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.

  • Analysis
  • Published:

The 'glutamate switch' provides a link between ATPase activity and ligand binding in AAA+ proteins

Nature Structural & Molecular Biology volume 15, pages 1223–1227 (2008)Cite this article

Abstract

AAA+ proteins carry out diverse functions in cells. In most cases, their ATPase activity is tightly regulated by protein partners and target ligands, but the mechanism for this control has remained unclear. We have identified a conserved link between the ligand binding and ATPase sites in AAA+ proteins. This link, which we call the 'glutamate switch', regulates ATPase activity directly in response to the binding of target ligands by controlling the orientation of the conserved glutamate residue in the DExx motif, switching it between active and inactive conformations. The reasons for this level of control of the ATPase activity are discussed in the context of the biological processes catalyzed by AAA+ proteins.

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

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

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

Figure 1: Essential residues in the active site of ATPases.
Figure 2: ATPase active sites showing the conformations of the glutamate residue.
Figure 3: Conservation of the glutamate switch in AAA+ proteins.
Figure 4: Link between the glutamate switch motif and the ligand binding site.
Figure 5: Overall mechanism of two well-characterized AAA+ protein–catalyzed reactions.

Similar content being viewed by others

Accession codes

Accessions

Protein Data Bank

References

  1. Kunau, W.H. et al. Two complementary approaches to study peroxisome biogenesis in Saccharomyces cerevisiae: forward and reversed genetics. Biochimie 75, 209–224 (1993).

    Article  CAS  PubMed  Google Scholar 

  2. 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 

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

    Article  CAS  PubMed  Google Scholar 

  4. Erzberger, J.P. & Berger, J.M. Evolutionary relationships and structural mechanisms of AAA+ proteins. Annu. Rev. Biophys. Biomol. Struct. 35, 93–114 (2006).

    Article  CAS  PubMed  Google Scholar 

  5. Browning, D.F. & Busby, S.J. The regulation of bacterial transcription initiation. Nat. Rev. Microbiol. 2, 57–65 (2004).

    Article  CAS  PubMed  Google Scholar 

  6. Ahnert, P., Picha, K.M. & Patel, S.S. A ring-opening mechanism for DNA binding in the central channel of the T7 helicase-primase protein. EMBO J. 19, 3418–3427 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Yoder, B.L. & Burgers, P.M. Saccharomyces cerevisiae replication factor C. I. Purification and characterization of its ATPase activity. J. Biol. Chem. 266, 22689–22697 (1991).

    CAS  PubMed  Google Scholar 

  8. Seybert, A. & Wigley, D.B. Distinct roles for ATP binding and hydrolysis at individual subunits of an archaeal clamp loader. EMBO J. 23, 1360–1371 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. 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).

    Article  CAS  PubMed  Google Scholar 

  10. Walker, J.E., Saraste, M., Runswick, M.J. & Gay, N.J. Distantly related sequences in the α- and β-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J. 1, 945–951 (1982).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Mogk, A. et al. Roles of individual domains and conserved motifs of the AAA+ chaperone ClpB in oligomerization, ATP hydrolysis, and chaperone activity. J. Biol. Chem. 278, 17615–17624 (2003).

    Article  CAS  PubMed  Google Scholar 

  12. Joly, N., Rappas, M., Wigneshweraraj, S.R., Zhang, X. & Buck, M. Coupling nucleotide hydrolysis to transcription activation performance in a bacterial enhancer binding protein. Mol. Microbiol. 66, 583–595 (2007).

    Article  CAS  PubMed  Google Scholar 

  13. Rappas, M., Schumacher, J., Niwa, H., Buck, M. & Zhang, X. Structural basis of the nucleotide driven conformational changes in the AAA+ domain of transcription activator PspF. J. Mol. Biol. 357, 481–492 (2006).

    Article  CAS  PubMed  Google Scholar 

  14. Abrahams, J.P., Leslie, A.G., Lutter, R. & Walker, J.E. Structure at 2.8 Å resolution of F1-ATPase from bovine heart mitochondria. Nature 370, 621–628 (1994).

    Article  CAS  PubMed  Google Scholar 

  15. Sallai, L. & Tucker, P.A. Crystal structure of the central and C-terminal domain of the σ54-activator ZraR. J. Struct. Biol. 151, 160–170 (2005).

    Article  CAS  PubMed  Google Scholar 

  16. Lee, S.Y. et al. Regulation of the transcriptional activator NtrC1: structural studies of the regulatory and AAA+ ATPase domains. Genes Dev. 17, 2552–2563 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Rappas, M. et al. Structural insights into the activity of enhancer-binding proteins. Science 307, 1972–1975 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Chaney, M. et al. Binding of transcriptional activators to sigma 54 in the presence of the transition state analog ADP-aluminum fluoride: insights into activator mechanochemical action. Genes Dev. 15, 2282–2294 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Bowman, G.D., O'Donnell, M. & Kuriyan, J. Structural analysis of a eukaryotic sliding DNA clamp-clamp loader complex. Nature 429, 724–730 (2004).

    Article  CAS  PubMed  Google Scholar 

  20. Seybert, A., Singleton, M.R., Cook, N., Hall, D.R. & Wigley, D.B. Communication between subunits within an archaeal clamp-loader complex. EMBO J. 25, 2209–2218 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Gaudier, M., Schuwirth, B.S., Westcott, S.L. & Wigley, D.B. Structural basis of DNA replication origin recognition by an ORC protein. Science 317, 1213–1216 (2007).

    Article  CAS  PubMed  Google Scholar 

  22. Dueber, E.L., Corn, J.E., Bell, S.D. & Berger, J.M. Replication origin recognition and deformation by a heterodimeric archaeal Orc1 complex. Science 317, 1210–1213 (2007).

    Article  CAS  PubMed  Google Scholar 

  23. Zhang, X. et al. Structure of the AAA ATPase p97. Mol. Cell 6, 1473–1484 (2000).

    Article  CAS  PubMed  Google Scholar 

  24. Matias, P.M., Gorynia, S., Donner, P. & Carrondo, M.A. Crystal structure of the human AAA+ protein RuvBL1. J. Biol. Chem. 281, 38918–38929 (2006).

    Article  CAS  PubMed  Google Scholar 

  25. Bochtler, M. et al. The structures of HsIU and the ATP-dependent protease HsIU-HsIV. Nature 403, 800–805 (2000).

    Article  CAS  PubMed  Google Scholar 

  26. Trame, C.B. & McKay, D.B. Structure of Haemophilus influenzae HslU protein in crystals with one-dimensional disorder twinning. Acta Crystallogr. D Biol. Crystallogr. 57, 1079–1090 (2001).

    Article  CAS  PubMed  Google Scholar 

  27. Davies, J.M., Brunger, A.T. & Weis, W.I. Improved structures of full-length p97, an AAA ATPase: implications for mechanisms of nucleotide-dependent conformational change. Structure 16, 715–726 (2008).

    Article  CAS  PubMed  Google Scholar 

  28. Schlee, S., Groemping, Y., Herde, P., Seidel, R. & Reinstein, J. The chaperone function of ClpB from Thermus thermophilus depends on allosteric interactions of its two ATP-binding sites. J. Mol. Biol. 306, 889–899 (2001).

    Article  CAS  PubMed  Google Scholar 

  29. Hattendorf, D.A. & Lindquist, S.L. Cooperative kinetics of both Hsp104 ATPase domains and interdomain communication revealed by AAA sensor-1 mutants. EMBO J. 21, 12–21 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Singleton, M.R. et al. Conformational changes induced by nucleotide binding in Cdc6/ORC from Aeropyrum pernix. J. Mol. Biol. 343, 547–557 (2004).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Yoo, S.J. et al. Purification and characterization of the heat shock proteins HslV and HslU that form a new ATP-dependent protease in Escherichia coli. J. Biol. Chem. 271, 14035–14040 (1996).

    Article  CAS  PubMed  Google Scholar 

  33. Dean, F.B. et al. Simian virus 40 (SV40) DNA replication: SV40 large T antigen unwinds DNA containing the SV40 origin of replication. Proc. Natl. Acad. Sci. USA 84, 16–20 (1987).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. 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 

  35. White, P.W. et al. Characterization of recombinant HPV6 and 11 E1 helicases: effect of ATP on the interaction of E1 with E2 and mapping of a minimal helicase domain. J. Biol. Chem. 276, 22426–22438 (2001).

    Article  CAS  PubMed  Google Scholar 

  36. Joly, N., Burrows, P.C. & Buck, M. An intramolecular route for coupling ATPase activity in AAA+ proteins for transcription activation. J. Biol. Chem. 283, 13725–13735 (2008).

    Article  CAS  PubMed  Google Scholar 

  37. Schepers, A. & Diffley, J.F. Mutational analysis of conserved sequence motifs in the budding yeast Cdc6 protein. J. Mol. Biol. 308, 597–608 (2001).

    Article  CAS  PubMed  Google Scholar 

  38. Sollner, T., Bennett, M.K., Whiteheart, S.W., Scheller, R.H. & Rothman, J.E. A protein assembly-disassembly pathway in vitro that may correspond to sequential steps of synaptic vesicle docking, activation, and fusion. Cell 75, 409–418 (1993).

    Article  CAS  PubMed  Google Scholar 

  39. Rappas, M., Bose, D. & Zhang, X. Bacterial enhancer-binding proteins: unlocking σ54-dependent gene transcription. Curr. Opin. Struct. Biol. 17, 110–116 (2007).

    Article  CAS  PubMed  Google Scholar 

  40. Collaborative Computational Project, Number 4. The, CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50, 760–763 (1994).

Download references

Acknowledgements

This work was funded by the Wellcome Trust and Biotechnology and Biological Sciences Research (X.Z.) and Cancer Research UK (D.B.W.).

Author information

Authors and Affiliations

  1. Division of Molecular Biosciences, Department of Life Sciences, Centre for Structural Biology, Faculty of Natural Sciences, Imperial College London, London, SW7 2AZ, UK

    Xiaodong Zhang

  2. Cancer Research UK Clare Hall Laboratories, The London Research Institute, Blanche Lane, South Mimms, Potters Bar, Hertfordshire, EN6 3LD, UK

    Dale B Wigley

Authors
  1. Xiaodong Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Dale B Wigley
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Xiaodong Zhang or Dale B Wigley.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Zhang, X., Wigley, D. The 'glutamate switch' provides a link between ATPase activity and ligand binding in AAA+ proteins. Nat Struct Mol Biol 15, 1223–1227 (2008). https://doi.org/10.1038/nsmb.1501

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nsmb.1501

This article is cited by

Search

Advanced 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