Electrostatics in the active site of an α-amylase

European Journal of Biochemistry

Volumn 264, Issue 3, 1999, Pages 816-824

  Nielsen, Jens E ^b   Beier, Lars ^a   Otzen, Daniel ^c   Borchert, Torben V ^a   Frantzen, Henrik B ^a   Andersen, Kim V ^a   Svendsen, Allan ^a  

^a NOVO NORDISK A S   (Denmark)

^b EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^c NONE

Author keywords

Amylase; Active site; Electrostatics; pH activity profile; Protein engineering

Indexed keywords

AMYLASE;

ARTICLE; BACILLUS LICHENIFORMIS; CATALYSIS; ELECTRICITY; ENZYME ACTIVE SITE; ENZYME ACTIVITY; HYDROGEN BOND; NONHUMAN; PH; PRIORITY JOURNAL; SITE DIRECTED MUTAGENESIS;

ALPHA-AMYLASE; BACILLUS; CATALYTIC DOMAIN; ELECTROSTATICS; ENZYME STABILITY; HYDROGEN BONDING; HYDROGEN-ION CONCENTRATION; MODELS, MOLECULAR; MUTAGENESIS, SITE-DIRECTED; PROTEIN CONFORMATION; PROTEIN ENGINEERING;

BACILLUS LICHENIFORMIS;

EID: 0033568136     PISSN: 00142956     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1432-1327.1999.00664.x     Document Type: Article

References (51)

1. 1. Warshel, A., Naray-Szabo, G., Sussman, F. & Hwang, J.K. (1989) How do serine proteases really work? Biochemistry 28, 2639-3637.
2. 2. Sinnot, M.L. (1990) Catalytic mechanisms of enzymic glycosyl transfer. Chem. Rev. 90, 1171-1202.
3. 3. McCarter, J.D. & Withers, S.G. (1994) Mechanisms of enzymatic glycoside hydrolysis. Curr. Opin. Struct. Biol. 4, 885-892.
4. 4. Pickersgill, R.W., Goodenough, P.W., Summer, I.G. & Collins, M.E. (1988) The electrostatic fields in the active-site clefts of actinidin and papain. Biochem. J. 254, 235-238.
5. 5. Fang, T.-Y. & Ford, C. (1998) Protein engineering of Aspergillus awamori glucoamylase to increase its pH optimum. Protein Eng. 11, 383-388.
6. a of the general acid/base carboxyl group of a glycosidase cycles during catalysis: a 13C-NMR study of Bacillus circulans xylanase. Biochemistry 35, 9958-9966.
7. 7. Almo, S.C., Smith, D.L., Danishefsky, A.T. & Ringe, D. (1994) The structural basis for the altered substrate specificity of the R292D active site mutant of aspartate aminotransferase from E. coli. Protein Eng. 7, 405-412.
8. a of the catalytic residue His-102 of the recombinant ribonuclease from Bacillus amyloliquefaciens (Barnase). Proteins 24, 370-378.
9. 9. Perutz, M.F. (1978) Electrostatic effects in proteins. Science 201, 1187-1191.
10. 10. Fersht, A.R., Shi, J.P., Knill-Jones, J., Lowe, D.M., Wilkinson, A.J., Blow, D.M., Brick, P.M., Carter, P., Waye, M.M. & Winter, G. (1985) Hydrogen bonding and biological specificity analysed by protein engineering. Nature 314, 235-238.
11. 11. Sharp, K.A. & Honig, B. (1990) Electrostatic interactions in macromolecules. Annu. Rev. Biophys. Chem. 19, 301-332.
12. 12. Graf, L., Jancso, A., Szilagyi, L., Hegyi, G., Pinter, K., Naray-Szabo, G., Hepp. J., Medzihradszky, K. & Rutter, W.J. (1988) Electrostatic complementarity within the substrate-binding pocket of trypsin. Proc. Natl Acad. Sci. USA 85, 4961-4965.
13. 13. Klapper, I., Hagstrom, R., Fine, R., Sharp, K. & Honig, B. (1986) Focusing of electric fields in the active site of Cu-Zn superoxide dismutase: effects of ionic strength and amino-acid modification. Proteins 1, 47-59.
14. 14. Nicholls, A., Sharp, K. & Honig, B. (1991) Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11, 281-296.
15. 15. Madura, J.D., Briggs, J.M., Wade, R.C., Davis, M.E., Luty, B.A., Ilin, A., Antosiewicz, J., Gilson, M.K., Bagheri, B., Scott, L.R. & McCammon, J.A. (1995) Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian dynamics program. Comput. Phys. Commun. 91, 57-95.
16. 16. Jackson, S.E. & Fersht, A.R. (1993) Contribution of long-range electrostatic interactions to the stabilization of the catalytic transition state of the serine protease subtilisin BPN'. Biochemistry 32, 13909-13916.
17. 17. Linderstrøm-Lang, K. & Nielsen, S.O. (1959) Acid-base equilibria of proteins. In Electrophoresis (Bier, M., ed.), pp. 35-89. Academic, New York.
18. 18. Fisher, C.L., Cabelli, D.E., Tainer, J.A., Hallewell, R.A. & Getzoff, E.D. (1994) The role of arginine 143 in the electrostatics and mechanism of Cu,Zn superoxide dismutase: computational and experimental evaluation by mutational analysis. Proteins 19, 24-34.
19. 19. Schreiber, G. & Fersht, A.R. (1996) Rapid, electrostatically assisted association of proteins. Nat. Struct. Biol. 3, 427-431.
20. a of an active-site glutamic acid residue in Bacillus circulans xylanase. Eur. J. Biochem. 232, 839-843.
21. 1H NMR. Biophys. J. 66, 1180-1194.
22. 22. Kunugi, S., Hirohara, H. & Ise, N. (1982) pH and temperature dependences of thermolysin catalysis. Catalytic role of zinc-coordinated water. Eur. J. Biochem. 124, 157-163.
23. 23. Kiick, D.M., Harris, B.G. & Cook, P.F. (1986) Protonation mechanism and location of rate-determining steps for the Ascaris suum nicotinamide adenine dinucleotide-malic enzyme reaction from isotope effects and pH studies. Biochemistry 25, 227-236.
24. 24. Guzman-Maldano, H. & Predes-Lopez (1995) Amylolytic enzymes and products derived from starch; a review. Crit. Rev. Food Nutr. 36 (5), 373-403.
25. 25. Knegtel. R.M.A., Strokopytov, B., Penninga, D., Faber, O.G., Roozeboom, H.J., Kalk, K.H., Dijkhuizen, L. & Dijkstra, B.W. (1995) Crystallographic studies of the interaction of cyclodextrin glycosyltransferase from Bacillus circulans strain 251 with natural substrates and products. J. Biol. Chem. 270, 29256-29264.
26. 26. Qian, M., Haser, R., Buisson, G., Duee, E. & Payan, F. (1994) The active center of a mammalian α-amylase. Structure of the complex of a pancreatic α-amylase with a carbohydrate inhibitor refined to 2.2-Ä resolution. Biochemistry 33, 6284-6294.
27. 27. McCarter, J.D. & Withers, S.G. (1996) Unequivocal identification of Asp-214 as the catalytic nucleophile of Saccharomyces cerevisiae α-glucosidase using 5-fluoro glycosyl fluorides. J. Biol. Chem. 271 (12), 6689-6894.
28. 28. MacGregor, E.A. (1993) Relationships between structure and activity in the α-amylase family of starch-metabolising enzymes. Starch 7, 232-237.
29. 29. Svensson, B. (1994) Protein engineering in the α-amylase family: catalytic mechanism, substrate specificity, and stability. Plant Mol. Biol. 25, 141-157.
30. 30. Boel, E., Brady, L., Brzozowski, A.M., Derewenda, Z., Dodson, G.G., Jensen, V.J., Petersen, S.B., Swift, H., Thim, L. & Woldike, H.F. (1990) Calcium binding in α-amylases: an X-ray diffraction study at 2.1-Å resolution of two enzymes from Aspergillus. Biochemistry 29, 6244-6249.
31. 31. Machius, M., Wiegand, G. & Huber, R. (1995) Crystal structure of calcium-depleted Bacillus licheniformis α-amylase at 2.2-Å resolution. J. Mol. Biol. 246, 545-559.
32. 32. Gilles, C., Astier, J.-P., Marchis-Mouren, G., Cambillau, C. & Payan, F. (1996) Crystal structure of pig pancreatic α-amylase isoenzyme II, in complex with the carbohydrate inhibitor acarbose. Eur. J. Biochem. 238, 561-569.
33. 33. Larson, S.B., Greenwood, A., Cascio, D., Day, J. & McPherson, A. (1994) Refined molecular structure of pig pancreatic α-amylase at 2.1-Å resolution. J. Mol. Biol. 235, 1560-1584.
34. 34. Ramasubbu, N., Paloth, V., Luo, Y., Brayer, G.D. & Levine, M.J. (1996) Structure of human salivary α-amylase at 1.6-Å resolution: implications for its role in the oral cavity. Acta Crystallogr., Sect. D 52, 435-446.
35. 35. Aghajari, N., Feller, F., Gerday, G. & Haser, R. (1998) Crystal structures of the psycrophilic α-amylase from Alteromonas haloplanctis in its native form and complexed with an inhibitor. Protein Sci. 7, 564-572.
36. 36. Machius, M., Declerck, N., Huber, R. & Wiegand, G. (1998) Activation of Bacillus licheniformis α-amylase through a disorder → order transition of the substrate-binding site mediated by a calcium-sodium-calcium metal triad. Structure 6, 281-292.
37. 37. Svensson, B. & Søgaard, M. (1993) Mutational analysis of glycosylase function. J. Biotechnol. 29, 1-37.
38. 38. Davies, G.J. & Henrissat, H. (1995) Structures and mechanisms of glycosyl hydrolases. Structure 3, 853-859.
39. 38a. Takase, K., Matsumoto, T., Mizuno, H. & Yamane, K. (1992) Site-directed mutagenesis of active site residues in Bacillus subtilis α-amylase. Biochim. Biophys. Acta 1120, 281-288.
40. 39. Davies, G.J., Wilson, K.S. & Henrissat, B. (1997) Nomenclature for sugar-binding subsites in glycosyl hydrolases, Biochem. J. 321, 557-559.
41. 39a. Declerck, N., Joyet, P., Trosset, J.-Y., Garnier, J. & Gaillardin, C. (1995) Hyberthermostable mutants of Bacillus licheniformis α-amylase: multiple amino acid replacements and molecular modeling. Protein Eng. 8 (10), 1029-1037.
42. 40. Klein, C., Hollender, J., Bender, H. & Schulz, G.E. (1992) Catalytic center of cyclodextrin glycosyltransferase derived from X-ray structure analysis combined with site-directed mutagenesis. Biochemistry 31, 8740-8746.
43. 40a. Takase, K. (1993) Effect of mutation of an amino acid residue near the catalytic site on the activity of Bacillus stearothermophilus α-amylase. Eur. J. Biochem. 211, 899-902.
44. 41. Strokopytov, B., Penninga, D., Rozeboom, H.J., Kalk, K.H., Dijkhuizen, L. & Dijkstra, B.W. (1995) X-ray structure of cyclodextrin glycosyltransferase complexed with acarbose. Implications for the catalytic mechanism of glycosidases. Biochemistry 34, 2234-2240.
45. 41a. Søgaard, M., Kadziola, A., Haser, R. & Svensson, B. (1993) Site-directed mutagenesis of histidine 93, aspartic acid 180, glutamic acid 205, histidine 290, and aspartic acid 291 at the active site and tryptophan 279 at the raw starch binding site in barley α-amylase 1. J. Biol. Chem. 268 (30), 22480-22484.
46. 42. Krengel, U. & Dijkstra, B.W. (1996) Three-dimensional structure of endo-1,4-beta-xylanase I from Aspergillus niger: molecular basis for its low pH optimum. J. Mol. Biol. 263, 70-78.
47. 43. Vriend, G. (1990) WHAT IF: a molecular modeling and drug design program. J. Mol. Graphics 8, 52-56.
48. 44. Chinea, G., Padron, G., Hooft, R.W.W., Sander, C. & Vriend, G. (1995) The use of position-specific rotamers in model building by homology. Proteins 23, 415-421.
49. 45. Honig, B., Sharp, K. & Yang, A.-S. (1993) Macroscopic models of aqueous solutions: biological and chemical applications. J. Phys. Chem. 97, 1101-1109.
50. a shifts for aspartic acid: relevance to protein mechanisms. Biopolymers 34, 889-896.
51. 47. Antosiewicz, J., McCammon, J.A. & Gilson, M.K. (1994) Prediction of pH-dependent properties of proteins. J. Mol. Biol. 238, 415-436.