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Oligosaccharide substrate binding in Escherichia coli maltodextrin phosphorylase

Nature Structural Biology volume 4, pages 405–412 (1997)Cite this article

Abstract

The crystal structure of E. coli maltodextrin phosphorylase co-crystallized with an oligosaccharide has been solved at 3.0 Å resolution, providing the first structure of an oligosaccharide bound at the catalytic site of an α-glucan phosphorylase. An induced fit mechanism brings together two domains across the catalytic site tunnel. A stacking interaction between the glucosyl residue and the aromatic group of a tyrosine residue at a sub-site remote (8 Å) from the catalytic site provides a key element in substrate recognition; mutation of this residue to Ala decreases the kcat/Km by 104. Extrapolation of the results to substrate binding across the site of attack by phosphorolysis indicates a likely alteration in the glycosidic torsion angles from their preferred values, an alteration that appears to be important for the catalytic mechanism.

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References

  1. Quiocho, F.A. Carbohydrate binding proteins: tertiary structures and protein sugar interactions. Ann. Rev. Biochem. 55, 287–315 (1986).

    Article  CAS  Google Scholar 

  2. Johnson, L.N. et al. Protein-oligosaccharide interactions: lysozyme, phosphorylase, amylases. Curr. Topics Microbiol. Immunol. 139, 81–134 (1988).

    CAS  Google Scholar 

  3. Vyas, N.K. Atomic features of protein-carbohydrate interactions. Curr. Opin. Struct. Biol. 1, 732–740 (1991).

    Article  CAS  Google Scholar 

  4. Weiss, W.I. & Drickamer, K. Structural basis of lectin-carbohydrate recognition. Ann. Rev. Biochem. 65, 441–473 (1996).

    Article  Google Scholar 

  5. Qian, M., Haser, R., Buisson, G., Duee, E. & Payan, F. The active centre of a mammalian α-amylase. Structure of the complex of a pancreatic α-amylase with a carbohydrate inhibitor refined to 2.2Å resolution. Biochemistry 33, 6284–6294 (1994).

    Article  CAS  Google Scholar 

  6. Alzari, P.M., Souchon, H. & Dominguez, R. The crystal structure of endoglucanase CelA, a family 8 glycosl hydrolase from Clostridium thermocellum. Structure 4, 265–275 (1996).

    Article  CAS  Google Scholar 

  7. Dutzler, R., Wang, Y.-F., Rizkallah, P.J., Rosenbusch, J.P. & Schirmer, T. Crystal structure of various maltooligosaccharides bound to maltoporin reveal a specific sugar translocation pathway. Structure 4, 127–134 (1996).

    Article  CAS  Google Scholar 

  8. Nishio, M., Umezawa, Y., Hirota, M. & Takeuchi, Y., CH/π interaction significance in molecular recognition. Tetrahedron 51, 8665–8701 (1995).

    Article  CAS  Google Scholar 

  9. Johnson, L.N., Acharya, K.R., Jordan, M.D. & McLaughlin, P.J. The refined crystal structure of the phosphorylase-heptulose 2-phosphate-oligosaccharide-AMP complex. J.Mol. Biol. 211, 645–661 (1990).

    Article  CAS  Google Scholar 

  10. Martin, J.L., Withers, S.G. & Johnson, L.N. 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 

  11. Barford, D. & Johnson, L.N. The allosteric transition of glycogen phosphorylase. Nature 340, 609–614 (1989).

    Article  CAS  Google Scholar 

  12. Barford, D., Hu, S.-H. & Johnson, L.N. The structural mechanism for glycogen phosphorylase control by phosphorylation and by AMP. J. Mol. Biol. 218, 233–260 (1991).

    Article  CAS  Google Scholar 

  13. Sprang, S.R., Withers, S.G., Goldsmith, E.J., Fletterick, R.J. & Madsen, N.B. The structural basis for the association of phosphorylase b with AMP. Science 254, 1367–1371 (1991).

    Article  CAS  Google Scholar 

  14. Kasvinsky, P., Madsen, N.B., Fletterick, R.J. & Sygusch, J. X-ray crystallographic and kinetic studies of oligosaccharide binding to phosphorylase. J. Biol. Chem. 253, 1290–1296 (1978).

    CAS  PubMed  Google Scholar 

  15. Hu, H.-Y. & Gold, A.M. Kinetics of glycogen phosphorylase a with a series of semisynthetic, branched saccharides: a model for binding of polysaccharide substrates. Biochemistry 14, 2224–2230 (1975).

    Article  CAS  Google Scholar 

  16. Hajdu, J. et al. Catalysis in the crystal: synchrotron radiation studies with glycogen phosphorylase b. EMBO J. 6, 539–546 (1987).

    Article  CAS  Google Scholar 

  17. Raibaud, O. & Schwartz, M. Positive control of transcription initiation in bacteria. Ann. Rev. Genet. 18, 207–231 (1984).

    Article  Google Scholar 

  18. Schwartz, M. & Hofnung, M. La maltodextrine phosphorylase d'Escherichia coli. Eur. J. Biochem. 2, 132–145 (1967).

    Article  CAS  Google Scholar 

  19. Palm, D., Goerl, R. & Burger, K.J. Evolution of catalytic and regulatory sites in phosphorylase. Nature 313, 500–502 (1985).

    Article  CAS  Google Scholar 

  20. Becker, S., Schnackerz, K.D. & Schinzel, R. A study of binary complexes of Escherichia coli maltodextrin phosphorylase; α-D-glucose 1-methylenephosphonate as a probe of pyridoxal 5'-phosphate-substrate interactions. Biochim. Biophys. Acta 1243, 381–385 (1994).

    Article  Google Scholar 

  21. Davies, G.D., Tolley, S.P., Henrissat, B., Hjort, C. & Schulein, M. Structures of oligosaccharide-bound forms of the endoglucanas V from Humicola insolens at 1. 9Å resolution. Biochemistry 34, 16210–16220 (1995).

    Article  CAS  Google Scholar 

  22. Watson, K.A., Schinzel, R., Palm, D. & Johnson, L.N. The crystal structure of E. coli maltodextrin phosphorylase provides an explanation for the activity without control in this basic archetype of a phosphorylase. EMBOJ. 16, 1–14 (1997).

    Article  CAS  Google Scholar 

  23. Takusagawa, F. & Jacobson, R.A. The crystal structure of maltose. Acta Crystallogr. D34, 213 (1978).

  24. Drueckes, P., Boeck, B., Palm, D. & Schinzel, R. Mutational analysis of the oligosaccharide recognition site at the active site of Escherichia coli maltodextrin phosphorylase. Biochemistry 35, 6727–6734 (1996).

    Article  CAS  Google Scholar 

  25. Barford, D. & Johnson, L.N. The molecular mechanism for the tetrameric association of glycogen phosphorylase promoted by protein phosphorylation. Protein Sci. 1, 472–493 (1992).

    Article  CAS  Google Scholar 

  26. Meyer, F., Heilmeyer, L.M.G., Hashke, R.H. & Fischer, E.H. Control of phosphorylase in the glycogen particle. I. Isolation and characterisation of the protein glycogen complex. J.Biol. Chem. 245, 6642–6648 (1970).

    CAS  PubMed  Google Scholar 

  27. Johnson, L.N. et al. Glycogen phosphorylase b. in Allosteric Enzymes (ed. Herve, G.) 81–127 (CRC Press, Boca Raton, Florida, 1989).

    Google Scholar 

  28. Mitchell, E.P. et al. Ternary complex crystal structures of glycogen phosphorylase with a transition state analogue nojirimycin tetrazole and phosphate in the T and R states. Biochemistry 35, 7341–7355 (1996).

    Article  CAS  Google Scholar 

  29. Rees, D.A. & Smith, P.J.C. Polysaccharide conformation. Part IX. Monte Carlo calculation of conformational energies for disaccharides and comparison with experiment. J. Chem. Soc. Perkin II, 836–840 (1975).

  30. Mikami, B., Degano, M., Hehre, E.J. & Sacchettinin, J.C. Crystal structures of Soybean β-amylase reacted with β-maltose and maltal: active site components and their apparent roles in catalysis. Biochemistry 33, 7779–7787 (1994).

    Article  CAS  Google Scholar 

  31. Machius, M., Vertesy, L., Huber, R. & Wiegland, G. Carbohydrate and protein-based inhibitors of porcine pancreatic α-amylase: structure analysis and comparison of their binding characteristics. J. Mol. Biol. 260, 409–421 (1996).

    Article  CAS  Google Scholar 

  32. Barford, D. et al. Channels at the catalytic site of glycogen phosphorylase b: binding and kinetic studies with the β-glycosidase inhibitor D-gluconohydroximo-1,5-lactone N-phenylurethane. Biochemistry 27, 6733–6741 (1988).

    Article  CAS  Google Scholar 

  33. Johnson, L.N., Hu, S.-H. & Barford, D. Catalytic mechanism of glycogen phosphorylase. Faraday Disc. 93, 131–142 (1992).

    Article  CAS  Google Scholar 

  34. Palm, D., Klein, H.W., Schinzel, R., Buehner, M. & Helmreich, E.J.M. The role of pyridoxal-5'-phosphate in glycogen phosphorylase catalysis. Biochemistry 29, 1099–1107 (1990).

    Article  CAS  Google Scholar 

  35. Otwinowski, Z.DENZO. in Data Collection and Processing. (eds Sawyer, L., Isaacs, N. & Bailey, S.) 56–62, SERC Laboratory, Daresbury, Warrington, UK. DL/SC1/R34, 1993).

    Google Scholar 

  36. The CCP4 (Collaborative Computational Project Number 4) suite: programmes for protein crystallography. Acta Crystallogr. D50, 760–763 (1994).

  37. Navaza, J. AMoRe: an automated package for molecular replacement. Acta Crystallogr. A50, 157–163 (1990).

    Google Scholar 

  38. Brunger, A.T. X-PLOR: Version 3.1; a system for protein crystallography and NMR., (Yale University Press, New Haven, 1992).

    Google Scholar 

  39. Engh, R.A. & Huber, R. Accurate bond length and angle parameters for X-ray protein structure refinement. Acta Crystallogr. A47, 392–400 (1991).

    Article  CAS  Google Scholar 

  40. Cowtan, K. DM: an automated procedure for phase improvement by density modification. Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography 31, 34–38 (1994).

    Google Scholar 

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

    Article  CAS  Google Scholar 

  42. Ho, S.N., Hunt, H.D., Horton, R.M., Pullen, J.K. & Pease, L. Site-directed mutagenesis by overlap extension using the polymerase chain reaction. Gene 77, 51–59 (1989).

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Laboratory of Molecular Biophysics and Oxford Centre for Molecular Sciences, University of Oxford, Rex Richards Building, South Parks Road, Oxford, 0X1 3QU

    Marc O'Reilly, Kim A. Watson & Louise N. Johnson

  2. Physiologische Chemie I, Theodor-Boveri-lnstitutfur Biowissenschaften (Biozentrum), Universitat Wurzburg, Am Hubland, 97074, Wurzburg, Germany

    Reinhard Schinzel & Dieter Palm

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O'Reilly, M., Watson, K., Schinzel, R. et al. Oligosaccharide substrate binding in Escherichia coli maltodextrin phosphorylase. Nat Struct Mol Biol 4, 405–412 (1997). https://doi.org/10.1038/nsb0597-405

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