Abstract
Mass spectrometric screening reveals that an unmodified natural heptapeptide—human β-casomorphin-7, an internal sequence of human β-casein that possesses opioid-like activity—reacts with porcine pancreatic elastase to form an unusually stable acyl-enzyme complex at low pH. X-ray crystallographic analysis (to 1.9 Å resolution) at pH 5 shows continuous electron density linking the C-terminal isoleucine of β-casomorphin-7 to Ser 195 through an ester bond. The structure reveals a well defined water molecule (Wat 317), equidistant between the carbon of the ester carbonyl and Nε2 of His 57. Deprotonation of Wat 317 will produce a hydroxide ion positioned to attack the ester carbonyl through the favoured Bürgi-Dunitz trajectory.
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References
Blow, D.M. Structure and mechanism of chymotrypsin. Acc. Chem. Res. 9, 145–152 (1976).
Bode, W., Meyer, E., Jr. & Powers, J.C. Human leukocyte and porcine pancreatic elastase: X-ray crystal structures, mechanism, substrate specificity, and mechanism-based inhibitors. Biochemistry 28, 1951–1963 (1989).
Graf, L. Structural basis of serine protease action: the fourth dimension. in Natural Sciences and HumanThought (ed Zwilling) 139–148 (Springer-Verlag, Berlin, 1995).
Warshel, A. & Russell, S. Theoretical correlation of structure and energetics in the catalytic reaction of trypsin. J. Am, Chem. Soc. 108, 6569–6579 (1986).
Fothergill, M., Goodman, M.F., Petruska, J., Warshel, A. Structure-energy analysis of the role of metal ions in phosphodiester bond hydrolysis by DNA polymerase I. J. Am. Chem. Soc. 117, 11620–11627.
Dixon, M.M. & Matthews, B.W. Is γ-chymotrypsin a tetrapeptide acyl-enzyme adduct of α-chymotrypsin? Biochemistry 28, 7033–7038 (1989).
Harel, M., Su, C.-T., Frolow, F., Silman, I. & Sussman, J.L. γ-Chymotrypsin is a complex of α-chymotrypsin with its own autolysis products. Biochemistry 30, 5217–5225 (1991).
Dixon, M.M., Brennan, R.G. & Matthews, B.W. Structure of γ-chymotrypsin in the range pH 2.0 to pH 10.5 suggests that γ-chymotrypsin is a covalent acyl-enzyme adduct at low pH. Int. J, Biol. Macromol. 13, 89–96 (1991).
Singer, P.T., Smalås, A., Carty, R.P., Mangel, W.F. & Sweet, R.M. The hydrolytic water molecule in trypsin, revealed by time-resolved Laue crystallography. Science 259, 669–673 (1993).
Perona, J.J., Craik, C.S. & Fletterick, R.J. Locating the catalytic water molecule in serine proteases. Science 261, 620 (1993).
Singer, P.T., Smals, A., Carty, R.P., Mangel, W.F. & Sweet, R.M. Locating the water molecule in serine proteases: Response. Science 261, 621–622 (1993).
Ding, X., Rasmussen, B.F., Petsko, G.A. & Ringe, D. Direct structural observation of an acyl-enzyme intermediate in the hydrolysis of an ester substrate by elastase. Biochemistry 33, 9285–9293 (1994).
Blanchard, H. & James, M.N.G. A crystallographic re-investigation into the structure of Streptomyces griseus proteinase A reveals an acyl-enzyme intermediate. J. Mol. Biol. 241, 574–587 (1994).
Nohmi, T. & Fenn, F.J. Electrospray mass spectrometry of poly(ethylene glycols) with molecular weights up to five million. J. Am. Chem. Soc. 114, 3241–3246 (1992).
Aplin, R.T., Baldwin, J.E., Schofield, C.J. & Waley, S.G. Use of electrospray mass-spectrometry to directly observe an acyl-enzyme intermediate in beta-lactamase catalysis. FEBS Lett. 277, 212–214 (1990).
Ashton, D.S. et al. Some electrospray mass spectrometric evidence for the existence of covalent O-acyl enzyme intermediates. FEBS Lett. 292, 201–204 (1991).
Aplin, R.T., Robinson, C.V., Schofield C.J. & Westwood, N.J. An investigation into the mechanism of elastase inhibition by cephalosporins using electrospray ionisation mass spectrometry. Tetrahedron 49, 10903–10912 (1993).
Greenberg, R., Groves, M.L. & Dower, H.J. Human β-casein. J. Biol. Chem. 259, 5132–5138 (1984).
β-Casomorphins and Related Peptides (eds Nyberg, F. & Brantl, V.) (Fyris-Tryck AB, Uppsala, Sweden, 1990).
Del Mar, E.G., Largman, C., Brodrick, J.W., Fassett, M. & Geokas, M.C. Substrate specificity of human pancreatic elastase 2. Biochemistry 19, 468–472 (1980).
Meyer, E., Cole, G., Radhakrishnan, R. & Epp, O. Structure of native porcine pancreatic elastase at 1.65 Å resolution. Acta Cryst. B44, 26–38 (1988).
Teschemacher, H. & Koch, G. & Koch, G. β-Casomorphins: possible physiological significance., in β-Casomorphins and related peptides (eds Nyberg, F. & Brantl, V.) 143–149 (Fyris-Tryck AB, Uppsala, Sweden, 1990).
Taira, T., Hilakivi, L.A., Aalto, J. & Hilakivi, I. Effect of beta-casomorphin on neonatal sleep in rats. Peptides 11, 1–4 (1990). 30. Thompson, R.C. Binding of peptides to elastase: implication for the mechanism of substrate hydrolysis. Biochemistry 13, 5495–5501 (1974).
Thompson, R.C. Binding of peptides to elastase: implication for the mechanism of substrate hydrolysis. Biochemistry 13, 5495–5501 (1974).
James, M.N.G., Sielecki, A.R., Brayer, G.D., Delbaere, L.T. & Bauer, C.A. Structures of product and inhibitor complexes of Streptomyces griseus protease A at 1.8 Å resolution. J. Mol. Biol. 144, 43–88 (1980).
Brügi, H.B., Dunitz, J.D. & Shefter, E. Geometrical reaction coordinates. II. Nucleophilic addition to a carbonyl group. J. Am. Chem. Soc. 95, 5065–5067 (1973).
Maveyraud, L., Massova, I., Birck, C., Miyashita, K., Samama, J-P. & Mobashery, S. Crystal structure of 6a-(hydroxymethyl)penicillanate complexed to the TEM-1 β-lactamase from Esherichia coli: evidence on the mechanism of action of a novel inhibitor designed by a computer-aided process. J. Am. Chem. Soc. 118, 7435–7447 (1996).
Hagmann, W.K. et al. Prevention of human leukocyte elastase-mediated lung damage by 3-alkyl-4-azetidinones. Bioorg. Med. Chem. Letts. 1, 545–550 (1991).
Edwards, P.D., Meyer, E.F., Jr., Vijayalakshmi, J., Tuthill, P.A., Andisik, D.A., Gomes, B. & Strimpler, A. Design, synthesis, and kinetic evaluation of a unique class of elastase inhibitors, the peptidyl α-ketobenzoxazoles, and the X-ray crystal structure of the covalent complex between porcine pancreatic elastase and Ac-Ala-Pro-Val-2-benzoxazole. J. Am. Chem. Soc. 114, 1854–1863 (1992).
Lineweaver, H. & Burk, D. The determination of enzyme dissociation constants. J. Am. Chem. Soc. 56, 658–666 (1934).
Dixon, M. The determination of enzyme inhibitor constants. Biochem. J. 55, 170–171 (1953).
Cornish-Bowden, A. A simple graphical method for determining the inhibition constants of mixed, uncompetitive and non-competitive inhibitors. Biochem. J. 137, 143–144 (1974).
Otwinowski, Z. Oscillation data reduction program. in Data Collection and Processing (eds Sawyer, L., Isaacs, N.W. & Bailey, S.) 55–62 (DL/SCI/R34, Daresbury Laboratory, Warrington, U.K., 1993).
Brünger, A.T., Kuriyan, J. & Karplus, M. Cystallographic R-factor refinement by molecular dynamics. Science 235, 458–460 (1987).
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).
Kraulis, P.J. Molscript - a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946–950 (1991).
Merritt, E.A. & Murphy, M.E.P. Raster3d Version 2.0 - A program for photorealistic molecular graphics. Acta Crystallogr. D50, 869–873 (1994).
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Wilmouth, R., Clifton, I., Robinson, C. et al. Structure of a specific acyl-enzyme complex formed between β-casomorphin-7 and porcine pancreatic elastase. Nat Struct Mol Biol 4, 456–462 (1997). https://doi.org/10.1038/nsb0697-456
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DOI: https://doi.org/10.1038/nsb0697-456
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