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Parallel evolution in two homologues of phosphorylase

Nature Structural Biology volume 1, pages 681–690 (1994)Cite this article

Abstract

The structure of the unphosphorylated, inactive form of yeast glycogen phosphorylase has been determined to a resolution of 2.6 Å. The structure is similar to the phosphorylated, active form of muscle phosphorylase in the orientations of the subunits and catalytic residues, but resembles the inactive muscle enzyme in the closed, or substrate excluding, orientation of the two domains. Part of the unique yeast amino-terminal extension of 40 residues binds near the catalytic site of the second subunit in the homodimer, preventing the domain movement required for substrate access. Phosphorylation may displace the amino terminus from the active site, allowing the domains to separate.

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References

  1. Hwang, P.K. & Fletterick, R.J. Convergent and divergent evolution of regulatory sites in eukaryotic phosphorylases. Nature 324, 80–84 (1986).

    Article  CAS  Google Scholar 

  2. Hudson, J.W., Golding, G.B. & Crerar, M.M. Evolution of Allosteric Control in Glycogen Phosophorylase. J. molec. Biol. 234, 700–721 (1993).

    Article  CAS  Google Scholar 

  3. Rath, V.L. Allosteric Mechanisms in Phosphorylases. (University of California, San Francisco, 1991).

    Google Scholar 

  4. Becker, J.-O., Wingender-Drissen, R. & Schiltz, E. Purification and Properties of Phosphorylase from Baker's Yeast. Arch. Biochem. Biophys. 225, 667–678 (1983).

    Article  CAS  Google Scholar 

  5. Sprang, S.R. et al. Structural changes in glycogen phosphorylase induced by phsophorylation. Nature 336, 215–221 (1988).

    Article  CAS  Google Scholar 

  6. Martin, J.L., Johnson, L.N. & Withers, S.G. Comparison of the binding of glucose and glucose 1-phosphate derivatives to T-state glycogen phosphorylase b. Biochemistry. 29, 10745–10757 (1990).

    Article  CAS  Google Scholar 

  7. Johnson, L.N., Barford, D., Acharya, R., Oikonomakos, N.G. & Martin, J.L. Allosteric Regulation of Glycogen Phosphoryase. (Robert A Welch Foundation, Houston, Texas, 1992).

    Google Scholar 

  8. Sprang, S., Goldsmith, E. & Fletterick, R. Structure of the Nucleotide Activation Switch in Glycogen Phosphorylase a. Science 237, 1012–1019 (1987).

    Article  CAS  Google Scholar 

  9. Johnson, L.N. et al. in Allosteric Enzymes (eds Hervé, G.L.) 81–128 (CRC Reviews, 1989).

    Google Scholar 

  10. Johnson, L.N., Acharya, K.R., Jordan, M.D. & McLaughlin, P.J. Refined Structure of the Phosphorylase-Heptulose 2-Phosphate-Oligosaccharide-AMP Complex. J. Molec. Biol. 645–661 (1990).

  11. Ziegler, K.J. & Schwartz, A.C. Participation of proteinase yscA in the in vitro formation of the smaller subunit of glycogen phosphorylase in extracts of Saccharomyces cerevisiae. Yeast 7, 925–931 (1991).

    Article  CAS  Google Scholar 

  12. Leonidas, D.D. et al. The ammonium sulfate activation of phosphorylase b. FEBS Letts. 261, 23–27 (1990).

    Article  CAS  Google Scholar 

  13. Hurley, J.H., Dean, A.M., Koshland, D.E., Jr & Stroud, R.M. Regulation of Isocitrate Dehydrogenase Involves No Long-Range Conformational Change in the Free Enzyme. J. biol. Chem. 265, 3599–3602 (1990).

    CAS  PubMed  Google Scholar 

  14. Rath, V.L., Hwang, P.K. & Fletterick, R.J. Purification and Crystallization of glycogen phosphorylase from Saccharomyces cerevisiae. J. molec. Biol. 225, 1027–1034 (1992).

    Article  CAS  Google Scholar 

  15. Xuong, N.-H., Nielsen, C., Hamlin, R. & Anderson, D. Strategy for Data Collection from Protein Crystals Using a Multiwire Counter Area Dectector Diffractometer. J. appl. Crystallogr. 18, 342–350 (1985).

    Article  Google Scholar 

  16. Howard, A.J., Nielsen, C. & Xuong, N.-H. in Methods in Enzymology (eds. Wyckoff, H.W., Hirs, C.H. & Timasheff, S.N.) 452–472 (Academic Press, Orlando, Florida, 1985).

    Google Scholar 

  17. CCP4. The SERC (UK) Collaborative Computing Project No. 4, A Suite of Programs for Protein Crystallography. (Daresbury Laboratory, Warrington, UK, 1979).

  18. Rossmann, M.G. The Molecular Replacement Method (Gordon and Breach, New York, 1972).

    Google Scholar 

  19. Brunger, A.T. Extension of Molecular Replacement: a New Search Strategy Based on Patterson Correlation Refinement. Acta crystallogr. A46, 46–57 (1990).

    Article  CAS  Google Scholar 

  20. Brunger, A.T. X-PLOR Manual, Version 3.1 (Yale University Press, New Haven and London, 1992).

    Google Scholar 

  21. Brunger, A.T., Kuriyan, J. & Karplus, M. Crystallographic R Factor Refinement by Molecular Dynamics. Science 235, 458–460 (1987).

    Article  CAS  Google Scholar 

  22. Jones, T.A. A Graphics Model Building and Refinement System for Macromolecules. J. Appl. crystallogr. 11, 268–272 (1978).

    Article  CAS  Google Scholar 

  23. Acharya, K.R., Stuart, D.I., Varvill, K.M. & Johnson, L.N. Glycogen Phosphorylase b: Description of the Protein Structure. (World Scientific Publishing Co., Inc., Teaneck, New Jersey, 1990).

    Google Scholar 

  24. Sprang, S.R., Withers, S.G., Goldsmith, E.J., Fletterick, R.J. & Madsen, N.B. Structural basis for the activation of glycogen phosphorylase b by adenosine monophosphate. Science 254, 1367–1371 (1991).

    Article  CAS  Google Scholar 

  25. Barford, D., Hu, S. & Johnson, L.N. Structural Mechanism for Glycogen Phosphorylase Control by Phosphorylation and AMP. J. molec. Biol. 218, 233–260 (1991).

    Article  CAS  Google Scholar 

  26. Goldsmith, E.J., Sprang, S.R., Hamlin, R., Xuong, N.-H. & Fletterick, R.J. Domain Separation in the Activation of Glycogen Phosophorylase a. Science 245, 528–532 (1989).

    Article  CAS  Google Scholar 

  27. Barford, D. & Johnson, L.N. The allosteric transition of glycogen phosphorylase. Nature 340, 609–616 (1989).

    Article  CAS  Google Scholar 

  28. Fauman, E.B. (University of California, San Francisco, 1993).

  29. Browner, M.B., Fauman, E.B. & Fletterick, R.J. Tracking Conformational States in Allosteric Transitions of Phosphorylase. Biochemistry. 31, 11297–11304 (1992).

    Article  CAS  Google Scholar 

  30. Lee, B. & Richards, F.M. The Interpretation of Protein Structures: Estimation of Static Inaccessibility. J. molec. Biol. 55, 379–400 (1971).

    Article  CAS  Google Scholar 

  31. Chothia, C., Levitt, M. & Richardson, D. Helix to Helix Packing in Proteins. J. molec. Biol 145, 215–220 (1981).

    Article  CAS  Google Scholar 

  32. Richards, F.M. & Kundrot, C.E. Identification of Structural Motifs from Protein Coordinate Data: Secondary Structure and First-Level Supersecondary Structure. Proteins: Struct. Funct. Genet. 3, 71–84 (1988).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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Author notes

  1. Virginia L. Rath

    Present address: Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, P. O. Box 208114, New Haven, Connecticut, 06520-8114, USA

Authors and Affiliations

  1. Department of Biochemistry and Biophysics, University of California, San Francisco, California, 94143-0448, USA

    Robert J. Fletterick

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  1. Virginia L. Rath
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  2. Robert J. Fletterick
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Rath, V., Fletterick, R. Parallel evolution in two homologues of phosphorylase. Nat Struct Mol Biol 1, 681–690 (1994). https://doi.org/10.1038/nsb1094-681

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  • DOI: https://doi.org/10.1038/nsb1094-681

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