Modeling study on a hydrolytic mechanism of class A β-lactamases

Journal of Medicinal Chemistry

Volumn 39, Issue 11, 1996, Pages 2207-2218

  Ishiguro, Masaji ^a,b   Imajo, Seiichi ^a  

^a SUNTORY LTD   (Japan)

^b SUNTORY INSTITUTE FOR BIOORGANIC RESEARCH   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BETA LACTAMASE; PENICILLIN DERIVATIVE;

ARTICLE; COMPLEX FORMATION; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; DEACYLATION; ENZYME ACTIVATION; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME KINETICS; ENZYME MECHANISM; HYDROGEN BOND; HYDROLYSIS; MOLECULAR MODEL; NONHUMAN; REACTION ANALYSIS;

AMINO ACID SEQUENCE; BETA-LACTAMASES; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; HYDROGEN BONDING; HYDROLYSIS; KINETICS; MODELS, MOLECULAR; PENICILLIN G; PROTEIN CONFORMATION; SERINE; STAPHYLOCOCCUS AUREUS;

EID: 0029896566     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm9506027     Document Type: Article

References (55)

1. Ambler, R. P. The Structure of β-Lactamases. Philos. Trans. R. Soc. London B 1980, 289, 321-331.
2. Herzberg, O. Refined Crystal Structure of β-Lactamase from Staphylococcus aureus PC1 at 2.0 Å Resolution. J. Mol. Biol. 1991, 217, 701-719.
3. Knox, J. R.; Moews, P. C. β-Lactamase of Bacillus licheniformis 749/C. Refinement at 2Å Resolution and Analysis of Hydration. J. Mol. Biol. 1991, 220, 435-455.
4. Herzberg, O.; Moult, J. Bacterial Resistance to β-Lactam Antibiotics: Crystal Structure of β-Lactamase from Staphylococcus aureus PC1 at 2.5 Å Resolution. Science 1987, 236, 694-701.
5. Gibson, R. M.; Christensen, H.; Waley, S. G. Site-Directed Mutagenesis of β-Lactamase I. Single and Double Mutants of Glu-166 and Lys-73 Biochem. J. 1990, 272, 613-619.
6. Jacob, F.; Joris, B.; Lepage, S.; Dusart, J.; Frère, J.-M. Pole of the Conserved Amino Acids of the 'SDN' Loop (Ser130,Asp131 and Asn132) in a Class A β-Lactamase Studied by Site-Directed Mutagenesis. Biochem. J. 1990, 277, 399-406.
7. Lamotte-Brasseur, J.; Dive, G.; Dideberg, O.; Charlier, P.; Frère, J.-M.; Ghuysen, J.-M. Mechanism of Acyl Transfer by the Class A Serine β-Lactamase of Streptomyces albus G. Biochem. J. 1991, 279, 213-221.
8. Fonze, E.; Charlier, P.; To'th, Y.; Vermeire, M.; Raquet, X.; Dubus, A.; Frère, J.-M. TEM1 β-Lactamase Structure Solved by Molecular Replacement and refined Structure of the S235A Mutant. Acta Crystallogr. 1995, D51, 682-694.
9. Adachi, H.; Ohta, T.; Matsuzawa, H. Site-Directed Mutants, at Position 166, of RTEM-1 β-Lactamase That Form a Stable Acyl-Enzyme Intermediate with Penicillin. J. Biol. Chem. 1991, 266, 3186-3191.
10. Escobar, W. A.; Tan, A. K.; Fink, A. L. Site-Directed Mutagenesis of β-Lactamase Leading to Accumulation of a Catalytic Intermediate. Biochemistry 1991, 30, 10783-10787.
11. Delaire, M.; Lenfant, F.; Labia, R.; Masson, J.-M. Site-Directed Mutagenesis on TEM-1 β-Lactamase: Role of Glul66 in Catalysis and Substrate Binding. Protein Eng. 1991, 4, 805-810.
12. 166 of Class A β-Lactamases FEBS Lett. 1993, 332, 93-98.
13. Lobkovsky, E.; Moews, P. C.; Liu, H.; Zhao, H.; Frère, J.-M.; Knox, J. R. Evolution of an Enzyme Activity: Crystallographic Structure at 2-Å Resolution of Cephalosporinase from the AmpC Gene of Enterobacter cloacae P99 and Comparison with a Class A Penicillinase. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 11257-11261.
14. Ellerby, L. M.; Escobar, W. A.; Fink, A. L.; Michinson, C.; Wells, J. A. The Role of Lysine-234 in β-Lactamase Catalysis Probed by Site-Directed Mutagenesis. Biochemistry 1990, 29, 5797-5806.
15. Lenfant, F.; Labia, R.; Masson, J.-M. Replacement of Lysine 234 Affects Transition State Stabilization in the Active Site of β-Lactamase TEM1. J. Biol. Chem. 1991, 266, 17187-17194.
16. Matagne, A.; Frère, J.-M. Contribution of Mutant Analysis to the Understanding of Enzyme Catalysis: The Case of Class A β-Lactamases. Biochim. Biophys. Acta 1995, 1246, 109-127.
17. Dideberg, O.; Charlier, P.; Wery, J. P.; Dehottay, P.; Dusart, J.; Erpicum, T.; Frère, J.-M.; Ghuysen, J.-M. The Crystal Structure of the β-Lactamase of Streptomyces albus G at 0.3nm Resolution. Biochem. J. 1987, 245, 911-919.
18. Strynadka, N. C. J.; Adachi, H.; Jensen, S. E.; Johns, K.; Sielecki, A.; Betzel, C.; Sutoh, K.; James, M. N. G. Molecular Structure of the Acyl-Enzyme Intermediate in β-Lactam Hydrolysis at 1.7 Å Resolution. Nature 1992, 359, 700-705.
19. Jelsch, C.; Mourey, L.; Masson, J.-M.; Samama, J.-P. Crystal Structure of Escherichia coli TEM1 β-Lactamase at 1.8 Å Resolution. PROTEINS: Struct. Funct. Genet. 1993, 16, 364-383.
20. Chen, C. C. H.; Herzberg, O. Inhibition of β-Lactamase by Clavulanate. Trapped Intermediates in Cryocrystallographic Studies. J. Mol. Biol. 1992, 224, 1103-1113.
21. Chen, C. C. H.; Rahil, J.; Pratt, R. F.; Herzberg, O. Structure of a Phosphonate-Inhibited β-Lactamase. An Analog of the Tetrahedral Transition State/Intermediate of β-Lactam Hydrolysis. J. Mol. Biol. 1993, 234, 165-178.
22. Knox, J. R.; Moews, P. C.; Escobar, W. A.; Fink, A. L. A Catalytically-Impaired Class A β-Lactamase: 2 Å Crystal Structure and Kinetics of the Bacillus licheniformis E166A Mutant. Protein Eng. 1993, 6, 11-18.
23. Herzberg, O.; Kapadia, G.; Blanco, B.; Smith, T. S.; Coulson, A. Structural Basis for the Inactivation of the P54 Mutant of β-Lactamase from Staphylococcus aureus PC1. Biochemistry 1991, 30, 9503-9509.
24. Matagne, A.; Lamotte-Brasseur, J.; Dive, G.; Knox, J. R.; Frère, J.-M. Interactions Between Active-Site-Serine β-Lactamases and Compounds Bearing a Methoxy Side Chain on the α-Face of the β-Lactam Ring: Kinetic and Molecular Modeling Studies. Biochem. J. 1993, 293, 607-611.
25. Escobar, W. A.; Tan, A. K.; Lewis, E. R.; Fink, A. L. Site-Directed Mutagenesis of Glutamate-166 in β-Lactamase Leads to a Branched Path Mechanism. Biochemistry 1994, 33, 7619-7626.
26. Blaney, J. M.; Crippen, G. M.; Dearing, A.; Dixon, J. S. DGEOM-Distance Geometry. QCPE 1990, No. 590.
27. Weiner, S. J.; Kollman, P. A.; Case, D. A.; Singh, U. C.; Ghio, C.; Alagona, G.; Profeta, S., Jr.; Weiner, P. A New Force Field for Molecular Mechanical Simulation of Nucleic Acids and Proteins. J. Am. Chem. Soc. 1984, 106, 765-784.
28. Cohen, N. C. β-Lactam Antibiotics: Geometrical Requirements for Antibacterial Activities. J. Med. Chem. 1983, 26, 259-264.
29. Boles, M. O.; Girren, R. J.; Gane, P. A. C. The Structure of Amoxycillin Trihydrate and a Comparison with the Structures of Ampicillin. Acta Crystallogr. Sect. B 1978, 34, 461.
30. Mohamadi, F.; Richards, N. G. J.; Guida, W. C.; Liskamp, R.; Lipton, M.; Caufield, C.; Chang, G.; Hendrickson, T.; Still, W. C. Macromodel - An Integrated Software for Modeling Organic and Bioorganic Molecules Using Molecular Mechanics. J. Comput. Chem. 1990, 11, 440-467.
31. Dewar, M. J. S.; Zoebisch, E. G.; Healy, E. F.; Stewart, J. J. P. AM1: A New General Purpose Quantum Mechanical Molecular Model. J. Am. Chem. Soc. 1985, 107, 3902-3909.
32. Juteau, J.-M.; Billings, E.; Knox, J. R.; Levesque, R. C. Site-Saturation Mutagenesis and Three-Dimensional Modeling of ROB-1 Define a Substrate Binding Role of Ser130 in Class A β-Lactamases. Protein Eng. 1992, 5, 693-701.
33. Huletsky, A.; Knox, J. R.; Levesque, R. C. Role of Ser-238 and Lys-240 in the Hydrolysis of Third-generation Cephalosporins by SHV-type β-Lactamases Probed by Site-directed Mutagenesis and Three-dimensional Modeling. J. Biol. Chem. 1993, 268, 3690-3697
34. Kelly, J. A.; Moews, P. C.; Frère, J.-M.; Ghuysen, J.-M. Penicillin Target Enzyme and the Antibiotic Binding Site. Science 1982, 479-481.
35. Wei, Y.; Schottel, J. L.; Derewenda, U.; Swenson, L.; Patker, S.; Derewenda, Z. S. A Novel Variant of the Catalytic Triad in the Streptomyces scabies esterase. Nature: Struct. Biol. 1995, 2, 218-223.
36. Laws, A. P.; Layland, N. J.; Proctor, D. G.; Page, M. I. The Role of the Carboxy Group in β-Lactam Antibiotics and Lysine 234 in β-Lactamase I. J. Chem. Soc., Perkin Trans. 2 1993, 17-21.
37. Gilli, P.; Bertolasi, V.; Ferretti, V.; Gilli, G. Covarent Nature of the Strong Homonuclear Hydrogen Bond. Study of the O-H-O System by Crystal Structure Correlation Methods. J. Am. Chem. Soc. 1994, 116, 909-915.
38. Cartwright, S. J.; Tan, A. K.; Frank, A. L. Trapping the Acyl-enzyme Intermediate in β-Lactamase I Catalysis. Biochem. J. 1989, 263, 905-912.
39. 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 1993, 259, 669-673.
40. Gouaux, J. E.; Krause, K. L.; Lipscomb, W. N. The Catalytic Mechanism of Escherichia coli aspartate Carbamoyltransferase: A Molecular Modeling Study. Biochem. Biophys. Res. Commun. 1987, 142, 893-897.
41. Jeltsch, A.; Alves, J.; Wolfes, H.; Maas, G.; Pingould, A. Substrate-Assisted Catalysis in the Cleavage of DNA by the EcoRI and EcoRV Restriction Enzymes. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 8499-8503.
42. Perona, J. J.; Rould, M. A.; Steitz, T. A. Structural Basis for Transfer RNA Aminoacylation by Escherichia coli glutaminyl-tRNA Synthetase. Biochemistry 1993, 32, 8758-8771.
43. Cavarelli, J.; Eriani, G.; Rees, B.; Ruff, M.; Boeglin, M.; Mitschler, A.; Martin, F.; Gangloff, J.; Thierry, J.-C.; Moras, D. The Active Site of Yeast Aspartyl-tRNA Synthetase: Structural and Functional Aspects of the Aminoacylation. EMBO J. 1994, 13, 327-337.
44. ras and Other GTP-Binding Proteins. Nature: Struct. Biol. 1995, 2, 36-44.
45. Zafaralla, G.; Moashery, S. Facilitation of the Δ2→Δ1 Pyrroline Tautomerization of Carbapenem Antibiotics by the Highly Conserved Arginine-244 of Class A β-Lactamases During the Course of Turnover. J. Am. Chem. Soc. 1992, 114, 1505-1506.
46. Easton, C. J.; Knowles, J. R. Inhibition of the RTEM β-Lactamase from Escherichia coli. Interaction of the Enzyme with Derivatives of Olivanic Acid. Biochemistry 1982, 21, 2857-2862.
47. Charnas, R. L.; Knowles, J. R. Inhibition of the RTEM β-Lactamase from Escherichia coli. Interaction of Enzyme with Derivatives of Olivanic Acid. Biochemistry 1981, 20, 2732-2737.
48. Knowles, J. R. Penicillin resistance: The Chemistry of β-Lactamase Inhibition. Acc. Chem. Res. 1985, 18, 97-104.
49. Imtiaz, U., Billings; E.; Knox, J. R.; Manavathu, E. K.; Lerner, S. A.; Mobashery, S. Inactivation of Class A β-Lactamases by Clavulanic Acid: The Role of Arginine-244 in a Proposed Nonconcerted Sequence of Events. J. Am. Chem. Soc. 1993, 115, 4435-4442.
50. Vijayakumar, S.; Ravishanker, G.; Pratt, R. F.; Beveridge, D. L. Molecular Dynamics Simulation of a Class A β-Lactamases: Structural and Mechanistic Implications J. Am. Chem. Soc. 1995, 117, 1722-1730.
51. Oefner, C.; D'Arcy, A.; Daly, J. J.; Gubernator, K.; Charnas, R. L.; Heinze, I.; Hubschwerlen, C.; Winkler, F. K. Refined Crystal Structure of β-Lactamase from Citrobacter freundii indicates a Mechanism for β-Lactam Hydrolysis. Nature 1990, 343, 284-288.
52. Dubus, A.; Normark, S.; Kania, M.; Page, M. G. P. The Role of Tyrosine 150 in Catalysis of β-Lactam Hydrolysis by Amp C β-Lactamase from Escherichia coli Investigated by Site-Directed Mutagenesis. Biochemistry 1994, 33, 8577-8586.
53. Monnaie, D.; Dubus, A.; Frère, J.-M. The Role of Lysine-67 in a Class C β-Lactamase is Mainly Electrostatic. Biochem. J. 1994, 302, 1-4.
54. Tsukamoto, K.; Tachibana, K.; Yamazaki, N.; Ishii, Y.; Ujiie, K.; Nishida, N.; Sawai, T. Role of Lysine-67 in the Active Site of Class C β-Lactamase from Citrobacter freundii GN346. Eur. J. Biochem. 1990, 188, 15-22.
55. Tsukamoto, K.; Nishida, N.; Tsuruoka, M.; Sawai, T. Function of the Conserved Triad Residues in the Class C β-Lactamase from Citrobacter freundii GN346. FEBS Lett. 1990, 277, 243-246.