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Structure-based design of a lysozyme with altered catalytic activity

Abstract

Here we show that the substitution Thr 26→His in the active site of T4 lysozyme causes the product to change from the α- to the β-anomer. This implies an alteration in the catalytic mechanism of the enzyme. From the change in product, together with inspection of relevant crystal structures, it is inferred that wild-type T4 lysozyme is an anomer-inverting enzyme with a single displacement mechanism in which water attacks from the α-side of the substrate. In contrast, the mutant T26H is an anomer-retaining enzyme with an apparently double displacement mechanism in which a water molecule attacks from the opposite side of the substrate. The results also show that the mechanism of wild-type T4 lysozyme differs from that of hen egg-white lysozyme even though both enzymes are presumed to have evolved from a common precursor.

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References

  1. Bowie, J.U., Reidhaar-Olson, J.F., Lim, W.A. & Sauer, R.T. Deciphering the message in protein sequences: Tolerance to amino acid substitutions. Science 247, 1306–1310 (1990).

    Article  CAS  Google Scholar 

  2. Matthews, B.W. Structural and genetic analysis of protein stability. A. Rev. Biochem. 62, 139–160 (1993).

    Article  CAS  Google Scholar 

  3. Grütter, M.G., Weaver, L.H. & Matthews, B.W. Goose lysozyme structure: an evolutionary link between hen and bacteriophage lysozymes? Nature 303, 828–831 (1983).

    Article  Google Scholar 

  4. Blake, C.C.F. et al. Structure of hen egg-white lysozyme. A three-dimensional Fourier synthesis at 2 Å resolution. Nature 206, 757–761 (1965).

    Article  CAS  Google Scholar 

  5. Matthews, B.W. & Remington, S.J. The three-dimensional structure of the lysozyme from bacteriophage T4. Proc. natn. Acad. Sci. U.S.A. 71, 4178–4182 (1974).

    Article  CAS  Google Scholar 

  6. Svensson, B. & Søgaard, M. Mutational analysis of glycosylase function. J. Biotechnology 29, 1–37 (1993).

    Article  CAS  Google Scholar 

  7. Jacobson, R.H., Zhang, X.-J., DuBose, R.F. & Matthews, B.W. Three-dimensional structure of β-galactosidase from E. coli. Nature 369, 761–766 (1994).

    Article  CAS  Google Scholar 

  8. Jenkins, J., Leggio, L.L., Harris, G. & Pickersgill, R. & Pickersgill, R β-Glucosidase, β-galactosidase, family A cellulases, family F xylanases and two barley glycanases form a superfamily of enzymes with 8-fold β/α architecture and with two conserved glutamates near the carboxy-terminal ends of β-strands four and seven. FEBS Lett. 362, 281–285 (1995).

    Article  CAS  Google Scholar 

  9. Weaver, L.H., Grütter, M.G. & Matthews, B.W. The refined structures of goose lysozyme and its complex with a bound trisaccharide show that the “goose-type” lysozymes lack a catalytic aspartase residue. J. molec. Biol. 245, 54–68 (1995).

    Article  CAS  Google Scholar 

  10. Koshland, D.E. Stereochemistry and the mechanism of enzymatic reactions. Biol. Rev. 28, 416–436 (1953).

    Article  CAS  Google Scholar 

  11. Phillips, D.C. The hen egg-white lysozyme molecule. Proc. natn. Acad. Sci.U.S.A. 57, 484–495 (1967).

    Article  CAS  Google Scholar 

  12. Sinnott, M.L. Catalytic mechanisms of enzymic glycosyl transfer. Chem. Rev. 90, 1171–1202 (1990).

    Article  CAS  Google Scholar 

  13. Strynadka, N.C.J. & James, M.N.G. Lysozyme revisited: crystallographic evidence for distortion of an N-acetylmuramic acid residue bound in site D. J. molec. Biol. 220, 401–424 (1991).

    Article  CAS  Google Scholar 

  14. Anand, N.N., Stephen, E.R. & Narang, S.A. Mutation of active site residues in synthetic T4-lysozyme gene and their effect on lytic activity. Biochem. biophys. Res. Commun. 153, 862–868 (1988).

    Article  CAS  Google Scholar 

  15. Malcolm, B.A. et al. Site-directed mutagenesis of the catalytic residues Asp-52 and Glu-35 of chicken egg white lysozyme. Proc. natn. Acad. Sci. U.S.A. 86, 133–137 (1989).

    Article  CAS  Google Scholar 

  16. Hardy, L.W. & Poteete, A.R. Reexamination of the role of Asp20 in catalysis by bacteriophage T4 lysozyme. Biochemistry 30, 9457–9463 (1991).

    Article  CAS  Google Scholar 

  17. Rennell, D., Bouvier, S.E., Hardy, L.W. & Poteete, A.R. Systematic mutation of bacteriophage T4 lysozyme. J. molec. Biol. 222, 67–87 (1991).

    Article  CAS  Google Scholar 

  18. Shoichet, B.K., Baase, W.A., Kuroki, R. & Matthews, B.W. A relationship between protein stability and protein function. Proc. natn. Acad. Sci. U.S.A. 92, 452–456 (1995).

    Article  CAS  Google Scholar 

  19. Kuroki, R., Weaver, L.H. & Matthews, B.W. A covalent enzyme-substrate intermediate with saccharide distortion in a mutant T4 lysozyme. Science 262, 2030–2033 (1993).

    Article  CAS  Google Scholar 

  20. Bienkowska, K. & Taylor, A. Low-molecular-weight substrate for the lysozyme of T4 bacteriophage. Eur. J. Biochem. 96, 581–584 (1979).

    Article  CAS  Google Scholar 

  21. Glauner, B. Separation and quantification of muropeptides with high-performance liquid chromatography. Anal. Biochem. 172, 451–464 (1988).

    Article  CAS  Google Scholar 

  22. Dahlquist, F.W., Borders, C.L., Jacobson, G. & Raftery, M.A. The stereospecificity of human, hen, and papaya lysozymes. Biochemistry 8, 694–700 (1969).

    Article  CAS  Google Scholar 

  23. Weaver, L.H. & Matthews, B.W. Structure of bacteriophage T4 lysozyme refined at 1.7 Å resolution. J. molec. Biol. 193, 189–199 (1987).

    Article  CAS  Google Scholar 

  24. Tomme, P. et al. Identification of a histidyl residue in the active center of endoglucanase D from Clostridium thermocellum. J. biol. Chem. 266, 10313–10318 (1991).

    CAS  PubMed  Google Scholar 

  25. Py, B., Bortoli-German, I., Haiech, J., Chippaux, M. & Barras, F. Cellulase EGZ of Erwinia chrysanthemi: Structural organization and importance of His 98 and Glu 133 residues for catalysis. Protein Engng. 4, 325–333 (1991).

    Article  CAS  Google Scholar 

  26. Nickbarg, E.B., Davenport, R.C., Petsko, G.A. & Knowles, J.R. Triosephosphate isomerase: Removal of a putatively electrophilic histidine residue results in a subtle change in catalytic mechanism. Biochemistry 27, 5948–5960 (1988).

    Article  CAS  Google Scholar 

  27. Wang, Q., Graham, R.W., Trimbur, D., Warren, R.A.J. & Withers, S.G. Changing enzymatic reaction mechanisms by mutagenesis: Conversion of a retaining glucosidase to an inverting enzyme. J. Am. chem. Soc. 116, 11594–11595 (1994).

    Article  CAS  Google Scholar 

  28. Muchmore, D.C., Mclntosh, L.P., Russell, C.B., Anderson, D.E. & Dahlquist, F.W. Expression and 15N labelling of proteins for proton and nitrogen-15 NMR. Meths Enzymol. 177, 44–73 (1989).

    Article  CAS  Google Scholar 

  29. Poteete, A.R., Dao-pin, S., Nicholson, H. & Matthews, B.W. Second-site revertants of an inactive T4 lysozyme mutant restore activity structuring the active site cleft. Biochemistry 30, 1425–1432 (1991).

    Article  CAS  Google Scholar 

  30. Streisinger, G., Mukai, F., Dreyer, W.J., Miller, B. & Horiuchi, S. Mutations affecting the lysozyme of phage T4. Cold Spring Harb. Symp. quant. Biol. 26, 25–30 (1961).

    Article  CAS  Google Scholar 

  31. Tronrud, D.E., Ten Eyck, L.F. & Matthews, B.W. An efficient general-purpose least-squares refinement program for macromolecular structures. Acta Crystallogr. A43, 489–503 (1987).

    Article  CAS  Google Scholar 

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Kuroki, R., Weaver, L. & Matthews, B. Structure-based design of a lysozyme with altered catalytic activity. Nat Struct Mol Biol 2, 1007–1011 (1995). https://doi.org/10.1038/nsb1195-1007

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