH. J. Biol. Chem. 275, 7327–7336 (2000).

    CAS  PubMed  Google Scholar 

  21. Jarvis, T. C., Paul, L. S. & von Hippel, P. H. Structural and enzymatic studies of the T4 DNA replication system. I. Physical characterization of the polymerase accessory protein complex. J. Biol. Chem. 264, 12709–12716 (1989).The subunit composition of the T4 phage clamp loader is determined in this paper.

    CAS  PubMed  Google Scholar 

  22. Koonin, E. V. DnaC protein contains a modified ATP–binding motif and belongs to a novel family of ATPases including also DnaA. Nucleic Acids Res. 20, 1997 (1992).

    CAS  PubMed  PubMed Central  Google Scholar 

  23. Liu, J. et al. Structure and function of Cdc6/Cdc18: implications for origin recognition and checkpoint control. Mol. Cell 6, 637–648 (2000).

    CAS  PubMed  Google Scholar 

  24. Xiao, H., Naktinis, V. & O'Donnell, M. Assembly of a chromosomal replication machine: two DNA polymerases, a clamp loader, and sliding clamps in one holoenzyme particle. IV. ATP-binding site mutants identify the clamp loader. J. Biol. Chem. 270, 13378–13383 (1995).

    CAS  PubMed  Google Scholar 

  25. Turner, J., Hingorani, M. M., Kelman, Z. & O'Donnell, M. The internal workings of a DNA polymerase clamp-loading machine. EMBO J. 18, 771–783 (1999).Elucidates the roles of δ as the wrench and δ′ as a modifier of the wrench in response to ATP binding to γ.

    CAS  PubMed  PubMed Central  Google Scholar 

  26. Stewart, J., Hingorani, M. M., Kelman, Z. & O'Donnell, M. Mechanism of β-clamp opening by the δ-subunit of Escherichia coli DNA polymerase III holoenzyme. J. Biol. Chem. 276, 19182–19189 (2001).

    CAS  PubMed  Google Scholar 

  27. Jeruzalmi, D. et al. Mechanism of processivity clamp opening by the δ-subunit wrench of the clamp loader complex of E. coli DNA polymerase III. Cell 106, 417–428 (2001).This structure revealed not only the detailed nature of how δ binds β and cracks an interface, but also provides evidence for spring tension in β, indicating a mechanism for how the β-clamp might open up after one interface is cracked.

    CAS  PubMed  Google Scholar 

  28. Naktinis, V., Onrust, R., Fang, L. & O'Donnell, M. Assembly of a chromosomal replication machine: two DNA polymerases, a clamp loader, and sliding clamps in one holoenzyme particle. II. Intermediate complex between the clamp loader and its clamp. J. Biol. Chem. 270, 13358–13365 (1995).

    CAS  PubMed  Google Scholar 

  29. Leu, F. P. & O'Donnell, M. Interplay of clamp loader subunits in opening the β sliding clamp of Escherichia coli DNA polymerase III holoenzyme. J. Biol. Chem. 276, 47185–47194 (2001).

    CAS  PubMed  Google Scholar 

  30. Ahmadian, M. R., Stege, P., Scheffzek, K. & Wittinghofer, A. Confirmation of the arginine-finger hypothesis for the GAP-stimulated GTP-hydrolysis reaction of Ras. Nature Struct. Biol. 4, 686–689 (1997).The arginine-finger model for the GTPase-activating-protein–Ras interaction is confirmed in this paper. The arginine-finger model has guided the thinking of how some proteins use NTPs, including the AAA+ proteins.

    CAS  PubMed  Google Scholar 

  31. Walker, J. R. et al. Escherichia coli DNA polymerase III τ- and γ-subunit conserved residues required for activity in vivo and in vitro. J. Bacteriol. 182, 6106–6113 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  32. Lenzen, C. U., Steinmann, D., Whiteheart, S. W. & Weis, W. I. Crystal structure of the hexamerization domain of N-ethylmaleimide-sensitive fusion protein. Cell 94, 525–536 (1998).

    CAS  PubMed  Google Scholar 

  33. Yu, R. C., Jahn, R. & Brunger, A. T. NSF N-terminal domain crystal structure: models of NSF function. Mol. Cell 4, 97–107 (1999).

    CAS  PubMed  Google Scholar 

  34. Zhang, X. et al. Structure of the AAA ATPase p97. Mol. Cell 6, 1473–84 (2000).

    CAS  PubMed  Google Scholar 

  35. Onrust, R., Stukenberg, P. T. & O'Donnell, M. Analysis of the ATPase subassembly which initiates processive DNA synthesis by DNA polymerase III holoenzyme. J. Biol. Chem. 266, 21681–21686 (1991).

    CAS  PubMed  Google Scholar 

  36. Hingorani, M. M. & O'Donnell, M. ATP binding to the Escherichia coli clamp loader powers opening of the ring-shaped clamp of DNA polymerase III holoenzyme. J. Biol. Chem. 273, 24550–24563 (1998).

    CAS  PubMed  Google Scholar 

  37. Lee, S. H., Kwong, A. D., Pan, Z. Q. & Hurwitz, J. Studies on the activator 1 protein complex, an accessory factor for proliferating cell nuclear antigen-dependent DNA polymerase δ. J. Biol. Chem. 266, 594–602 (1991).

    CAS  PubMed  Google Scholar 

  38. Tsurimoto, T. & Stillman, B. Replication factors required for SV40 DNA replication in vitro. I. DNA structure-specific recognition of a primer-template junction by eukaryotic DNA polymerases and their accessory proteins. J. Biol. Chem. 266, 1950–1960 (1991).

    CAS  PubMed  Google Scholar 

  39. Fien, K. & Stillman, B. Identification of replication factor C from Saccharomyces cerevisiae: a component of the leading-strand DNA replication complex. Mol. Cell. Biol. 12, 155–163 (1992).

    CAS  PubMed  PubMed Central  Google Scholar 

  40. Shiomi, Y. et al. ATP-dependent structural change of the eukaryotic clamp-loader protein, replication factor C. Proc. Natl Acad. Sci. USA 97, 14127–14132 (2000).

    CAS  PubMed  Google Scholar 

  41. Uhlmann, F., Gibbs, E., Cai, J., O'Donnell, M. & Hurwitz, J. Identification of regions within the four small subunits of human replication factor C required for complex formation and DNA replication. J. Biol. Chem. 272, 10065–10071 (1997).

    CAS  PubMed  Google Scholar 

  42. Uhlmann, F., Cai, J., Gibbs, E., O'Donnell, M. & Hurwitz, J. Deletion analysis of the large subunit p140 in human replication factor C reveals regions required for complex formation and replication activities. J. Biol. Chem. 272, 10058–10064 (1997).

    CAS  PubMed  Google Scholar 

  43. Fotedar, R. et al. A conserved domain of the large subunit of replication factor C binds PCNA and acts like a dominant negative inhibitor of DNA replication in mammalian cells. EMBO J. 15, 4423–4433 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  44. Cai, J. et al. A complex consisting of human replication factor C p40, p37, and p36 subunits is a DNA-dependent ATPase and an intermediate in the assembly of the holoenzyme. J. Biol. Chem. 272, 18974–18981 (1997).

    CAS  PubMed  Google Scholar 

  45. Ellison, V. & Stillman, B. Reconstitution of recombinant human replication factor C (RFC) and identification of an RFC subcomplex possessing DNA-dependent ATPase activity. J. Biol. Chem. 273, 5979–5987 (1998).

    CAS  PubMed  Google Scholar 

  46. Uhlmann, F. et al. In vitro reconstitution of human replication factor C from its five subunits. Proc. Natl Acad. Sci. USA 93, 6521–6526 (1996).

    CAS  PubMed  Google Scholar 

  47. Oyama, T., Ishino, Y., Cann, I. K., Ishino, S. & Morikawa, K. Atomic structure of the clamp loader small subunit from Pyrococcus furiosus. Mol. Cell. 8, 455–463 (2001).The crystal structure of the small RFC subunit from Pyrococcus furiosus is determined and is similar to the γ-trimer of γ 3 δδ′.

    CAS  PubMed  Google Scholar 

  48. Guenther, B., Onrust, R., Sali, A., O'Donnell, M. & Kuriyan, J. Crystal structure of the δ′-subunit of the clamp-loader complex of E. coli DNA polymerase III. Cell 91, 335–345 (1997).

    CAS  PubMed  Google Scholar 

  49. Rush, J. et al. The 44P subunit of the T4 DNA polymerase accessory protein complex catalyzes ATP hydrolysis. J. Biol. Chem. 264, 10943–10953 (1989).

    CAS  PubMed  Google Scholar 

  50. Fuller, R. S., Funnell, B. E. & Kornberg, A. The dnaA protein complex with the E. coli chromosomal replication origin (oriC) and other DNA sites. Cell 38, 889–900 (1984).

    CAS  PubMed  Google Scholar 

  51. Matsui, M., Oka, A., Takanami, M., Yasuda, S. & Hirota, Y. Sites of dnaA protein-binding in the replication origin of the Escherichia coli K-12 chromosome. J. Mol. Biol. 184, 529–533 (1985).

    CAS  PubMed  Google Scholar 

  52. Speck, C., Weigel, C. & Messer, W. From footprint to toeprint: a close-up of the DnaA box, the binding site for the bacterial initiator protein DnaA. Nucleic Acids Res. 25, 3242–3247 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  53. Carr, K. M. & Kaguni, J. M. Stoichiometry of DnaA and DnaB protein in initiation at the Escherichia coli chromosomal origin. J. Biol. Chem. 276, 44919–44925 (2001).The most recent measurement of DnaA stoichiometry of binding to oriC . This overcomes the challenge of DnaA aggregation and determines that five DnaA molecules bind to oriC , and correspond to five DnaA-binding sites in oriC.

    CAS  PubMed  Google Scholar 

  54. Bramhill, D. & Kornberg, A. Duplex opening by dnaA protein at novel sequences in initiation of replication at the origin of the E. coli chromosome. Cell 52, 743–755 (1988).This is the first report of origin unwinding by the replication initiator, DnaA, a crucial step for initiation of DNA replication.

    CAS  PubMed  Google Scholar 

  55. Gille, H. & Messer, W. Localized DNA melting and structural pertubations in the origin of replication, oriC, of Escherichia coli in vitro and in vivo. EMBO J. 10, 1579–1584 (1991).

    CAS  PubMed  PubMed Central  Google Scholar 

  56. Funnell, B. E., Baker, T. A. & Kornberg, A. In vitro assembly of a prepriming complex at the origin of the Escherichia coli chromosome. J. Biol. Chem. 262, 10327–10334 (1987).

    CAS  PubMed  Google Scholar 

  57. Fang, L., Davey, M. J. & O'Donnell, M. Replisome assembly at oriC, the replication origin of E. coli, reveals an explanation for initiation sites outside an origin. Mol. Cell 4, 541–553 (1999).

    CAS  PubMed  Google Scholar 

  58. Woelker, B. & Messer, W. The structure of the initiation complex at the replication origin, oriC, of Escherichia coli. Nucleic Acids Res. 21, 5025–5033 (1993).

    CAS  PubMed  PubMed Central  Google Scholar 

  59. Hwang, D. S. & Kornberg, A. Opening of the replication origin of Escherichia coli by DnaA protein with protein HU or IHF. J. Biol. Chem. 267, 23083–23086 (1992).

    CAS  PubMed  Google Scholar 

  60. Speck, C. & Messer, W. Mechanism of origin unwinding: sequential binding of DnaA to double- and single-stranded DNA. EMBO J. 20, 1469–1476 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  61. Lee, D. G. & Bell, S. P. ATPase switches controlling DNA replication initiation. Curr. Opin. Cell. Biol. 12, 280–285 (2000).

    CAS  PubMed  Google Scholar 

  62. Speck, C., Weigel, C. & Messer, W. ATP- and ADP-dnaA protein, a molecular switch in gene regulation. EMBO J. 18, 6169–6176 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  63. Katayama, T., Kubota, T., Kurokawa, K., Crooke, E. & Sekimizu, K. The initiator function of DnaA protein is negatively regulated by the sliding clamp of the E. coli chromosomal replicase. Cell 94, 61–71 (1998).Links the regulation of initiation of DNA replication to the replicative polymerase, ensuring that reinitiation cannot occur once DNA synthesis has begun.

    CAS  PubMed  Google Scholar 

  64. Kurokawa, K. et al. A stimulation factor for hydrolysis of ATP bound to DnaA protein, the initiator of chromosomal DNA replication in Escherichia coli. Biochem. Biophys. Res. Commun. 243, 90–95 (1998).

    CAS  PubMed  Google Scholar 

  65. Kato, J. & Katayama, T. Hda, a novel DnaA-related protein, regulates the replication cycle in Escherichia coli. EMBO J. 20, 4253–4262 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  66. Davey, M. J., Fang, L., McInerney, P., Georgescu, R. E. & O'Donnell, M. The DnaC helicase loader is a dual ATP/ADP switch protein. EMBO J. 21, 3148–3159 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  67. Wickner, S. & Hurwitz, J. Interaction of Escherichia coli dnaB and dnaC(D) gene products in vitro. Proc. Natl Acad. Sci. USA 72, 921–925 (1975).

    CAS  PubMed  Google Scholar 

  68. Kobori, J. A. & Kornberg, A. The Escherichia coli dnaC gene product III. Properties of the dnaB-dnaC protein complex. J. Biol. Chem. 257, 13770–13775 (1982).

    CAS  PubMed  Google Scholar 

  69. Bell, S. P. & Stillman, B. ATP-dependent recognition of eukaryotic origins of DNA replication by a multiprotein complex. Nature 357, 128–134 (1992).In a landmark discovery, this report describes the purification and characterization of the origin recognition complex (ORC), the replication initiator in eukaryotic cells.

    CAS  Google Scholar 

  70. Liang, C., Weinreich, M. & Stillman, B. ORC and Cdc6p interact and determine the frequency of initiation of DNA replication in the genome. Cell 81, 667–676 (1995).

    CAS  PubMed  Google Scholar 

  71. Kelly, T. J. et al., The fission yeast cdc18+ gene product couples S phase to START and mitosis. Cell 74, 371–382 (1993).Fission yeast cdc18 (called Cdc6 in other organisms) is discovered and shown to be essential for control of the replication cycle.

    CAS  PubMed  Google Scholar 

  72. Klemm, R. D., Austin, R. J. & Bell, S. P. Coordinate binding of ATP and origin DNA regulates the ATPase activity of the origin recognition complex. Cell 88, 493–502 (1997).

    CAS  PubMed  Google Scholar 

  73. Vashee, S., Simancek, P., Challberg, M. D. & Kelly, T. J. Assembly of the human origin recognition complex. J. Biol. Chem. 276, 26666–26673 (2001).

    CAS  PubMed  Google Scholar 

  74. Lee, D. G., Makhov, A. M., Klemm, R. D., Griffith, J. D. & Bell, S. P. Regulation of origin recognition complex conformation and ATPase activity: differential effects of single-stranded and double-stranded DNA binding. EMBO J. 19, 4774–4782 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  75. Zou, L., Mitchell, J. & Stillman, B. CDC45, a novel yeast gene that functions with the origin recognition complex and Mcm proteins in initiation of DNA replication. Mol. Cell. Biol. 17, 553–563 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  76. Nishitani, H., Lygerou, Z., Nishimoto, T. & Nurse, P. The Cdt1 protein is required to license DNA for replication in fission yeast. Nature 404, 625–628 (2000).

    CAS  PubMed  Google Scholar 

  77. Maiorano, D., Moreau, J. & Mechali, M. XCDT1 is required for the assembly of pre-replicative complexes in Xenopus laevis. Nature 404, 622–625 (2000).

    CAS  PubMed  Google Scholar 

  78. Cocker, J. H., Piatti, S., Santocanale, C., Nasmyth, K. & Diffley, J. F. An essential role for the Cdc6 protein in forming the pre-replicative complexes of budding yeast. Nature 379, 180–182 (1996).

    CAS  PubMed  Google Scholar 

  79. Donovan, S., Harwood, J., Drury, L. S. & Diffley, J. F. Cdc6p-dependent loading of Mcm proteins onto pre-replicative chromatin in budding yeast. Proc. Natl Acad. Sci. USA 94, 5611–5616 (1997).This paper identifies Cdc6 as an important factor for Mcm assembly onto origin DNA in yeast cells.

    CAS  PubMed  Google Scholar 

  80. Adachi, Y., Usukura, J. & Yanagida, M. A globular complex formation by Nda1 and the other five members of the MCM protein family in fission yeast. Genes Cells 2, 467–479 (1997).

    CAS  PubMed  Google Scholar 

  81. Schwacha, A. & Bell, S. P. Interactions between two catalytically distinct MCM subgroups are essential for coordinated ATP hydrolysis and DNA replication. Mol. Cell 8, 1093–1104 (2001).Biochemical characterization of the Mcm2–7 complex from budding yeast. The authors establish the complexities of ATP hydrolysis by Mcm2–7 and describe the activities of various subcomplexes.

    CAS  PubMed  Google Scholar 

  82. Schulte, D., Richter, A., Burkhart, R., Musahl, C. & Knippers, R. Properties of the human nuclear protein p85Mcm. Expression, nuclear localization and interaction with other Mcm proteins. Eur. J. Biochem. 235, 144–151 (1996).

    CAS  PubMed  Google Scholar 

  83. Thommes, P., Kubota, Y., Takisawa, H. & Blow, J. J. The RLF-M component of the replication licensing system forms complexes containing all six MCM/P1 polypeptides. EMBO J. 16, 3312–3319 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  84. Labib, K., Tercero, J. A. & Diffley, J. F. Uninterrupted MCM2-7 function required for DNA replication fork progression. Science 288, 1643–1647 (2000).

    CAS  PubMed  Google Scholar 

  85. Lee, J. K. & Hurwitz, J. Isolation and characterization of various complexes of the minichromosome maintenance proteins of Schizosaccharomyces pombe. J. Biol. Chem. 275, 18871–18878 (2000).

    CAS  PubMed  Google Scholar 

  86. Ishimi, Y. A. DNA helicase activity is associated with an MCM4,-6, and-7 protein complex. J. Biol. Chem. 272, 24508–24513 (1997).

    CAS  PubMed  Google Scholar 

  87. Aparicio, O. M., Weinstein, D. M. & Bell, S. P. Components and dynamics of DNA replication complexes in S. cerevisiae: redistribution of MCM proteins and Cdc45p during S phase. Cell 91, 59–69 (1997).

    CAS  Google Scholar 

  88. Kim, S., Dallmann, H. G., McHenry, C. S. & Marians, K. J. τ couples the leading- and lagging-strand polymerases at the Escherichia coli DNA replication fork. J. Biol. Chem. 271, 21406–21412 (1996).

    CAS  PubMed  Google Scholar 

  89. Kelman, Z., Lee, J. K. & Hurwitz, J. The single minichromosome maintenance protein of Methanobacterium thermoautotrophicum ΔH contains DNA helicase activity. Proc. Natl Acad. Sci USA 96, 14783–14788 (1999).

    CAS  PubMed  Google Scholar 

  90. Chong, J. P., Hayashi, M. K., Simon, M. N., Xu, R. M. & Stillman, B. A double-hexamer archaeal minichromosome maintenance protein is an ATP-dependent DNA helicase. Proc. Natl Acad. Sci. USA 97, 1530–1535 (2000).Establishes (along with refs 89 and 91 ) that this archaeal MCM is a processive helicase, strengthening the argument that its eukaryotic counterparts form the replicative helicase. This report further demonstrates that the archaeal MCM is a ring-shaped double hexamer.

    CAS  PubMed  Google Scholar 

  91. Shechter, D. F., Ying, C. Y. & Gautier, J. The intrinsic DNA helicase activity of Methanobacterium thermoautotrophicum δ H minichromosome maintenance protein. J. Biol. Chem. 275, 15049–15059 (2000).

    CAS  PubMed  Google Scholar 

  92. Putnam, C. D. et al. Structure and mechanism of the RuvB Holliday junction branch migration motor. J. Mol. Biol. 311, 297–310 (2001).

    CAS  PubMed  Google Scholar 

  93. Niedenzu, T., Roleke, D., Bains, G., Scherzinger, E. & Saenger, W. Crystal structure of the hexameric replicative helicase RepA of plasmid RSF1010. J. Mol. Biol. 306, 479–487 (2001).

    CAS  Google Scholar 

  94. Story, R. M. & Steitz, T. A. Structure of the recA protein–ADP complex. Nature 355, 374–376 (1992).

    CAS  PubMed  Google Scholar 

  95. Yuzhakov, A., Kelman, Z. & O'Donnell, M. Trading places on DNA—a three-point switch underlies primer handoff from primase to the replicative DNA polymerase. Cell 96, 153–163 (1999).

    CAS  PubMed  Google Scholar 

  96. Xiao, H., Dong, Z. & O'Donnell, M. DNA polymerase III accessory proteins. IV. Characterization of chi and psi. J. Biol. Chem. 268, 11779–117784 (1993).

    CAS  PubMed  Google Scholar 

  97. Dallmann, H. G. & McHenry, C. S. DnaX complex of Escherichia coli DNA polymerase III holoenzyme. Physical characterization of the DnaX subunits and complexes. J. Biol. Chem. 270, 29563–29569 (1995).

    CAS  PubMed  Google Scholar 

  98. O'Donnell, M. & Studwell, P. S. Total reconstitution of DNA polymerase III holoenzyme reveals dual accessory protein clamps. J. Biol. Chem. 265, 1179–1187 (1990).

    CAS  PubMed  Google Scholar 

  99. Kelman, Z., Yuzhakov, A., Andjelkovic, J. & O'Donnell, M. Devoted to the lagging strand–the χ subunit of DNA polymerase III holoenzyme contacts SSB to promote processive elongation and sliding clamp assembly. EMBO J. 17, 2436–2449 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  100. Erzberger, J. P., Pirruccello, M. M. & Berger, J. M. The structure of bacterial DnaA: implications for general mechanisms underlying DNA replication. EMBO J. 21, 4763–4773 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

This work was supported in part by the Howard Hughes Medical Institute and the National Institutes of Health.

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Author notes

  1. David Jeruzalmi

    Present address: Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, 01238, USA

Authors and Affiliations

  1. Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, 10021, New York, USA

    Megan J. Davey & Mike O'Donnell

  2. Departments of Molecular and Cell Biology, and Chemistry, Howard Hughes Medical Institute, The University of California, Berkeley, 94720, California, USA

    David Jeruzalmi & John Kuriyan

  3. Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, 94720, California, USA

    David Jeruzalmi & John Kuriyan

Authors
  1. Megan J. Davey
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Correspondence to Mike O'Donnell.

Related links

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DATABASES

LocusLink

Cdc18

Cdc6

Cdt1

Mcm2

Mcm3

Mcm4

Mcm5

Mcm6

Mcm7

N-ethylmaleimide-sensitive fusion protein

Orc1

Orc2

Orc3

Orc4

Orc5

Orc6

Replication factor C

<i>Saccharomyces</i> genome database

Rfc1

Rfc2

Rfc3

Rfc4

Rfc5

Glossary

SLIDING CLAMP

A ring-shaped oligomer that encircles double-stranded DNA and slides along it. It confers processivity to replicative polymerases by tightly coupling the polymerase to DNA.

CLAMP LOADER

A multi-protein machine that acts catalytically to open a clamp and then place the clamp around primed DNA in an ATP-dependent process.

REPLICASE

A DNA polymerase with accessory subunits, including clamp and clamp loader.

ORIGIN OF REPLICATION

The site at which replication is initiated and usually where a replication initiator binds.

REPLICATIVE HELICASE

A ring-shaped protein that encircles single-stranded DNA and unwinds double-stranded DNA ahead of it. Replicative helicases are typically hexamers.

SENSOR-1 MOTIF

This motif is conserved in the AAA+ family of proteins and other NTPases and encodes a helix that might be positioned to respond to nucleotide binding within the same protein. It is also thought to be analogous to the switch II helix in small GTP-binding proteins.

WALKER-A AND -B MOTIFS

Found in many NTPases, these motifs are important for nucleotide binding and hydrolysis and come into contact with the phosphates of the bound nucleotide. The Walker-A motif is also known as the P loop.

SENSOR-2 MOTIF

This motif is conserved in the AAA+ proteins and is proposed to respond to nucleotide binding and hydrolysis. It is also thought to be analogous to the cap domain of adenylate cyclase.

SRC/F MOTIFS

These motifs are found within the Box VII motif (described in Box 1) that encode the putative arginine finger of clamp-loader subunits (SRC motif) and MCM proteins (SRF motif).

ARGININE FINGER

Consists of a catalytic arginine that forms part of an active site in some NTPases and is thought to function by stabilizing the transition state. Arginine fingers are usually supplied from a different subunit than the subunit that binds the nucleotide.

PRE-REPLICATIVE COMPLEX

A complex that forms on origins before the initiation of DNA replication. Its components in eukaryotes are known to include ORC, Cdc6, Cdt1 and Mcm2–7.

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Davey, M., Jeruzalmi, D., Kuriyan, J. et al. Motors and switches: AAA+ machines within the replisome. Nat Rev Mol Cell Biol 3, 826–835 (2002). https://doi.org/10.1038/nrm949

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