A theoretical study on the activation of Ser70 in the acylation mechanism of cephalosporin antibiotics

Biophysical Chemistry

Volumn 114, Issue 2-3, 2005, Pages 103-113

  Ke, Yi Yu ^a   Lin, Thy Hou ^a  

^a NATIONAL TSING HUA UNIVERSITY   (Taiwan)

Author keywords

Acylation mechanism; Proton transfer; Quantum mechanics; Reaction mechanism; Transition states; lactamase

Indexed keywords

BETA LACTAMASE; CEPHALOSPORIN;

ACYLATION; ARTICLE; BACILLUS LICHENIFORMIS; CHEMICAL REACTION; CONTROLLED STUDY; ENERGY TRANSFER; ENZYME ACTIVATION; LIGAND BINDING; MATHEMATICAL COMPUTING; NONHUMAN; POLARIZATION; PRIORITY JOURNAL; PROTON TRANSPORT; QUANTUM CHEMISTRY; THEORETICAL STUDY; X RAY ANALYSIS;

BACILLUS LICHENIFORMIS;

EID: 14844345076     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bpc.2004.11.007     Document Type: Article

References (34)

1. S. Kovacevic, B.J. Weigel, M.B. Tobin, T.D. Ingolia, and J.R. Miller Cloning, characterization, and expression in Escherichia coli of the streptomyces clavuligerus gene encoding deacetoxycephalosporin C synthetase J. Bacteriol. 171 1989 754 760
2. J.L. Barredo, and J.F. Martin Genes directly involved in the biosynthesis of beta-lactam antibiotics Microbiologia 7 1991 1 12
3. T. Hashizume, M. Sanada, S. Nakagawa, and N. Tanaka Alteration in expression of Serratia marcescens porins associated with decreased outer membrane permeability J. Antimicrob. Chemother. 31 1993 21 28
4. J. Mitsuyama, R. Hiruma, A. Yamaguchi, and T. Sawai Identification of porins in outer membrane of Proteus, Morganella, and Providencia spp. and their role in outer membrane permeation of beta-lactams Antimicrob. Agents Chemother. 31 1987 379 384
5. F.P. Tally, G.J. Cuchural Jr., and M.H. Malamy Mechanisms of resistance and resistance transfer in anaerobic bacteria: factors influencing antimicrobial therapy Rev. Infect. Dis. 1 1984 260 269
6. H.C. Neu Contribution of beta-lactamases to bacterial resistance and mechanisms to inhibit beta-lactamases Am. J. Med. 79 1985 2 12
7. J.T. Smith, J.M. Hamilton-Miller, and R. Knox Bacterial resistance to penicillins and cephalosporins J. Pharm. Pharmacol. 21 1969 337 358
8. R.P. Ambler, A.F. Coulson, J.M. Frére, J.M. Ghuysen, B. Jaurin, B. Joris, R. Levesque, G. Tiraby, and S.G. Waley A standard numbering scheme for the class A beta-lactamases Biochem. J. 276 1991 269 270
9. J. Lamotte-Brasseur, G. Dive, O. Dideberg, P. Charlier, J.M. Frére, and J.M. Ghuysen Mechanism of acyl transfer by the class A serine β-lactamase of Streptomyces albus G Biochem. J. 279 1991 213
10. S. Wolfe, C.-K. Kim, and K. Yang Ab initio molecular orbital calculation on the neutral and methanolysis of azetidinones, including catalysis water, relationship to the mechanism of action of β-lactam antibiotics Can. J. Chem. 72 1994 1014 1032
11. N. Diaz, D. Suarez, T.L. Sordo, and K.M. Merz Jr. Acylation of Class A beta-lactamase by penicillins: a theoretical examination of the role of serine 130 and the -lactam carboxylate group J. Phys. Chem., B 105 2001 11302 11313
12. N.C. Strynadka, R. Martin, S.E. Jensen, M. Gold, and J.B. Jones Structure-based design of a potent transition state analogue for TEM-1 beta-lactamase Nat. Struct. Biol. 3 1996 688 695
13. N.C. Strynadka, H. Adachi, S.E. Jensen, K. Johns, A. Sielecki, C. Betzel, K. Sutoh, and M.N. James Molecular structure of the acyl-enzyme intermediate in beta-lactam hydrolysis at 1.7 A resolution Nature 359 1992 700 705
14. Y.C. Leung, C.V. Robinson, R.T. Aplin, and S.G. Waley Site-directed mutagenesis of beta-lactamase I: role of Glu-166 Biochem. J. 229 1994 671 678
15. G. Minasov, X. Wang, and B.K. Shoichet An ultrahigh resolution structure of TEM-1 -lactamase suggests a role for Glu166 as the general base in acylation J. Am. Chem. Soc. 124 2002 5333
16. J. Pitarch, J-.L. Pascual-Ahuir, E. Silla, and I. Tuñón A quantum mechanics/molecular mechanism study of the acylation reaction of TEM1 β-lactamase and penicillance J. Chem. Soc., Perkin Trans. 2 2000 761 767
17. J.C. Hermann, L. Ridder, A.J. Mulholland, and H.-D. Holtje Identification of Glu166 as the general base in the acylation reaction of class A -lactamases through QM/MM modeling J. Am. Chem. Soc. 125 2003 9590 9591
18. C. Damblon, X. Raquet, L.Y. Lian, J. Lamotte-Brasseur, E. Fonze, P. Charlier, G.C. Roberts, and J.M. Frere The catalytic mechanism of beta-lactamases: NMR titration of an active-site lysine residue of the TEM-1 enzyme Proc. Natl. Acad. Sci. U. S. A. 93 1996 1747 1752
19. P.J. GoodFord A computational procedure for determining energetically favorable binding sites on biologically important macromolecules J. Med. Chem. 28 1985 849 857
20. E. Fonzé, M. Vanhove, G. Dive, E. Sauvage, J.M. Frère, and P. Charlier Crystal structures of the Bacillus licheniformis BS3 class A -lactamase and of the acyl-enzyme adduct formed with cefoxitin Biochemistry 41 2002 1877 1885
21. R.A. Sayle, and E.J. Milner-Whilte RASMOL: biomolecular graphics for all Trends Biochem. Sci. 20 1995 374 382
22. Insight II Program, Biosym/MSI, San Diego, CA, (1995).
23. Sybyl, version 6.8, Tripos: St. Louis, MO.
24. J. Gasteiger, and M. Marsili Iterative partial equalization of orbital electronegativity-a rapid access to atomic charges Tetrahedron 36 1980 3219 3228
25. T.A. Halgren, R.B. Murphy, R.A. Friesner, H.S. Beard, L.L. Frye, W.T. Pollard, and J.L. Banks Glide: a new approach for rapid, accurate docking and scoring: 2. Enrichment factors in database screening J. Med. Chem. 2004 (ASAP Article)
26. Gaussian 98., Revision A.6., M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman, V.G. Zakrzewski, J.A. Montgomery, R.E. Stratmann Jr., J.C. Burant, S. Dapprich, J.M. Millam, A.D. Daniels, K.N. Kudin, M.C. Strain, O. Farkas, J. Tomasi, V. Barone, M. Cossi, R. Cammi, B. Mennucci, C. Pomelli, C. Adamo, S. Clifford, J. Ochterski, G.A. Petersson, P.Y. Ayala, Q. Cui, K. Morokuma, D.K. Malick, A.D. Rabuck, K. Raghavachari, J.B. Foresman, J. Cioslowski, J.V. Ortiz, B.B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. Gomperts, R.L. Martin, D.J. Fox, T. Keith, M.A. Al-Laham, C.Y. Peng, A. Nanayakkara, C. Gonzalez, M. Challacombe, P.M.W. Gill, B. Johnson, W. Chen, M.W. Wong, J.L. Andres, C. Gonzalez, M. Head-Gordon, E.S. Replogle, J.A. Pople, Gaussian, Pittsburgh, PA, 1998.
27. N. Tsuda, M. Hata, T. Hoshino, and M. Tsuda Ab initio study of the role of lysine 16 for the molecular switching mechanism of Ras protein p21 Biophys. J. 32 1999 3287 3292
28. M. Hata, Y. Fujii, M. Ishii, T. Hoshino, and M. Tsuda Catalytic mechanism of class A beta-lactamase: I. The role of Glu166 and Serl30 in the deacylation reaction Chem. Pharm. Bull. (Tokyo) 48 2000 447 453
29. C. Gonzalez, and H.B. Schlegel An improved algorithm for reaction path following J. Chem. Phys. 90 1989 2154
30. S. Miertus, and J. Tomasi Approximate evaluations of the electrostatic free energy and internal energy changes in solution processes Chem. Phys. 65 1982 239 245
31. a calculations for Class A β-lactamase: methodological and mechanistic implications J. Biophys. 73 1997 2416 2426
32. a Calculation for class A β-lactamase: influence of substrate binding Protein Sci. 8 1999 404 409
33. a, MM, and QM studies of mechanisms of beta-lactamases and penicillin-binding proteins: acylation step J. Comput. Chem. 23 2002 1559 1576
34. R.M. Gibson, H. Christensen, and S.G. Waley Site-directed mutagenesis of beta-lactamase I single and double mutants of Glu-166 and Lys-73 Biochem. J. 272 1990 613 619