pK(a) Calculations for class A β-lactamases: Influence of substrate binding

Protein Science

Volumn 8, Issue 2, 1999, Pages 404-409

  Lamotte Brasseur, Josette ^a,b   Lounnas, Valère ^b   Raquet, Xavier ^c   Wade, Rebecca C ^b  

^a UNIVERSITY OF LIÈGE   (Belgium)

^b EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^c Max Delbruck Laboratorium der Max Planck Gesellschaft   (Germany)

Author keywords

Mechanism; pK(a) calculations; Poisson Boltzmann electrostatics; Protein modeling; lactamases

Indexed keywords

BETA LACTAM; BETA LACTAMASE; GLUTAMIC ACID; LYSINE; CEFALOTIN; DRUG DERIVATIVE; PENICILLIN G;

ACYLATION; ANTIBIOTIC RESISTANCE; ARTICLE; ENZYME ACTIVE SITE; ENZYME MECHANISM; ENZYME STABILITY; ENZYME SUBSTRATE COMPLEX; PKA; PRIORITY JOURNAL; CHEMICAL MODEL; PH; STATISTICAL MODEL;

BACTERIA (MICROORGANISMS);

BETA-LACTAMASES; CEPHALOTHIN; HYDROGEN-ION CONCENTRATION; LYSINE; MODELS, CHEMICAL; MODELS, STATISTICAL; PENICILLIN G;

EID: 0032586776     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.8.2.404     Document Type: Article

References (36)

1. as in proteins. Biochemistry 35:7819-7833.
2. Brannigan J, Matagne A, Jacob F, Damblon C, Joris B, Klein D, Spratt B, Frère JM. 1991. The mutation Lys234His yields a class A β-lactamase with a novel pH-dependence. Biochem J 278:673-678.
3. Damblon C, Raquet X, Lian LY, Lamotte-Brasseur J, Fonzé E, Charlier P, Roberts GCK, Frère JM. 1996. The catalytic mechanism of β-lactamases: NMR titration of an active-site lysine residue of the TEM-1 enzyme. Proc Natl Acad Sci USA 93:1747-1752.
4. Davis ME, McCammon JA. 1989. Solving the finite difference linearized Poisson-Boltzmann equation: A comparison of relaxation and conjugate gradient methods. J Comput Chem 10:386-391.
5. Davis ME, McCammon JA. 1991. Dielectric boundary smoothing in finite difference solutions of the Poisson equation: An approach to improve accuracy and convergence. J Comput Chem 12:909-912.
6. Delaire M, Lenfant F, Labia R, Masson JM. 1991. Site-directed mutagenesis on TEM-1 β-lactamase: Role of Glu166 in catalysis and substrate binding. Protein Eng 4:805-810.
7. as of ionizable groups in proteins. J Phys Chem 100:17373-17387.
8. Dideberg O, Charlier P, Wéry JP, Dehottay P, Dusart J, Erpicum T, Frère JM, Ghuysen JM. 1987. The crystal structure of the β-lactamase of Streptomyces albus G at 0.3 nm resolution. Biochem J 245:911-919.
9. Escobar WA, Tan AK, Fink AL. 1991. Site-directed mutagenesis of β-lactamase I - Single and double mutants of Glu166 and Lys73. Biochem J 272:613-619.
10. Fonzé E, Charlier P, To'th Y, Vermeire M, Raquet X, Dubus A, Frère JM. 1995. TEM1 β-lactamase structure solved by molecular replacement and refined structure of the S235A mutant. Acta Crystallogr D51:682-694.
11. Gibson RM, Christensen H, Waley SG. 1990. Site-directed mutagenesis of β-lactamase I - Single and double mutants of Glu166 and Lys73. Biochem J 272:613-619.
12. Guillaume G, Vanhove M, Lamotte-Brasseur J, Ledent P, Jamin M, Joris B, Frère JM. 1997. Site-directed mutagenesis of glutamate 166 in two β-lactamases - Kinetic and molecular modeling studies. J Biol Chem 272: 5438-5444.
13. Herzberg O. 1991. Refined crystal structure of β-lactamase from Staphylococcus aureus PC1 at 2.0 Å resolution. J Mol Biol 217:701-719.
14. Herzberg O, Moult J. 1987. Bacterial resistance to β-lactam antibiotics: Crystal structure of β-lactamase from Staphylococcus aureus PC1 at 2.5 Å resolution. Science 236:694-701.
15. Hooft RW, Sander C, Vriend G. 1996. Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures. Proteins Struct Funct Genet 26:363-376.
16. Jorgensen WL, Tirado-Rives J. 1988. The OPLS potential functions for proteins-Energy minimization for crystals of cyclic peptides and crambin. J Am Chem Soc 110:1657-1666.
17. Knox JR, Moews PC, Escobar WA, Fink AL. 1993. A catalytically impaired class A β-lactamase: The 2 Å crystal structure and kinetics of the Bacillus licheniformis E166A mutant. Protein Eng 6:11-18.
18. Lamotte-Brasseur J, Dive G, Dideberg O, Charlier P, Frère JM, Ghuysen JM. 1991. Mechanism of acyl transfer by the class A serine β-lactamase of Streptomyces albus G. Biochem J 279:213-221.
19. Laws A, Page M. 1989. The effect of the carboxy group on the chemical and β-lactamase reactivity of β-lactam antibiotics. J Chem Soc Perkin Trans 11:1577-1581.
20. Lee B, Richards FM. 1971. The interpretation of protein structures: Estimation of static accessibility. J Mol Biol 55:379-400.
21. Lobkovsky E, Moews PC, Hansong L, Zao H, Frère JM, Knox JR. 1993. 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 USA 90:11257-11261.
22. Madura JD, Briggs JM, Wade RC, Davis ME, Luty BA, Ilin A, Antosiewicz J, Gilson MK, Bagheri B, Scott LR, McCammon JA. 1995. Electrostatics and diffusion of molecules in solution: Simulations with the University of Houston Brownian Dynamics program. Comp Phys Comm 92:57-95.
23. Massova I, Mobashery S. 1998. Kinship and diversification of bacterial penicillin-binding proteins and β-lactamases. Antimicrob Agents Chemother 42:1-17.
24. Matagne A, Dubus A, Galleni M, Frère JM. 1999. The β-lactamase cycle: A tale of selective pressure and bacterial ingenuity. Nat Prod Rep 16. Forthcoming.
25. Matagne A, Lamotte-Brasseur J, Dive G, Knox JR, Frère JM. 1993. 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 293:607-611.
26. Maveyraud L, Pratt RF, Samama JP. 1998. Crystal structure of an acylation transition-state analog of the TEM-1 β-lactamase - Mechanistic implications for class A β-lactamases. Biochemistry 37:2622-2628.
27. Maveyraud L, Saves I, Burlet-Schiltz O, Swaren P, Masson JM, Delaire M, Mourey L, Promé JC, Samama JP. 1996. Structural basis of extended spectrum TEM β-lactamases - Crystallographic, kinetic, and mass spectrometric investigations of enzyme mutants. J Biol Chem 271:10842-10849.
28. Moews PC, Knox JR, Dideberg O, Charlier P, Frère JM. 1990. β-Lactamase of Bacillus licheniformis 749/C at 2 Å resolution. Proteins Struct Funct Genet 7:156-171.
29. Pearlman D, Case DA, Caldwell JA, Ross WS, Cheathman TE, Ferguson DM, Seibel GL, Singh UC, Weiner PK, Kollman PA. 1995. AMBER 4.1. San Francisco: University of California San Francisco.
30. Raquet X, Lamotte-Brasseur J, Bouillenne F, Frère JM. 1997a. A disulfide bridge near the active site of carbapenem-hydrolyzing class A β-lactamases might explain their unusual substrate profile. Proteins Struct Funct Genet 27:47-58.
31. a calculations for class A β-lactamases: Methodological and mechanistic implications. Biophys J 73:2416-2426.
32. Strynadka NCJ, Adachi H, Jensen SE, Johns K, Sielecki A, Betzel C, Sutoh K, James MNJ. 1992. Molecular structure of the acyl-enzyme intermediate in β-lactam hydrolysis at 1.7 Å resolution. Nature 359:700-705.
33. Swaren P, Maveyraud L, Guillet V, Masson JM, Mourey L, Samama JP. 1995. Electrostatic analysis of TEM-1 β-lactamase: Effect of substrate binding, steep potential gradients, and consequences of site-directed mutations. Structure 3:603-613.
34. Varetto L, De Meester F, Monnaie D, Marchand-Brynaert J, Dive G, Jacob F, Frère JM. 1991. The importance of the negative charge of β-lactam compounds in the interactions with active-site serine DD-peptidases and β-lactamases. Biochem J 278:801-807.
35. Vijayakumar S, Ravishanker G, Pratt RF, Beveridge DL. 1995. Mechanism of acyl transfer by the class A serine β-lactamase of Streptomyces albus G. J Am Chem Soc 117:1722-1730.
36. Zawadzke LE, Chen CCH, Banerjee S, Li Z, Wäsch S, Kapadia G, Moult J, Herzberg O. 1996. Elimination of the hydrolytic water molecule in the class Aβ-lactamase mutant: Crystal structure and kinetics. Biochemistry 35:16475-16482.