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The 2.4 Å crystal structure of the bacterial chaperonin GroEL complexed with ATPγS

Nature Structural Biology volume 3, pages 170–177 (1996)Cite this article

Abstract

GroEL is a bacterial chaperonin of 14 identical subunits required to help fold newly synthesized proteins. The crystal structure of GroEL with ATPγS bound to each subunit shows that ATP binds to a novel pocket, whose primary sequence is highly conserved among chaperonins. Interaction of Mg2+ and ATP involves phosphate oxygens of the α-, β- and γ-phosphates, which is unique for known structures of nucleotide-binding proteins. Although bound ATP induces modest conformational shifts in the equatorial domain, the stereochemistry that functionally coordinates GroEL's affinity for nucleotides, polypeptide, and GroES remains uncertain.

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References

  1. Hendrix, R.W. Purification and properties of groE, a host protein involved in bacteriophage assembly. J. Mol. Biol. 129, 375–392 (1979).

    Article  CAS  Google Scholar 

  2. Hemmingsen, S.M., et al. Homologous plant and bacterial proteins chaperone oligomeric protein assembly. Nature 333, 330–334 (1988).

    Article  CAS  Google Scholar 

  3. McMullin, T.W. & Hallberg, R.L. A highly evolutionary conserved mitochondrial protein is structurally related to the protein encoded by the Escherichia coli groEL gene. Mol. Cell. Biol. 8, 371–380 (1988).

    Article  CAS  Google Scholar 

  4. Trent, J.D., Nimmesgern, E., Wall, J.S., Hartl, F.U. & Norwich, A.L. A molecular chaperone from a thermophilic archaebacterium is related to the eukaryotic protein t-complex polypeptide-1. Nature 354, 490–493 (1991).

    Article  CAS  Google Scholar 

  5. Gao, Y., Thomas, J.O., Chow, R.L., Lee, G.H. & Cowan, N.J. A cytoplasmic chaperonin that catalyzes beta-actin folding. Cell 69, 1043–1050 (1992).

    Article  CAS  Google Scholar 

  6. Hendrick, J.P. & Hartl, F.U. Molecular chaperone functions of heat-shock proteins. Ann. Rev. Biochem. 62, 349–84 (1993).

    Article  CAS  Google Scholar 

  7. Horwich, A.L. & Willison, K.R. Protein folding in the cell: functions of two families of molecular chaperone, hsp 60 and TF55-TCP1. Phil. Trans. Royal Soc. Lond. B339, 313–25 (1993).

    Google Scholar 

  8. Lund, P. The chaperonin cycle and protein folding. Bioessays 16, 229–31 (1994).

    Article  CAS  Google Scholar 

  9. Braig, K. et al. The crystal structure of the bacterial chaperonin GroEL at 2.8 Å. Nature 371, 578–86 (1994).

    Article  CAS  Google Scholar 

  10. Ellis, R.J. & van der Vies, S.M. Molecular chaperones. Ann. Rev. Biochem. 60, 321–47 (1991).

    Article  CAS  Google Scholar 

  11. Gething, M.J. & Sambrook, J. Protein folding in the cell. Nature 355, 33–45 (1992).

    Article  CAS  Google Scholar 

  12. Hartl, F.U. & Martin, J. Molecular chaperones in cellular protein folding. Curr. Opin. Struct. Biol. 5, 92–102 (1995).

    Article  CAS  Google Scholar 

  13. Landry, S.J. & Gierasch, L.M. The chaperonin GroEL binds a polypeptide in an alpha-helical conformation. Biochemistry 30, 7359–62 (1991).

    Article  CAS  Google Scholar 

  14. Richarme, G. & Kohiyama, M. Amino acid specificity of the Escherichia coli chaperone GroEL (heat shock protein 60). J. Biol. Chem. 269, 7095–7098 (1994).

    CAS  PubMed  Google Scholar 

  15. Hayer, H.M., Ewbank, J.J., Creighton, T.E. & Hartl, F.U. Conformational specificity of the chaperonin GroEL for the compact folding intermediates of alpha-lactalbumin. EMBO J. 13, 3192–202 (1994).

    Article  Google Scholar 

  16. Zahn, R. et al. Thermodynamic partitioning model for hydrophobic binding of polypeptides by GroEL. I. GroEL recognizes the signal sequences of beta-lactamase precursor. J. Mol. Biol. 242, 150–164 (1994).

    Article  CAS  Google Scholar 

  17. Lin, Z., Schwartz, F.P. & Eisenstein, E. The hydrophobic nature of GroEL-substrate binding. J. Biol. Chem. 270, 1011–1014 (1995).

    Article  CAS  Google Scholar 

  18. Langer, T., Pfeifer, G., Martin, J., Baumeister, W. & Hartl, F.U. Chaperonin-mediated protein folding: GroES binds to one end of the GroEL cylinder, which accommodates the protein substrate within its central cavity. EMBO J. 11, 4757–4765 (1992).

    Article  CAS  Google Scholar 

  19. Saibil, H.R., et al. ATP induces large quarternary rearrangements in a cage-like chaperonin structure. Curr. Biol. 3, 265–273 (1993).

    Article  CAS  Google Scholar 

  20. Braig, K., Simon, M., Furuya, F., Hainfeld, J.F. & Horwich, A.L. A polypeptide bound by the chaperonin groEL is localized within a central cavity. Proc. Natl. Acad. Sci. USA 90, 3978–3982 (1993).

    Article  CAS  Google Scholar 

  21. Ishii, N., Taguchi, H., Sasabe, H. & Yoshida, M. Folding intermediate binds to the bottom of bullet-shaped holo-chaperonin and is readily accessible to antibody. J. Mol. Biol. 236, 691–696 (1994).

    Article  CAS  Google Scholar 

  22. Fenton, W.A., Kashi, Y., Furtak, K. & Horwich, A.L. Residues in chaperonin GroEL required for polypeptide binding and release. Nature 371, 614–619 (1994).

    Article  CAS  Google Scholar 

  23. Chen, S. et al. Location of a folding protein and shape changes in GroEL-GroES complexes imaged by cryo-electron microscopy. Nature 371, 261–264 (1994).

    Article  CAS  Google Scholar 

  24. Martin, J., Mayhew, M., Langer, T. & Hartl, F.U. The reaction cycle of GroEL and GroES in chaperonin-assisted protein folding. Nature 366, 228–233 (1993).

    Article  CAS  Google Scholar 

  25. Weissman, J.S., Kashi, Y., Fenton, W.A. & Horwich, A.L. GroEL-mediated protein folding proceeds by multiple rounds of binding and release of nonnative forms. Cell 78, 693–702 (1994).

    Article  CAS  Google Scholar 

  26. Hansen, J.E. & Gafni, A. Fluorescence detection of conformational changes in GroEL induced by thermal switching and nucleotide binding. J. Biol. Chem. 269, 6286–6289 (1994).

    CAS  PubMed  Google Scholar 

  27. Read, R. Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Crystallogr. A42, 140–149 (1986).

    Article  CAS  Google Scholar 

  28. Brünger, A.T. XPLOR Version 3.1 Manual (1993).

  29. Kim, S., Willison, K. & Horwich, A.L. Cytosolic chaperonin subunits have a conserved ATPase domain but diverged polypeptide-binding domains. Trends Biochem. Sci. 19, 543–548 (1994).

    Article  CAS  Google Scholar 

  30. Walker, J.E., Saraste, M., Runswick, M.J. & Gay, N.J. Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J. 1, 945–51 (1982).

    Article  CAS  Google Scholar 

  31. Steitz, T.A. & Story, R.M. A general structural mechanism of coupling NTP to other processes. Robert A. Welch Foundn. Conf. Chem. Res XXXVI, 173–186 (1992).

    Google Scholar 

  32. Diamant, S., Azem, A., Weiss, C. & Goloubinoff, P. Increased efficiency of GroE-assisted protein folding by manganese ions. J. Biol. Chem. 270, 28387–28391 (1995).

    Article  CAS  Google Scholar 

  33. Guerger, M.J., MacGillavry, C.H., Henry, N.F.M., Lonsdale, K. & Rieck, G.D. International Tables for X-ray Crystallography 257–269 (The Kynoch Press, Birmingham, England, 1968).

    Google Scholar 

  34. Todd, M.J., Viitanen, P.V. & Lorimer, G.H. Hydrolysis of adenosine 5′-triphosphate by Escherichia coli GroEL: effects of GroES and potassium ion. Biochemistry 32, 8560–8567 (1993).

    Article  CAS  Google Scholar 

  35. Viitanen, P.V. et al. Chaperonin-facilitated refolding of ribulose-bisphosphate carboxylase and ATP hydrolysis by chaperonin 60 (groEL) are K+ dependent. Biochemistry 29, 5665–5671 (1990).

    Article  CAS  Google Scholar 

  36. Mendoza, J.A., Rogers, E., Lorimer, G.H. & Horowitz, P.M. Chaperonins facilitate the in vitro folding of monomeric mitochondrial rhodanese. J. Biol. Chem. 266, 13044–13049 (1991).

    CAS  Google Scholar 

  37. Weiss, C. & Goloubinoff, P. A mutant at position 87 of the groel chaperonin is affected in protein binding and atp hydrolysis. J. Biol. Chem. 270, 13956–13960 (1995).

    Article  CAS  Google Scholar 

  38. Yifrach, O. & Horovitz, A. Two lines of allosteric communication in the oligomeric chaperonin GroEL are revealed by the single mutation Arg 196→Ala. J. Mol. Biol. 243, 397–401 (1994).

    Article  CAS  Google Scholar 

  39. Horovitz, A., Bochkareva, E.S., Kovalenko, O. & Girshovich, A.S. Mutation Ala 2→Ser destabilizes intersubunit interactions in the molecular chaperone GroEL. J. Mol. Biol. 231, 58–64 (1993).

    Article  CAS  Google Scholar 

  40. Luo, G.X. & Horowitz, P.M. The stability of the molecular chaperonin cpn60 is affected by site-directed replacement of cysteine 518. J. Biol. Chem. 269, 32151–32154 (1994).

    CAS  PubMed  Google Scholar 

  41. Otwinowski, Z. & Minor, W. The HKL Program Suite. Meth. Enz. In the press

  42. Jones, T.A. CCP4 Study Weekend, Molecular Replacement 91–105 (eds Dodson, E.J., Glover, S. & Wolf, W.) 91–105 (SERC Daresbury Laboratory, UK, 1992).

    Google Scholar 

  43. Jones, T.A., Zou, J.Y., Cowan, S.W. & Kjeldgaard . Improved methods for binding protein models in electron density maps and the location of errors in these models. Acta crystallogr. A47, 110–119 (1991).

    Article  CAS  Google Scholar 

  44. Luthy, R., Bowie, J.U. & Eisenberg, D. Assessment of protein models with three-dimensional profiles. Nature 356, 83–5 (1992).

    Article  CAS  Google Scholar 

  45. Braig, K., Adams, P.D. & Brünger, A.T. Conformational variability in the refined structure of the chaperonin GroEL at 2. 8 Å resolution. Nature Struct. Biol. 2, 1083–1094 (1995).

    Article  CAS  Google Scholar 

  46. 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. Cryst. 26, 283–291 (1993).

    Article  CAS  Google Scholar 

  47. Carson, M. Ribbons 2.0. J.Appl.Crystallogr. 24, 958–961 (1991).

    Article  Google Scholar 

  48. Martin, J., Geromanos, S., Tempst, P. & Hartl, F.U. Identification of nucleotide-binding regions in the chaperonin proteins GroEL and GroES. Nature 366, 279–82 (1993).

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Department of Genetics, Yale University School of Medicine, Boyer Center, 295 Congress Avenue, New Haven, Connecticut, 06510, USA

    David C. Boisvert & Arthur L. Norwich

  2. Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, Boyer Center, 295 Congress Avenue, New Haven, Connecticut, 06510, USA

    Jimin Wang, Zbyszek Otwinowski & Paul B. Sigler

  3. The Howard Hughes Medical Institute, Yale University School of Medicine, Boyer Center, 295 Congress Avenue, New Haven, Connecticut, 06510, USA

    Arthur L. Norwich & Paul B. Sigler

  4. Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas, 75235, USA

    Zbyszek Otwinowski

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Boisvert, D., Wang, J., Otwinowski, Z. et al. The 2.4 Å crystal structure of the bacterial chaperonin GroEL complexed with ATPγS. Nat Struct Mol Biol 3, 170–177 (1996). https://doi.org/10.1038/nsb0296-170

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