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The structure of bovine F1-ATPase in complex with its regulatory protein IF1

Nature Structural & Molecular Biology volume 10, pages 744–750 (2003)Cite this article

Abstract

In mitochondria, the hydrolytic activity of ATP synthase is prevented by an inhibitor protein, IF1. The active bovine protein (84 amino acids) is an α-helical dimer with monomers associated via an antiparallel α-helical coiled coil composed of residues 49–81. The N-terminal inhibitory sequences in the active dimer bind to two F1-ATPases in the presence of ATP. In the crystal structure of the F1−IF1 complex at 2.8 Å resolution, residues 1–37 of IF1 bind in the αDP-βDP interface of F1-ATPase, and also contact the central γ subunit. The inhibitor opens the catalytic interface between the αDP and βDP subunits relative to previous structures. The presence of ATP in the catalytic site of the βDP subunit implies that the inhibited state represents a pre-hydrolysis step on the catalytic pathway of the enzyme.

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Figure 1: The dimeric bovine F1-ATPase–IF1 complex.
Figure 2: Regions of the electron density map of the F1−IF1 complex.
Figure 3: Stereo view of the contacts between F1-ATPase and IF1.
Figure 4: Conformational changes in the F1−IF1 complex relative to the reference state of F1-ATPase.
Figure 5: The catalytic interface between subunits αDP and βDP in the reference state structure of F1-ATPase and in the F1−IF1 complex.
Figure 6: The inhibition of the ATP hydrolytic activity of ATP synthase by IF1.

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References

  1. Boyer, P.D. The ATP synthase: a splendid molecular machine. Annu. Rev. Biochem. 66, 717–749 (1997).

    Article  CAS  Google Scholar 

  2. Walker, J.E. ATP synthesis by rotary catalysis (Nobel lecture). Angew. Chem. Int. Edn. Engl. 37, 2309–2319 (1998).

    Article  Google Scholar 

  3. Senior, A.E., Nadanaciva, S. & Weber, J. The molecular mechanism of ATP synthesis by F1Fo-ATP synthase. Biochim. Biophys. Acta 1553, 188–211 (2002).

    Article  CAS  Google Scholar 

  4. Collinson, I.R. et al. ATP synthase from bovine heart mitochondria. In vitro assembly of a stalk complex in the presence of F1-ATPase and in its absence. J. Mol. Biol. 242, 408–421 (1994).

    CAS  PubMed  Google Scholar 

  5. Karrasch, S. & Walker, J.E. Novel features in the structure of bovine ATP synthase. J. Mol. Biol. 290, 379–384 (1999).

    Article  CAS  Google Scholar 

  6. Rubinstein, J. & Walker, J.E. ATP synthase from Saccharomyces cerevisiae: location of the OSCP subunit in the peripheral stalk region. J. Mol. Biol. 321, 613–619 (2002).

    Article  CAS  Google Scholar 

  7. Stock, D., Leslie, A.G.W. & Walker, J.E. Molecular architecture of the rotary motor in ATP synthase. Science 286, 1700–1705 (1999).

    Article  CAS  Google Scholar 

  8. Gibbons, C., Montgomery, M.G., Leslie, A.G.W. & Walker, J.E. The structure of the central stalk in bovine F1-ATPase at 2.4 Å resolution. Nat. Struct. Biol. 7, 1055–1061 (2000).

    Article  CAS  Google Scholar 

  9. Abrahams, J.P., Leslie, A.G.W., 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  Google Scholar 

  10. Pullman, M.E. & Monroy, G.C. A soluble heat stable protein in mitochondria from bovine heart that inhibits ATP hydrolase activity. J. Biol. Chem. 238, 3762–3769 (1963).

    CAS  PubMed  Google Scholar 

  11. Green, D.W. & Grover, G.J. The IF1 inhibitor protein of the mitochondrial F1Fo-ATPase. Biochim. Biophys. Acta 1458, 343–355 (2000).

    Article  CAS  Google Scholar 

  12. van Raaij, M.J. et al. The ATPase inhibitor protein from bovine heart mitochondria: the minimal inhibitory sequence. Biochemistry 35, 15618–15625 (1996).

    Article  CAS  Google Scholar 

  13. Gordon-Smith, D.J. et al. Solution structure of a C-terminal coiled-coil domain from bovine IF1: the inhibitor protein of F1-ATPase. J. Mol. Biol. 308, 325–339 (2001).

    Article  CAS  Google Scholar 

  14. Cabezon, E., Runswick, M.J., Leslie, A.G.W. & Walker, J.E. The structure of bovine IF1, the regulatory subunit of mitochondrial F1-ATPase. EMBO J. 20, 6990–6996 (2001).

    Article  CAS  Google Scholar 

  15. Cabezon, E., Arechaga, I., Butler, P.J.G. & Walker, J.E. Dimerization of bovine F1-ATPase by binding the inhibitor protein, IF1 . J. Biol. Chem. 275, 28353–28355 (2000).

    Article  CAS  Google Scholar 

  16. Cabezon, E., Butler, P.J.G., Runswick, M.J. & Walker, J.E. Modulation of the oligomerization state of the bovine F1-ATPase inhibitor protein, IF1, by pH. J. Biol. Chem. 275, 25460–25464 (2000).

    Article  CAS  Google Scholar 

  17. Rouslin, W. Protonic inhibition of the mitochondrial oligomycin-sensitive adenosine 5′-triphosphatase in ischemic and autolyzing cardiac muscle. Possible mechanism for the mitigation of ATP hydrolysis under nonenergizing conditions. J. Biol. Chem. 258, 9657–9661 (1983).

    CAS  PubMed  Google Scholar 

  18. Rouslin, W. Factors affecting the reactivation of the oligomycin-sensitive adenosine 5′-triphosphatase and the release of ATPase inhibitor protein during the re-energization of intact mitochondria from ischemic cardiac muscle. J. Biol. Chem. 262, 3472–3476 (1987).

    CAS  PubMed  Google Scholar 

  19. Rouslin, W. & Broge, C.W. Regulation of mitochondrial matrix pH and adenosine 5′-triphosphatase activity during ischemia in slow heart-rate hearts. Role of Pi/H+ symport. J. Biol. Chem. 264, 15224–15229 (1989).

    CAS  PubMed  Google Scholar 

  20. Mimura, H., Hashimoto, T., Yoshida, Y., Ichikawa, N. & Tagawa, K. Binding of an intrinsic ATPase inhibitor to the interface between α- and β-subunits of F1Fo-ATPase upon de-energization of mitochondria. J. Biochem. (Tokyo) 113, 350–354 (1993).

    Article  CAS  Google Scholar 

  21. Jackson, P.J. & Harris, D.A. The mitochondrial ATP synthase inhibitor protein binds near the C terminus of the F1 β-subunit. FEBS Lett. 229, 224–228 (1988).

    Article  CAS  Google Scholar 

  22. Power, J., Cross, R.L. & Harris, D.A. Interaction of F1-ATPase, from ox heart mitochondria with its naturally occurring inhibitor protein. Studies using radio-iodinated inhibitor protein. Biochim. Biophys. Acta 724, 128–141 (1983).

    Article  CAS  Google Scholar 

  23. Milgrom, Y.M. When beef-heart mitochondrial F1-ATPase is inhibited by inhibitor protein a nucleotide is trapped in one of the catalytic sites. Eur. J. Biochem. 200, 789–795 (1991).

    Article  CAS  Google Scholar 

  24. Penin, F., Di Pietro, A., Godinot, C. & Gautheron, D.C. Fate of nucleotides bound to reconstituted Fo-F1 during adenosine 5′-triphosphate synthesis activation or hydrolysis: role of protein inhibitor and hysteretic inhibition. Biochemistry 27, 8969–8974 (1988).

    Article  CAS  Google Scholar 

  25. Pedersen, P.L., Schwerzmann, K. & Cintron, N.M. Regulation of the synthesis and hydrolysis of ATP in biological systems: role of peptide inhibitors of H+-ATPases. Curr. Top. Bioenerg. 11, 149–199 (1981).

    Article  CAS  Google Scholar 

  26. Boyer, P.D. The binding change mechanism for ATP synthase: some probabilities and possibilities. Biochim. Biophys. Acta 1140, 215–250 (1993).

    Article  CAS  Google Scholar 

  27. Nadanaciva, S., Weber, J., Wilke-Mounts, S. & Senior, A.E. Importance of F1-ATPase residue α-Arg376 for catalytic transition state stabilisation. Biochemistry 38, 15493–15499 (1999).

    Article  CAS  Google Scholar 

  28. Cabezon, E., Butler, P.J., Runswick, M.J., Carbajo, R.J. & Walker, J.E. Homologous and heterologous inhibitory effects of ATPase inhibitor proteins on F1-ATPases. J. Biol. Chem. 277, 41334–41341 (2002).

    Article  CAS  Google Scholar 

  29. Klionsky, D.J., Bruslow, W.S.A. & Simoni, R.D. In vivo evidence for the role of the ε-subunit as an inhibitor of the proton-translocating ATPase of Escherichia coli. J. Bacteriol. 160, 1055–1060 (1985).

    Google Scholar 

  30. Hausrath, A.C., Gruber, G., Matthews, B.W. & Capaldi, R.A. Structural features of the γ-subunit of the Escherichia coli F1-ATPase revealed by a 4.4 Å resolution map obtained by X-ray crystallography. Proc. Natl. Acad. Sci. USA 96, 13697–13702 (1999).

    Article  CAS  Google Scholar 

  31. Rodgers, A.J. & Wilce, M.C. Structure of the γ-ε complex of ATP synthase. Nat. Struct. Biol. 7, 1051–1054 (2000).

    Article  CAS  Google Scholar 

  32. Hausrath, A.C., Capaldi, R.A. & Matthews, B.W. The conformation of the ε- and γ-subunits within the Escherichia coli F1-ATPase. J. Biol. Chem. 276, 47227–47232 (2001).

    Article  CAS  Google Scholar 

  33. Tsunoda, S.P. et al. Large conformational changes of the ε-subunit in the bacterial F1Fo ATP synthase provide a ratchet action to regulate this rotary motor enzyme. Proc. Natl. Acad. Sci. USA 98, 6560–6564 (2001).

    Article  CAS  Google Scholar 

  34. Aggeler, R., Haughton, M.A. & Capaldi, R.A. Disulfide bond formation between the COOH-terminal domain of the β-subunits and the γ- and ε-subunits of the Escherichia coli F1-ATPase. Structural implications and functional consequences. J. Biol. Chem. 270, 9185–9191 (1995).

    Article  CAS  Google Scholar 

  35. Leslie, A.W.G. Joint CCP4 and ESF-EACMB Newsletter on Protein Crystallography Vol. 26 (Daresbury Laboratory, Warrington, UK, 1992).

    Google Scholar 

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

  37. Navaza, J. AmoRe: an automated package for molecular replacement. Acta Crystallogr. A 50, 157–163 (1994).

    Article  Google Scholar 

  38. Braig, K., Menz, R.I., Montgomery, M.G., Leslie, A.G.W. & Walker, J.E. Structure of bovine mitochondrial F1-ATPase inhibited by Mg2+ ADP and aluminum fluoride. Structure 8, 567–573 (2000).

    Article  CAS  Google Scholar 

  39. Brunger, A.T. et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. A 54, 905–921 (1998).

    Article  CAS  Google Scholar 

  40. Laskowski, R.A., MacArthur, M.W., Moss, D.S. & Thornton, J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283–291 (1993).

    Article  CAS  Google Scholar 

  41. 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 

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Acknowledgements

We thank the staff of beamline ID14 at European Synchrotron Radiation Facility (ESRF), Grenoble, for help with data collection. E.C. was supported during part of this work by a European Molecular Biology Organization Fellowship and by a TMR Marie Curie Research Training Grant from the European Community.

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Author notes

  1. Elena Cabezón

    Present address: Departamento De Biologia Molecular, Universidad De Cantabria, Santander, Spain

Authors and Affiliations

  1. The Medical Research Council Dunn Human Nutrition Unit, Hills Road, Cambridge, CB2 2XY, UK

    Elena Cabezón, Martin G Montgomery & John E Walker

  2. The Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, UK

    Andrew G W Leslie

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Correspondence to Andrew G W Leslie or John E Walker.

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Cabezón, E., Montgomery, M., Leslie, A. et al. The structure of bovine F1-ATPase in complex with its regulatory protein IF1. Nat Struct Mol Biol 10, 744–750 (2003). https://doi.org/10.1038/nsb966

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