Nature Structural Biology
3, 170 - 177 (1996)
doi:10.1038/nsb0296-170
The 2.4 Å crystal structure of the bacterial chaperonin GroEL complexed with ATP SDavid C. Boisvert1, Jimin Wang2, Zbyszek Otwinowski2, 4, Arthur L. Norwich1, 3
& Paul B. Sigler2, 3
1Department of Genetics, Yale University School of Medicine, Boyer Center, 295 Congress Avenue, New Haven, Connecticut 06510, USA
2Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, Boyer Center, 295 Congress Avenue, New Haven, Connecticut 06510, USA
3The Howard Hughes Medical Institute, Yale University School of Medicine, Boyer Center, 295 Congress Avenue, New Haven, Connecticut 06510, USA
4Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75235, USA GroEL is a bacterial chaperonin of 14 identical subunits required to help fold newly synthesized proteins. The crystal structure of GroEL with ATP S 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 -, - and -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. REFERENCES
- Hendrix, R.W. Purification and properties of groE, a host protein involved in bacteriophage assembly. J. Mol. Biol. 129, 375−392 (1979). | PubMed | ISI | ChemPort |
- Hemmingsen, S.M., et al. Homologous plant and bacterial proteins chaperone oligomeric protein assembly. Nature 333, 330−334 (1988). | Article | PubMed | ISI | ChemPort |
- 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). | PubMed | ISI | ChemPort |
- 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 | PubMed | ISI | ChemPort |
- 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). | PubMed | ISI | ChemPort |
- Hendrick, J.P. & Hartl, F.U. Molecular chaperone functions of heat-shock proteins. Ann. Rev. Biochem. 62, 349−84 (1993). | Article | PubMed | ISI | ChemPort |
- 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).
- Lund, P. The chaperonin cycle and protein folding. Bioessays 16, 229−31 (1994). | PubMed | ISI | ChemPort |
- Braig, K. et al. The crystal structure of the bacterial chaperonin GroEL at 2.8 Å. Nature 371, 578−86 (1994). | Article | PubMed | ISI | ChemPort |
- Ellis, R.J. & van der Vies, S.M. Molecular chaperones. Ann. Rev. Biochem. 60, 321−47 (1991). | Article | PubMed | ISI | ChemPort |
- Gething, M.J. & Sambrook, J. Protein folding in the cell. Nature 355, 33−45 (1992). | Article | PubMed | ISI | ChemPort |
- Hartl, F.U. & Martin, J. Molecular chaperones in cellular protein folding. Curr. Opin. Struct. Biol. 5, 92−102 (1995). | Article | PubMed | ISI | ChemPort |
- Landry, S.J. & Gierasch, L.M. The chaperonin GroEL binds a polypeptide in an alpha-helical conformation. Biochemistry 30, 7359−62 (1991). | PubMed | ISI | ChemPort |
- Richarme, G. & Kohiyama, M. Amino acid specificity of the Escherichia coli chaperone GroEL (heat shock protein 60). J. Biol. Chem. 269, 7095−7098 (1994). | PubMed | ISI | ChemPort |
- 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). | PubMed | ChemPort |
- 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 | PubMed | ISI | ChemPort |
- Lin, Z., Schwartz, F.P. & Eisenstein, E. The hydrophobic nature of GroEL-substrate binding. J. Biol. Chem. 270, 1011−1014 (1995). | Article | PubMed | ISI | ChemPort |
- 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). | PubMed | ISI | ChemPort |
- Saibil, H.R., et al. ATP induces large quarternary rearrangements in a cage-like chaperonin structure. Curr. Biol. 3, 265−273 (1993). | ISI | ChemPort |
- 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). | PubMed | ChemPort |
- 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 | PubMed | ISI | ChemPort |
- 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 | PubMed | ISI | ChemPort |
- 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 | PubMed | ISI | ChemPort |
- 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 | PubMed | ISI | ChemPort |
- 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). | PubMed | ISI | ChemPort |
- 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). | PubMed | ISI | ChemPort |
- Read, R. Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Crystallogr. A42, 140−149 (1986). | ChemPort |
- Brünger, A.T. XPLOR Version 3.1 Manual (1993).
- 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 | PubMed | ISI | ChemPort |
- 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). | PubMed | ISI | ChemPort |
- 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).
- 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 | PubMed | ISI | ChemPort |
- 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).
- 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). | PubMed | ISI | ChemPort |
- 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). | PubMed | ISI | ChemPort |
- 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). | PubMed | ISI | ChemPort |
- 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 | PubMed | ISI | ChemPort |
- 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 | PubMed | ISI | ChemPort |
- 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 | PubMed | ISI | ChemPort |
- 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). | PubMed | ISI | ChemPort |
- Otwinowski, Z. & Minor, W. The HKL Program Suite. Meth. Enz. In the press
- 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).
- 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). | ChemPort |
- Luthy, R., Bowie, J.U. & Eisenberg, D. Assessment of protein models with three-dimensional profiles. Nature 356, 83−5 (1992). | Article | PubMed | ISI | ChemPort |
- 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). | PubMed | ISI | ChemPort |
- 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 | ISI | ChemPort |
- Carson, M. Ribbons 2.0. J.Appl.Crystallogr. 24, 958−961 (1991). | Article |
- 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 | PubMed | ISI | ChemPort |
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