1
|
Judge A, Hu L, Sankaran B, Van Riper J, Venkataram Prasad BV, Palzkill T. Mapping the determinants of catalysis and substrate specificity of the antibiotic resistance enzyme CTX-M β-lactamase. Commun Biol 2023; 6:35. [PMID: 36635385 PMCID: PMC9837174 DOI: 10.1038/s42003-023-04422-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 01/04/2023] [Indexed: 01/14/2023] Open
Abstract
CTX-M β-lactamases are prevalent antibiotic resistance enzymes and are notable for their ability to rapidly hydrolyze the extended-spectrum cephalosporin, cefotaxime. We hypothesized that the active site sequence requirements of CTX-M-mediated hydrolysis differ between classes of β-lactam antibiotics. Accordingly, we use codon randomization, antibiotic selection, and deep sequencing to determine the CTX-M active-site residues required for hydrolysis of cefotaxime and the penicillin, ampicillin. The study reveals positions required for hydrolysis of all β-lactams, as well as residues controlling substrate specificity. Further, CTX-M enzymes poorly hydrolyze the extended-spectrum cephalosporin, ceftazidime. We further show that the sequence requirements for ceftazidime hydrolysis follow those of cefotaxime, with the exception that key active-site omega loop residues are not required, and may be detrimental, for ceftazidime hydrolysis. These results provide insights into cephalosporin hydrolysis and demonstrate that changes to the active-site omega loop are likely required for the evolution of CTX-M-mediated ceftazidime resistance.
Collapse
Affiliation(s)
- Allison Judge
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Liya Hu
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Banumathi Sankaran
- Department of Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Justin Van Riper
- Graduate Program in Chemical, Physical, and Structural Biology, Baylor College of Medicine, Houston, TX, USA
| | - B V Venkataram Prasad
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Timothy Palzkill
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA.
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA.
| |
Collapse
|
2
|
Knox R, Lento C, Wilson DJ. Mapping Conformational Dynamics to Individual Steps in the TEM-1 β-Lactamase Catalytic Mechanism. J Mol Biol 2018; 430:3311-3322. [PMID: 29964048 DOI: 10.1016/j.jmb.2018.06.045] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 06/14/2018] [Accepted: 06/22/2018] [Indexed: 10/28/2022]
Abstract
Conformational dynamics are increasingly recognized as being essential for enzyme function. However, there is virtually no direct experimental evidence to support the notion that individual dynamic modes are required for specific catalytic processes, apart from the initial step of substrate binding. In this work, we use a unique approach based on millisecond hydrogen-deuterium exchange mass spectrometry to identify dynamic modes linked to individual catalytic processes in the antibiotic resistance enzyme TEM-1 β-lactamase. Using a "good" substrate (ampicillin), a poorly hydrolyzed substrate (cephalexin) and a covalent inhibitor (clavulanate), we are able to isolate dynamic modes that are specifically linked to substrate binding, productive lactam ring hydrolysis and deacylation. These discoveries are ultimately translated into specific targets for allosteric TEM-1 inhibitor development.
Collapse
Affiliation(s)
- Ruth Knox
- Department of Chemistry, York University, Toronto, Canada M3J 1P3
| | - Cristina Lento
- Department of Chemistry, York University, Toronto, Canada M3J 1P3
| | - Derek J Wilson
- Department of Chemistry, York University, Toronto, Canada M3J 1P3; Center for Research in Mass Spectrometry, York University, Toronto, Canada M3J 1P3.
| |
Collapse
|
3
|
Yang J, Li Q, Bian L. Spectroscopic analysis and docking simulation on the recognition and binding of TEM-1 β-lactamase with β-lactam antibiotics. Exp Ther Med 2017; 14:3288-3298. [PMID: 28912880 DOI: 10.3892/etm.2017.4853] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Accepted: 03/17/2017] [Indexed: 11/05/2022] Open
Abstract
The interaction between TEM-1 β-lactamase and antibiotics is very important in the hydrolysis of antibiotics. In the present study, the recognition and binding of TEM-1 β-lactamase with three β-lactam antibiotics, including penicillin G, cefalexin and cefoxitin, was investigated by fluorescence and ultraviolet-visible absorption spectra in combination with molecular docking in the temperature range of 278-288 K and under simulated physiological conditions. The results demonstrated that the fluorescence emissions of TEM-1 β-lactamase were extinguished by static quenching and the energy of TEM-1 β-lactamase was transferred in a non-radioactive manner. The binding of TEM-1 β-lactamase with the three antibiotics was a spontaneously exothermic process, with binding constants of 1.41×107, 7.81×106 and 5.43×104 at 278 K. Furthermore, binding was driven by enthalpy change and the binding forces between them were mainly hydrogen bonding and Van der Waals forces. A TEM-1 β-lactamase only bound with one antibiotic at a time and the binding capacity between them was closely associated with the functional groups and flexibility in the antibiotics. In addition, a conformational change occurred in the TEM-1 β-lactamases when they bound with the three antibiotics and TEM-1 β-lactamase-antibiotic complexes were formed. The present study provided an insight into the recognition and binding of TEM-1 β-lactamase with β-lactam antibiotics, which may be helpful for designing a novel substrate for TEM-1 β-lactamase and developing novel antibiotics that are resistant to the enzyme.
Collapse
Affiliation(s)
- Jianting Yang
- Department of Traditional Chinese Medicine, College of Life Science, Northwest University, Xi'an, Shaanxi 710069, P.R. China.,Drug and Equipment Department, Weapon Industry 521 Hospital, Xi'an, Shaanxi 710065, P.R. China
| | - Qian Li
- Department of Traditional Chinese Medicine, College of Life Science, Northwest University, Xi'an, Shaanxi 710069, P.R. China
| | - Liujiao Bian
- Department of Traditional Chinese Medicine, College of Life Science, Northwest University, Xi'an, Shaanxi 710069, P.R. China
| |
Collapse
|
4
|
Meneksedag D, Dogan A, Kanlikilicer P, Ozkirimli E. Communication between the active site and the allosteric site in class A beta-lactamases. Comput Biol Chem 2013; 43:1-10. [DOI: 10.1016/j.compbiolchem.2012.12.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Revised: 11/22/2012] [Accepted: 12/03/2012] [Indexed: 11/16/2022]
|
5
|
Antunes NT, Frase H, Toth M, Mobashery S, Vakulenko SB. Resistance to the third-generation cephalosporin ceftazidime by a deacylation-deficient mutant of the TEM β-lactamase by the uncommon covalent-trapping mechanism. Biochemistry 2011; 50:6387-95. [PMID: 21696166 DOI: 10.1021/bi200403e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Glu166Arg/Met182Thr mutant of Escherichia coli TEM(pTZ19-3) β-lactamase produces a 128-fold increase in the level of resistance to the antibiotic ceftazidime in comparison to that of the parental wild-type enzyme. The single Glu166Arg mutation resulted in a dramatic decrease in both the level of enzyme expression in bacteria and the resistance to penicillins, with a concomitant 4-fold increase in the resistance to ceftazidime, a third-generation cephalosporin. Introduction of the second amino acid substitution, Met182Thr, restored enzyme expression to a level comparable to that of the wild-type enzyme and resulted in an additional 32-fold increase in the minimal inhibitory concentration of ceftazidime to 64 μg/mL. The double mutant formed a stable covalent complex with ceftazidime that remained intact for the entire duration of the monitoring, which exceeded a time period of 40 bacterial generations. Compared to those of the wild-type enzyme, the affinity of the TEM(pTZ19-3) Glu166Arg/Met182Thr mutant for ceftazidime increased by at least 110-fold and the acylation rate constant was augmented by at least 16-fold. The collective experimental data and computer modeling indicate that the deacylation-deficient Glu166Arg/Met182Thr mutant of TEM(pTZ19-3) produces resistance to the third-generation cephalosporin ceftazidime by an uncommon covalent-trapping mechanism. This is the first documentation of such a mechanism by a class A β-lactamase in a manifestation of resistance.
Collapse
Affiliation(s)
- Nuno T Antunes
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | | | | | | | | |
Collapse
|
6
|
Brown NG, Shanker S, Prasad BVV, Palzkill T. Structural and biochemical evidence that a TEM-1 beta-lactamase N170G active site mutant acts via substrate-assisted catalysis. J Biol Chem 2009; 284:33703-12. [PMID: 19812041 DOI: 10.1074/jbc.m109.053819] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
TEM-1 beta-lactamase is the most common plasmid-encoded beta-lactamase in Gram-negative bacteria and is a model class A enzyme. The active site of class A beta-lactamases share several conserved residues including Ser(70), Glu(166), and Asn(170) that coordinate a hydrolytic water involved in deacylation. Unlike Ser(70) and Glu(166), the functional significance of residue Asn(170) is not well understood even though it forms hydrogen bonds with both Glu(166) and the hydrolytic water. The goal of this study was to examine the importance of Asn(170) for catalysis and substrate specificity of beta-lactam antibiotic hydrolysis. The codon for position 170 was randomized to create a library containing all 20 possible amino acids. The random library was introduced into Escherichia coli, and functional clones were selected on agar plates containing ampicillin. DNA sequencing of the functional clones revealed that only asparagine (wild type) and glycine at this position are consistent with wild-type function. The determination of kinetic parameters for several substrates revealed that the N170G mutant is very efficient at hydrolyzing substrates that contain a primary amine in the antibiotic R-group that would be close to the Asn(170) side chain in the acyl-intermediate. In addition, the x-ray structure of the N170G enzyme indicated that the position of an active site water important for deacylation is altered compared with the wild-type enzyme. Taken together, the results suggest the N170G TEM-1 enzyme hydrolyzes ampicillin efficiently because of substrate-assisted catalysis where the primary amine of the ampicillin R-group positions the hydrolytic water and allows for efficient deacylation.
Collapse
Affiliation(s)
- Nicholas G Brown
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | | | | | | |
Collapse
|
7
|
Walsh AM, Mustafi D, Makinen MW, Lee RC. A surfactant copolymer facilitates functional recovery of heat-denatured lysozyme. Ann N Y Acad Sci 2006; 1066:321-7. [PMID: 16533935 DOI: 10.1196/annals.1363.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The triblock copolymer poloxamer 188 is a non-cytotoxic, nonionic surfactant with both hydrophobic and hydrophilic domains. We show that P188 is able to facilitate the recovery of catalytic activity of heat-denatured lysozyme in dilute solution at low molar ratios of P188:enzyme. Heat-denatured enzyme retained 55% of native activity. After treatment with P188, the enzyme's activity was 85% of native. Because of the low molar ratios used and the non-cytotoxic nature of the compound, P188 may be of potential use in burn therapy.
Collapse
Affiliation(s)
- Alexandra M Walsh
- Department of Surgery, University of Chicago Hospitals, MC 6035, 5841 S. Maryland Ave., Chicago, IL 60637, USA
| | | | | | | |
Collapse
|
8
|
Clark RL, Johnston BF, Suckling CJ, Mackay SP. A modelling study of a non-concerted hydrolytic cycloaddition reaction by the catalytic antibody H11. Bioorg Med Chem 2006; 14:2674-83. [PMID: 16378728 DOI: 10.1016/j.bmc.2005.11.042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2005] [Revised: 11/23/2005] [Accepted: 11/28/2005] [Indexed: 11/21/2022]
Abstract
H11 is the first antibody reported to have dual activity as a non-concerted, Diels-Alderase and hydrolytic catalyst. It was previously shown to catalyse the cycloaddition of acetoxybutadiene 1a to N-alkyl maleimides 2 to afford hydroxy-substituted bicyclic adducts 3 with a 30% ee of a major isomer. To better understand this mechanism and the partial stereospecificity, a homology model of H11 was constructed and used in docking studies to evaluate potential antibody-ligand complexes. The model suggested the hydrolytic nature of H11 was due to Glu 95H acting as a catalytic base, and evaluation of the shape complementarity of the proposed antibody-ligand complexes confirmed at a semi-quantitative level the observation that the major enantiomer is produced in a 30% ee.
Collapse
Affiliation(s)
- Rachel L Clark
- Department of Pharmaceutical Sciences, University of Strathclyde, Glasgow G4 0NR, UK
| | | | | | | |
Collapse
|
9
|
Roccatano D, Sbardella G, Aschi M, Amicosante G, Bossa C, Di Nola A, Mazza F. Dynamical aspects of TEM-1 beta-lactamase probed by molecular dynamics. J Comput Aided Mol Des 2005; 19:329-40. [PMID: 16184435 DOI: 10.1007/s10822-005-7003-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2005] [Accepted: 05/09/2005] [Indexed: 11/24/2022]
Abstract
The dynamical aspects of the fully hydrated TEM-1 beta-lactamase have been determined by a 5 ns Molecular Dynamics simulation. Starting from the crystallographic coordinates, the protein shows a relaxation in water with an overall root mean square deviation from the crystal structure increasing up to 0.17 nm, within the first nanosecond. Then a plateau is reached and the molecule fluctuates around an equilibrium conformation. The results obtained in the first nanosecond are in agreement with those of a previous simulation (Diaz et al., J. Am. Chem. Soc., (2003) 125, 672-684). The successive equilibrium conformation in solution shows an increased mobility characterized by the following aspects. A flap-like translational motion anchors the omega-loop to the body of the enzyme. A relevant part of the backbone dynamics implies a rotational motion of one domain relative to the other. The water molecules in the active site can exchange with different residence times. The H-bonding networks formed by the catalytic residues are frequently interrupted by water molecules that could favour proton transfer reactions. An additional simulation, where the aspartyl dyad D214-D233 was considered fully deprotonated, shows that the active site is destabilized.
Collapse
Affiliation(s)
- Danilo Roccatano
- Dipartimento di Chimica, Ingegneria Chimica e Materiali, Universitá degli Studi, V. Vetoio, 67010, L'Aquila, Italy
| | | | | | | | | | | | | |
Collapse
|
10
|
Vrielink A, Sampson N. Sub-Angstrom resolution enzyme X-ray structures: is seeing believing? Curr Opin Struct Biol 2004; 13:709-15. [PMID: 14675549 DOI: 10.1016/j.sbi.2003.10.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Recent technical advances in crystallographic analysis, particularly highly focused and high brilliance synchrotron beam lines, have significantly improved the resolutions that are attainable for many macromolecular crystal structures. The Protein Data Bank (http://www.rcsb.org/pdb/) contains an increasing number of atomic resolution structures, which are providing a wealth of structural information that was not previously visible in lower resolution electron density maps. Here, we review the importance of visualizing hydrogen atoms and multiple sidechain conformations or anisotropy, as well as substrate strain, at sub-Angstrom resolution. The additional structural features that are visible in the electron density maps as a result of atomic resolution data provide a better understanding of the catalytic mechanisms of cholesterol oxidase, ribonuclease A, beta-lactamase, serine proteases, triosephosphate isomerase and endoglucanase.
Collapse
Affiliation(s)
- Alice Vrielink
- Department of Molecular, Cellular and Developmental Biology, University of California, 1156 High Street, Santa Cruz, CA 95064, USA.
| | | |
Collapse
|
11
|
Mustafi D, Hofer JE, Huang W, Palzkill T, Makinen MW. Chromophoric spin-labeled beta-lactam antibiotics for ENDOR structural characterization of reaction intermediates of class A and class C beta-lactamases. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2004; 60:1279-1289. [PMID: 15134725 DOI: 10.1016/j.saa.2003.10.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2003] [Revised: 07/13/2003] [Accepted: 10/16/2003] [Indexed: 05/24/2023]
Abstract
The chromophoric spin-label substrate 6-N-[3-(2,2,5,5-tetramethyl-1-oxypyrrolin-3-yl)-propen-2-oyl]penicillanic acid (SLPPEN) was synthesized by acylation of 6-aminopenicillanic acid with the acid chloride of 3-(2,2,5,5-tetramethyl-1-oxypyrrolinyl)-2-propenoic acid and characterized by physical methods. By application of angle-selected electron nuclear double resonance (ENDOR), we have determined the molecular structure of SLPPEN in solution. SLPPEN exhibited UV absorption properties that allowed accurate monitoring of the kinetics of its enzyme-catalyzed hydrolysis. The maximum value of the (substrate-product) difference extinction coefficient was 2824 M(-1) cm(-1) at 275 nm compared to 670 M(-1) cm(-1) at 232 nm for SLPEN [J. Am. Chem. Soc. 117 (1995) 6739]. For SLPPEN, the steady-state kinetic parameters kcat and kcat/KM, determined under initial velocity conditions, were 637 +/- 36 s(-1) and 13.8 +/- 1.4 x 10(6) M(-1) s(-1), respectively, for hydrolysis catalyzed by TEM-1 beta-lactamase of E. coli, and 0.5 +/- 0.04 s(-1) and 3.9 +/- 0.4 x 10(4) M(-1) s(-1) for hydrolysis catalyzed by the beta-lactamase of Enterobacter cloacae P99. We have also observed "burst kinetics" for the hydrolysis of SLPPEN with P99 beta-lactamase, indicative of formation of an acylenzyme reaction intermediate. In DMSO:H2O (30:70, v:v) cryosolvent mixtures buffered to pH* 7.0, the half-life of the acylenzyme intermediate formed with the P99 enzyme at -5 degrees C was > or = 3 min, suitable for optical characterization. The observation of burst kinetics in the hydrolysis of SLPPEN catalyzed by P99 beta-lactamase suggests that this chromophoric spin-labeled substrate is differentially sensitive to active site interactions underlying the cephalosporinase and penicillinase reactivity of this class C enzyme.
Collapse
Affiliation(s)
- Devkumar Mustafi
- Department of Biochemistry and Molecular Biology, Cummings Life Science Center, The University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA.
| | | | | | | | | |
Collapse
|
12
|
Hermann JC, Ridder L, Mulholland AJ, Höltje HD. Identification of Glu166 as the general base in the acylation reaction of class A beta-lactamases through QM/MM modeling. J Am Chem Soc 2003; 125:9590-1. [PMID: 12904016 DOI: 10.1021/ja034434g] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bacterial class A beta-lactamases are responsible for the most known resistance against beta-lactam antibiotics. With the continuing rise in antibiotic resistance, improved knowledge of the mechanisms of action of these enzymes is needed in the development of effective therapeutic agents and strategies. The mechanism of the deacylation step in class A beta-lactamases is well accepted. In contrast, the mechanism of the acylation step has been uncertain, with several conflicting proposals put forward. We have modeled the acylation step in a class A beta-lactamase, using a combined quantum mechanics/molecular mechanics approach. The results provide an atomic level description of the reaction and show that Glu166 acts as the general base in the reaction, deprotonating Ser70 via an intervening water molecule. Ser70 acts as the nucleophile for attack on the lactam ring in a concerted reaction. The results do not rule out the importance of Lys73 in catalysis, in agreement with experimental data.
Collapse
Affiliation(s)
- Johannes C Hermann
- Institut für Pharmazeutische Chemie, Heinrich-Heine Universität Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | | | | | | |
Collapse
|
13
|
Díaz N, Sordo TL, Merz KM, Suárez D. Insights into the acylation mechanism of class A beta-lactamases from molecular dynamics simulations of the TEM-1 enzyme complexed with benzylpenicillin. J Am Chem Soc 2003; 125:672-84. [PMID: 12526667 DOI: 10.1021/ja027704o] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Herein, we present results from molecular dynamics MD simulations ( approximately 1 ns) of the TEM-1 beta-lactamase in aqueous solution. Both the free form of the enzyme and its complex with benzylpenicillin were studied. During the simulation of the free enzyme, the conformation of the Omega loop and the interresidue contacts defining the complex H-bond network in the active site were quite stable. Most interestingly, the water molecule connecting Glu166 and Ser70 does not exchange with bulk solvent, emphasizing its structural and catalytic relevance. In the presence of the substrate, Ser130, Ser235, and Arg244 directly interact with the beta-lactam carboxylate via H-bonds, whereas the Lys234 ammonium group has only an electrostatic influence. These interactions together with other specific contacts result in a very short distance ( approximately 3 A) between the attacking hydroxyl group of Ser70 and the beta-lactam ring carbonyl group, which is a favorable orientation for nucleophilic attack. Our simulations also gave insight into the possible pathways for proton abstraction from the Ser70 hydroxyl group. We propose that either the Glu166 carboxylate-Wat1 or the substrate carboxylate-Ser130 moieties could abstract a proton from the nucleophilic Ser70.
Collapse
Affiliation(s)
- Natalia Díaz
- Departamento de Química Física y Analítica, Universidad de Oviedo, C/ Julián Clavería 8, Spain
| | | | | | | |
Collapse
|
14
|
Majiduddin FK, Materon IC, Palzkill TG. Molecular analysis of beta-lactamase structure and function. Int J Med Microbiol 2002; 292:127-37. [PMID: 12195735 DOI: 10.1078/1438-4221-00198] [Citation(s) in RCA: 104] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The extensive and sometimes irresponsible use of beta-lactam antibiotics in clinical and agricultural settings has contributed to the emergence and widespread dissemination of antibiotic-resistant bacteria. Bacteria have evolved three strategies to escape the activity of beta-lactam antibiotics: 1) alteration of the target site (e.g. penicillin-binding protein (PBPs), 2) reduction of drug permeation across the bacterial membrane (e.g. efflux pumps) and 3) production of beta-lactamase enzymes. The beta-lactamase enzymes inactivate beta-lactam antibiotics by hydrolyzing the peptide bond of the characteristic four-membered beta-lactam ring rendering the antibiotic ineffective. The inactivation of the antibiotic provides resistance to the bacterium. Currently, there are over 300 beta-lactamase enzymes described for which numerous kinetic, structural, computational and mutagenesis studies have been performed. In this review, we discuss the recent work performed on the four different classes (A, B, C, and D) of beta-lactamases. These investigative advances further expand our knowledge about these complex enzymes, and hopefully, will provide us with additional tools to develop new inhibitors and antibiotics based on structural and rational designs.
Collapse
Affiliation(s)
- Fahd K Majiduddin
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | | | | |
Collapse
|
15
|
Minasov G, Wang X, Shoichet BK. An ultrahigh resolution structure of TEM-1 beta-lactamase suggests a role for Glu166 as the general base in acylation. J Am Chem Soc 2002; 124:5333-40. [PMID: 11996574 DOI: 10.1021/ja0259640] [Citation(s) in RCA: 161] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Although TEM-1 beta-lactamase is among the best studied enzymes, its acylation mechanism remains controversial. To investigate this problem, the structure of TEM-1 in complex with an acylation transition-state analogue was determined at ultrahigh resolution (0.85 A) by X-ray crystallography. The quality of the data was such as to allow for refinement to an R-factor of 9.1% and an R(free) of 11.2%. In the resulting structure, the electron density features were clear enough to differentiate between single and double bonds in carboxylate groups, to identify multiple conformations that are occupied by residues and loops, and to assign 70% of the protons in the protein. Unexpectedly, even at pH 8.0 where the protein was crystallized, the active site residue Glu166 is clearly protonated. This supports the hypothesis that Glu166 is the general base in the acylation half of the reaction cycle. This structure suggests that Glu166 acts through the catalytic water to activate Ser70 for nucleophilic attack on the beta-lactam ring of the substrate. The hydrolytic mechanism of class A beta-lactamases, such as TEM-1, appears to be symmetrical, as are the serine proteases. Apart from its mechanistic implications, this atomic resolution structure affords an unusually detailed view of the structure, dynamics, and hydrogen-bonding networks of TEM-1, which may be useful for the design of inhibitors against this key antibiotic resistance target.
Collapse
Affiliation(s)
- George Minasov
- Department of Molecular Pharmacology & Biological Chemistry, Northwestern University, 303 East Chicago Avenue, Chicago, Illinois 60611-3008, USA
| | | | | |
Collapse
|