Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Organization of the archaeal MCM complex on DNA and implications for the helicase mechanism

Abstract

The homomultimeric archaeal mini-chromosome maintenance (MCM) complex serves as a simple model for the analogous heterohexameric eukaryotic complex. Here we investigate the organization and orientation of the MCM complex of the hyperthermophilic archaeon Sulfolobus solfataricus (Sso) on model DNA substrates. Sso MCM binds as a hexamer and slides on the end of a 3′-extended single-stranded DNA tail of a Y-shaped substrate; binding is oriented so that the motor domain of the protein faces duplex DNA. Two candidate β-hairpin motifs within the MCM monomer have partially redundant roles in DNA binding. Notably, however, conserved basic residues within these motifs have nonequivalent roles in the helicase activity of MCM. On the basis of these findings, we propose a model for the mechanism of the helicase activity of MCM and note parallels with SV40 T antigen.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Two candidate β-hairpins in Sso MCM.
Figure 2: Biochemical characterization of Sso MCM.
Figure 3: Architecture of MCM and orientation on DNA.
Figure 4: Loading of Sso MCM onto DNA.
Figure 5: Cutaway model of MCM binding to DNA.

Similar content being viewed by others

Accession codes

Accessions

BINDPlus

Protein Data Bank

References

  1. Iyer, L.M., Leipe, D.D., Koonin, E.V. & Aravind, L. Evolutionary history and higher order classification of AAA plus ATPases. J. Struct. Biol. 146, 11–31 (2004).

    Article  CAS  Google Scholar 

  2. Kelman, L.M. & Kelman, Z. Archaea: an archetype for replication initiation studies? Mol. Microbiol. 48, 605–616 (2003).

    Article  CAS  Google Scholar 

  3. Chong, J.P.J., 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).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  7. You, Z.Y., Komamura, Y. & Ishimi, Y. Biochemical analysis of the intrinsic Mcm4-Mcm6-Mcm7 DNA helicase activity. Mol. Cell. Biol. 19, 8003–8015 (1999).

    Article  CAS  Google Scholar 

  8. 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).

    Article  CAS  Google Scholar 

  9. Lee, J.K. & Hurwitz, J. Processive DNA helicase activity of the minichromosome maintenance proteins 4, 6, and 7 complex requires forked DMA structures. Proc. Natl. Acad. Sci. USA 98, 54–59 (2001).

    Article  CAS  Google Scholar 

  10. Yu, X. et al. The Methanobacterium thermoautotrophicum MCM protein can form heptameric rings. EMBO Rep. 3, 792–797 (2002).

    Article  Google Scholar 

  11. Fletcher, R.J. et al. The structure and function of MCM from archaeal M. thermoautotrophicum. Nat. Struct. Biol. 10, 160–167 (2003).

    Article  CAS  Google Scholar 

  12. Pape, T. et al. Hexameric ring structure of the full-length archaeal MCM protein complex. EMBO Rep. 4, 1079–1083 (2003).

    Article  CAS  Google Scholar 

  13. Soultanas, P. & Wigley, D.B. Unwinding the 'Gordian knot' of helicase action. Trends Biochem. Sci. 26, 47–54 (2001).

    Article  CAS  Google Scholar 

  14. Laskey, R.A. & Madine, M.A. A rotary pumping model for helicase function of MCM proteins at a distance from replication forks. EMBO Rep. 4, 26–30 (2003).

    Article  CAS  Google Scholar 

  15. Kaplan, D.L. & O'Donnell, M. Twin DNA pumps of a hexameric helicase provide power to simultaneously melt two duplexes. Mol. Cell 15, 453–465 (2004).

    Article  CAS  Google Scholar 

  16. Li, D.W. et al. Structure of the replicative helicase of the oncoprotein SV40 large tumour antigen. Nature 423, 512–518 (2003).

    Article  CAS  Google Scholar 

  17. Gai, D.H., Zhao, R., Li, D.W., 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  Google Scholar 

  18. 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  Google Scholar 

  19. Chen, Y.J. et al. Structural polymorphism of Methanothermobacter thermautotrophicus MCM. J. Mol. Biol. 346, 389–394 (2005).

    Article  CAS  Google Scholar 

  20. Grainge, I., Scaife, S. & Wigley, D. Biochemical analysis of components of the pre-replication complex of Archaeoglobus fulgidus. Nucleic Acids Res. 31, 4888–4898 (2003).

    Article  CAS  Google Scholar 

  21. Shin, J.H., Jiang, Y., Grabowski, B., Hurwitz, J. & Kelman, Z. Substrate requirements for duplex DNA translocation by the eukaryal and archaeal minichromosome maintenance helicases. J. Biol. Chem. 278, 49053–49062 (2003).

    Article  CAS  Google Scholar 

  22. Kaplan, D.L., Davey, M.J. & O'Donnell, M. Mcm4,6,7 uses a “pump in ring” mechanism to unwind DNA by steric exclusion and actively translocate along a duplex. J. Biol. Chem. 278, 49171–49182 (2003).

    Article  CAS  Google Scholar 

  23. Johnson, E.M., Kinoshita, Y. & Daniel, D.C. A new member of the MCM protein family encoded by the human MCM8 gene, located contrapodal to GCD10 at chromosome band 20p12.3–13. Nucleic Acids Res. 31, 2915–2925 (2003).

    Article  CAS  Google Scholar 

  24. Maiorano, D., Cuvier, O., Danis, E. & Mechali, M. MCM8 is an MCM2–7-related protein that functions as a DNA helicase during replication elongation and not initiation. Cell 120, 315–328 (2005).

    Article  CAS  Google Scholar 

  25. Ellman, G.L. Tissue sulfhydryl groups. Arch. Biochem. Biophys. 82, 70–77 (1959).

    Article  CAS  Google Scholar 

  26. Poplawski, A., Grabowski, B., Long, S.F. & Kelman, Z. The zinc finger domain of the archaeal minichromosome maintenance protein is required for helicase activity. J. Biol. Chem. 276, 49371–49377 (2001).

    Article  CAS  Google Scholar 

  27. Schwede, T., Kopp, J., Guex, N. & Peitsch, M.C. SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res. 31, 3381–3385 (2003).

    Article  CAS  Google Scholar 

  28. Kaboord, B.F. & Benkovic, S.J. Dual role of the 44/62 protein as a matchmaker protein and DNA polymerase chaperone during assembly of the bacteriophage T4 holoenzyme complex. Biochemistry 35, 1084–1092 (1996).

    Article  CAS  Google Scholar 

  29. Trakselis, M.A., Berdis, A.J. & Benkovic, S.J. Examination of the role of the clamp-loader and ATP hydrolysis in the formation of the bacteriophage T4 polymerase holoenzyme. J. Mol. Biol. 326, 435–451 (2003).

    Article  CAS  Google Scholar 

  30. Selvin, P.R. Fluorescence resonance energy-transfer. Methods Enzymol. 246, 300–334 (1995).

    Article  CAS  Google Scholar 

  31. Hass, E., Katchalski-Katzir, E. & Steinberg, I.Z. Effect of the orientation of donor and acceptor on the probability of energy transfer involving electronic transitions of mixed polarization. Biochemistry 17, 5064–5070 (1978).

    Article  Google Scholar 

Download references

Acknowledgements

Work in the laboratory of S.D.B. is supported by the Medical Research Council. A.T.M. was additionally funded by Cambridge Clinical School. M.A.T. would also like to thank the Royal Society for generous funding. We thank N. Thorne for help with statistical distribution corrections and Z. Kelman for stimulating discussions.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Stephen D Bell.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Rights and permissions

Reprints and permissions

About this article

Cite this article

McGeoch, A., Trakselis, M., Laskey, R. et al. Organization of the archaeal MCM complex on DNA and implications for the helicase mechanism. Nat Struct Mol Biol 12, 756–762 (2005). https://doi.org/10.1038/nsmb974

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nsmb974

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing