Lysine carboxylation in proteins: OXA-10 β-lactamase

Proteins: Structure, Function and Genetics

Volumn 61, Issue 2, 2005, Pages 246-257

  Li, Jie ^a   Cross, Jason B ^a,d   Vreven, Thom ^c   Meroueh, Samy O ^b   Mobashery, Shahriar ^b   Schlegel, H Bernhard ^a,c  

^a WAYNE STATE UNIVERSITY   (United States)

^b UNIVERSITY OF NOTRE DAME   (United States)

^c GAUSSIAN INC   (United States)

^d Affinium Pharmaceuticals   (United States)

Author keywords

Carboxylation mechanism; Class D lactamase; Density functional calculations; ONIOM QM MM method; Penicillin binding proteins

Indexed keywords

AMINO ACID; BETA LACTAMASE; LYSINE; PENICILLIN BINDING PROTEIN;

ARTICLE; CARBOXYLATION; CATALYSIS; COMPLEX FORMATION; ENERGY; ENTHALPY; ENZYME ACTIVE SITE; ENZYME ACTIVITY; GAS; MOLECULAR MODEL; PHYSICAL PHASE; PRIORITY JOURNAL; QUANTUM MECHANICS; STEREOCHEMISTRY;

BETA-LACTAMASES; COMPUTATIONAL BIOLOGY; LYSINE; METHYLAMINES; MOLECULAR STRUCTURE; PROTEIN PROCESSING, POST-TRANSLATIONAL;

EID: 26444575837     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20596     Document Type: Article

References (84)

1. Jabri E, Carr MB, Hausinger RP, Karplus PA. The crystal structure of urease from Klebsiella aerogenes. Science 1995; 268(5213):998-1004.
2. Benning MM, Kuo JM, Raushel FM, Holden HM. Three-dimensional structure of the binuclear metal center of phosphotriesterase. Biochemistry 1995;34(25):7973-7978.
3. Shibata N, Inoue T, Fukuhara K, Nagara Y, Kitagawa R, Harada S, Kasai N, Uemura K, Kato K, Yokota A, Kai Y. Orderly disposition of heterogeneous small subunits in D-ribulose-1,5-bisphosphate carboxylase/oxygenase from spinach. J Biol Chem 1996;271(43):26449-26452.
4. Maveyraud L, Golemi D, Kotra LP, Tranier S, Vakulenko S, Mobashery S, Samama JP. Insights into class D beta-lactamases are revealed by the crystal structure of the OXA10 enzyme from Pseudomonas aeruginosa. Structure Fold Des 2000;8(12):1289-1298.
5. Golemi-Kotra D, Cha JY, Meroueh SO, Vakulenko SB, Mobashery S. Resistance to beta-lactam antibiotics and its mediation by the sensor domain of the transmembrane BlaR signaling pathway in Staphylococcus aureus. J Biol Chem 2003;278(20):18419-18425.
6. Sun T, Nukaga M, Mayama K, Braswell EH, Knox JR. Comparison of beta-lactamases of classes A and D: 1.5-Å crystallographic structure of the class D OXA-1 oxacillinase. Prot Sci 2003;12(1):82-91.
7. Birck C, Cha JY, Cross J, Schulze-Briese C, Meroueh SO, Schlegel HB, Mobashery S, Samama JP. X-ray crystal structure of the acylated beta-lactam sensor domain of BlaR1 from Staphylococcus aureus and the mechanism of receptor activation for signal transduction. J Am Chem Soc 2004;126:13945-13947.
8. Bush K, Mobashery S. How beta-lactamases have driven pharmaceutical drug discovery. From mechanistic knowledge to clinical circumvention. Adv Exp Med Biol 1998;456:71-98.
9. Kotra LP, Samama JP, Mobashery S. Structural aspects of β-lactamase evolution. In: Lewis A, Salyers AA, Haber H, Wax RG, editors. Bacterial resistance to antimicrobials, mechanisms, genetics, medical practice and public health. New York: Marcel Dekker, Inc.; 2002. p 123-159.
10. Lorimer GH, Badger MR, Andrews J. Rubisco carboxylation of lysine. Biochemistry 1976;15:529-536.
11. Shim H, Raushel FM. Self-assembly of the binuclear metal center of phosphotriesterase. Biochemistry 2000;39(25):7357-7364.
12. Thoden JB, Phillips GN, Jr., Neal TM, Raushel FM, Holden HM. Molecular structure of dihydroorotase: a paradigm for catalysis through the use of a binuclear metal center. Biochemistry 2001; 40(24):6989-6997.
13. Morollo AA, Petsko GA, Ringe D. Structure of a Michaelis complex analogue: propionate binds in the substrate carboxylate site of alanine racemase. Biochemistry 1999;38(11):3293-3301.
14. Golemi-Kotra D, Meroueh SO, Kim C, Vakulenko SB, Bulychev A, Stemmler AJ, Stemmler TL, Mobashery S. The importance of a critical protonation state and the fate of the catalytic steps in class A beta-lactamases and penicillin-binding proteins. J Biol Chem 2004;279(33):34665-34673.
15. Oliva M, Dideberg O, Field MJ. Understanding the acylation mechanisms of active-site serine penicillin-recognizing proteins: A molecular dynamics simulation study. Proteins 2003;53(1):88-100.
16. Golemi D, Maveyraud L, Vakulenko S, Samama JP, Mobashery S. Critical involvement of a carbamylated lysine in catalytic function of class D beta-lactamases. Proc Natl Acad Sci USA 2001;98(25):14280-14285.
17. Tien M, Berlett BS, Levine RL, Chock PB, Stadtman ER. Peroxynitrite-mediated modification of proteins at physiological carbon dioxide concentration: pH dependence of carbonyl formation, tyrosine nitration, and methionine oxidation. Proc Natl Acad Sci USA 1999;96(14):7809-7814.
18. Paetzel M, Danel F, de Castro L, Mosimann SC, Page MG, Strynadka NC. Crystal structure of the class D beta-lactamase OXA-10. Nat Struct Biol 2000;7(10):918-925.
19. Danel F, Frere JM, Livermore DM. Evidence of dimerisation among class D beta-lactamases: kinetics of OXA-14 beta-lactamase. Biochim Biophys Acta 2001;1546(1):132-142.
20. Gao J. Methods and applications of combined quantum mechanical and molecular mechanical potentials. In: Lipkowitz KB, Boyd DB, editors. Reviews in computational chemistry, vol. 7. New York: VCH; 1996. p 119-185.
21. Froese RDJ, Morokuma K. Hybrid methods. In: Schleyer PvR, Allinger NL, Kollman PA, Clark T, Schaefer III HF, Gasteiger J, Schreiner PR, editors. Encyclopedia of computational chemistry, vol. 2. Chichester: Wiley; 1998. p 1244-1257.
22. Monard G, Merz KM. Combined quantum mechanical/molecular mechanical methodologies applied to biomolecular systems. Acc Chem Res 1999;32(10):904-911.
23. Torrent M, Vreven T, Musaev DG, Morokuma K, Farkas O, Schlegel HB. Effects of the protein environment on the structure and energetics of active sites of metalloenzymes. ONIOM study of methane monooxygenase and ribonucleotide reductase. J Am Chem Soc 2002;124(2):192-193.
24. Maseras F, Morokuma K. Imomm - a new integrated ab initio + molecular mechanics geometry optimization scheme of equilibrium structures and transition states. J Comput Chem 1995;16(9): 1170-1179.
25. Dapprich S, Komaromi I, Byun KS, Morokuma K, Frisch MJ. A new ONIOM implementation in Gaussian98. Part I. The calculation of energies, gradients, vibrational frequencies and electric field derivatives. J Mol Struct-THEOCHEM 1999;462:1-21.
26. 1 excitation in bacteriorhodopsin with the ONIOM(MO:MM) hybrid method. Theor Chem Acc 2003;109:125-132.
27. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery JA, Vreven T, Kudin KN, Burant JC, Millam JM, Iyengar S, Tomasi J, Barone V, Mennucci B, Cossi M, Scalmani G, Rega N, Petersson GA, Ehara M, Toyota K, Hada M, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Kitao O, Nakai H, Honda Y, Nakatsuji H, Li X, Knox JE, Hratchian HP, Cross JB, Adamo C, Jaramillo J, Cammi R, Pomelli C, Gomperts R, Stratmann RE, Ochterski J, Ayala PY, Morokuma K, Salvador P, Dannenberg JJ, Zakrzewski VG, Dapprich S, Daniels AD, Strain MC, Farkas Ö, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Ortiz JV, Cui Q, Baboul AG, Clifford S, Cioslowski J, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Andres JL, Gonzalez C, Head-Gordon M, Replogle ES, Pople JA. Gaussian 01, Development Version (Revision B.02). Revision B.02. Pittsburgh, PA: Gaussian, Inc.; 2002.
28. Roothan CCJ. New developments in molecular orbital theory. Rev Mod Phys 1951;23:69-89.
29. Moller C, Plesset MS. Note on the approximation treatment for many-electron system. Phys Rev 1934;46:618-622.
30. Pople JA, Seeger R, Krishnan R. Variational configuration interaction methods and comparison with perturbation theory. Int J Quantum Chem 1977;11:149-163.
31. Becke AD. Density-functional exchange-energy approximation with correct asymptotic behavior. Phys Rev A 1988;38(6):3098-3100.
32. Becke AD. Density-functional thermochemistry. 3. The role of exact exchange. J Chem Phys 1993;98(7):5648-5652.
33. Lee CT, Yang WT, Parr RG. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron-density. Phys Rev B 1988;37:785-789.
34. Ditchfield R, Hehre WJ, Pople JA. Self-consistent molecular-orbital methods. IX. Extended Gaussian-type basis for molecular-orbital studies of organic molecules. J Chem Phys 1971;54:724-728.
35. Hariharan PC, Pople JA. Influence of polarization functions on MO hydrogenation energies. Theor Chim Acta 1973;28:213-222.
36. Mclean AD, Chandler GS. Contracted Gaussian basis sets for molecular calculations. I. Second row atoms, Z = 11-18. J Chem Phys 1980;72:5639-5648.
37. Krishnan R, Binkely JS, Seeger R, Pople JA. Self-consistent molecular orbital methods. XX. A basis set for correlated wave functions. J Chem Phys 1980;72:650-654.
38. Montgomery JA, Ochterski J, Petersson GA. A complete basis set model chemistry. IV. An improved atomic pair natural orbital method. J Chem Phys 1994;101:5900-5909.
39. Pople JA, Head-Gordon M, Raghavachari K. Quadratic configuration- interaction - a general technique for determining electron correlation energies. J Chem Phys 1987;87(10):5968-5975.
40. Barone V, Cossi M. Quantum calculation of molecular energies and energy gradients in solution by a conductor solvent model. J Phys Chem A 1998;102(11):1995-2001.
41. Tripos I. Sybyl 6.7. 1699 Sourth Hanley Rd., St. Louis, Missouri, 63144, USA.
42. Case DA, Pearlman DA, Caldwell JW, Cheatham III TE, Ross WS, Simmerling CL, Darden TA, Merz KM, Seibel GL, Cheng AL. AMBER 6. San Francisco: University of California; 1999.
43. Wang J, Cieplak P, Kollman PA. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J Comput Chem 2000;21:1049-1074.
44. Bayly CI, Cieplak P, Cornell WD, Kollman PA. A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges - the RESP model. J Chem Phys 1993;97: 10269-10280.
45. Darden T, York D, Pedersen L. Particle Mesh Ewald - an N.Log(N) method for Ewald sums in large systems. J Chem Phys 1993;98(12): 10089-10092.
46. Ryckaert J-P, Ciccotti G, Berendsen HJC. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 1977;23(3):327-341.
47. Vreven T, Morokuma K, Farkas O, Schlegel HB, Frisch MJ. Geometry optimization with QM/MM, ONIOM, and other combined methods. I. Microiterations and constraints. J Comput Chem 2003;24:760-769.
48. Kollman PA, Dixon R, Cornell WD, Fox T, Chipot C, Pohorille A. The development/application of a minimalist molecular mechanics force field using a combination of ab initio calculations and experimental data. In: Wilkinson A, Weiner P, van Gunsteren W, editors. Computation simulations of biomolecular systems, vol. 3. New York: Elsevier; 1997. p 83-96.
49. Dell'Amico DB, Calderazzo F, Labella L, Marchetti F, Pampaloni G. Converting carbon dioxide into carbamato derivatives. Chem Rev 2003;103(10):3857-3897.
50. Camacho F, Sanchez S, Pacheco R. Absorption of carbon dioxide at high partial pressures in 1-amino-2-propanol aqueous solution. Considerations of thermal effects. Ind Eng Chem Res 1997;36(10): 4358-4364.
51. Suda T, Iwaki T, Mimura T. Facile determination of dissolved species in CO2-amine-H2O system by NMR spectroscopy. Chem Lett 1996(9):777-778.
52. Xu S, Wang YW, Otto FD, Mather AE. Kinetics of the reaction of carbon dioxide with 2-amino-2-methyl-1-propanol solutions. Chem Eng Sci 1996;51(6):841-850.
53. Saha AK, Bandyopadhyay SS, Biswas AK. Kinetics of absorption of CO2 into aqueous-solutions of 2-amino-2-methyl-1-propanol. Chem Eng Sci 1995;50(22):3587-3598.
54. Hagewiesche DP, Ashour SS, Alghawas HA, Sandall OC. Absorption of carbon dioxide into aqueous blends of monoethanolamine and N-methyldiethanolamine. Chem Eng Sci 1995;50(7):1071-1079.
55. Rinker EB, Ashour SS, Sandall OC. Kinetics and modelling of carbon dioxide absorption into aqueous solutions of N-methyldiethanolamine. Chem Eng Sci 1995;50(5):755-768.
56. 2-biotin fixation. J Chem Soc Perkin Trans 2 1993(3):521-523.
57. 2 absorption in tertiary amines. Chem Eng Sci 1991;46(11):2927-2931.
58. Andres J, Bohm S, Moliner V, Silla E, Tunon I. A theoretical study of stationary structures for the addition of azide anion to tetrofuranosides: modeling the kinetic and thermodynamic controls by solvent effects. J Phys Chem 1994;98(28):6955-6960.
59. 2 and alkanolamines. Ind Eng Chem Res 2004;43(13):3413-3418.
60. Andres J, Moliner V, Krechl J, Silla E. A theoretical study of the effect of basis sets on stationary structures for the addition of carbon-dioxide to methylamine: a relation among geometries, energy status, and electronic structures. Int J Quantum Chem 1993;45(5):433-444.
61. 2 with dimethylamine. J Mol Struct 1997;404(1-2):105- 111.
62. Williams IH. Theoretical modeling of specific solvation effects upon carbonyl addition. J Am Chem Soc 1987;109(21):6299-6307.
63. Lledos A, Bertran J. Lactam-lactim tautomeric interconversion mechanism of 2-pyridone in aqueous solution. Tetra Lett 1981; 22(8):775-778.
64. Lledos A, Bertran J, Ventura ON. Water-chain intervention in the ketonization of vinyl alcohol. An ab initio study. Int J Quantum Chem 1986;30(4):467-477.
65. Ventura ON, Lledos A, Bonaccorsi R, Bertran J, Tomasi J. Theoretical study of reaction mechanisms for the ketonization of vinyl alcohol in gas phase and aqueous solution. Theor Chem Acta 1987;72(3):175-195.
66. 2 additions to ethylene. J Comput Chem 1987;8(4):481-488.
67. 2=C-NH) by water and water dimer. J Am Chem Soc 1983;105(12):3811-3815.
68. Nguyen MT, Hegarty AF. Molecular orbital study on the hydrolysis of ketene by water dimer: beta-carbon vs oxygen protonation. J Am Chem Soc 1984;106(6):1552-1557.
69. Antonczak S, Ruizlopez MF, Rivail JL. Ab initio analysis of water-assisted reaction mechanisms in amide hydrolysis. J Am Chem Soc 1994;116(9):3912-3921.
70. Pocker Y, Bjorkquist DW. Stopped-flow studies of carbon dioxide hydration and bicarbonate dehydration in water and water-d2. Acid-base and metal ion catalysis. J Am Chem Soc 1977;99(20): 6537-6543.
71. Palmer DA, Vaneldik R. The chemistry of metal carbonato and carbon-dioxide complexes. Chem Rev 1983;83(6):651-731.
72. Williams IH, Spangler D, Femec DA, Maggiora GM, Schowen RL. Theoretical models for transition-state structure and catalysis in carbonyl addition. J Am Chem Soc 1980;102(21):6619-6621.
73. Williams IH, Spangler D, Femec DA, Maggiora GM, Schowen RL. Theoretical models for solvation and catalysis in carbonyl addition. J Am Chem Soc 1983;105(1):31-40.
74. Nguyen MT, Ha TK. A theoretical study of the formation of carbonic acid from the hydration of carbon dioxide: a case of active solvent catalysis. J Am Chem Soc 1984;106(3):599-602.
75. Ruelle P. Ab initio study of the unimolecular pyrolysis mechanisms of formic-acid: additional comments based on refined calculations. J Am Chem Soc 1987;109(6):1722-1725.
76. Ruelle P, Kesselring UW, Namtran H. Ab initio quantum-chemical study of the unimolecular pyrolysis mechanisms of formic acid. J Am Chem Soc 1986;108(3):371-375.
77. 3 - the formation of (I) carbamic acid, (II) urea, and (III) carbonic-acid. J Comput Chem 1986;7(3):283-293.
78. Ventura ON, Coitino EL, Lledos A, Bertran J. Analysis of the gas-phase addition of water to formaldehyde: a semiempirical and ab initio study of bifunctional catalysis by H2O. J Comput Chem 1992;13(9):1037-1046.
79. Caplow M. Kinetics of carbamate formation and breakdown. J Am Chem Soc 1968;90:6795-6803.
80. Danckwerts PV, Sharma MM. The absorption of carbon dioxide into solutions of alkalis and amines. Ind Eng 1966;10:CE244.
81. Hikita H, Asai S, Ishidkawa H, Honda M. The kinetics of reactions of carbon dioxide with monoethanolamine, diethanolamine and triethanolamine by a rapid mixing method. Chem Eng J 1977;13: 7-12.
82. 2 into chemically reactive solutions at high temperatures. Chem Eng Sci 1971;26(9):1381-1390.
83. Nunge RJ, WGill WN. Gas-liquid kinetics: the absorption of carbon dioxide in diethanolamine. AIChE J 1963;9:469-474.
84. Maveyraud L, Golemi-Kotra D, Ishiwata A, Meroueh O, Mobashery S, Samama JP. High-resolution X-ray structure of an acyl-enzyme species for the class D OXA-10 beta-lactamase. J Am Chem Soc 2002;124(11):2461-2465.