1
|
Sun J, Boyle AL, Brünle S, Ubbink M. A low-barrier proton shared between two aspartates acts as a conformational switch that changes the substrate specificity of the β-lactamase BlaC. Int J Biol Macromol 2024; 278:134665. [PMID: 39134195 DOI: 10.1016/j.ijbiomac.2024.134665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 08/09/2024] [Accepted: 08/09/2024] [Indexed: 08/19/2024]
Abstract
Serine β-lactamases inactivate β-lactam antibiotics in a two-step mechanism comprising acylation and deacylation. For the deacylation step, a water molecule is activated by a conserved glutamate residue to release the adduct from the enzyme. The third-generation cephalosporin ceftazidime is a poor substrate for the class A β-lactamase BlaC from Mycobacterium tuberculosis but it can be hydrolyzed faster when the active site pocket is enlarged, as was reported for mutant BlaC P167S. The conformational change in the Ω-loop of the P167S mutant displaces the conserved glutamate (Glu166), suggesting it is not required for deacylation of the ceftazidime adduct. Here, we report the characterization of wild type BlaC and BlaC E166A at various pH values. The presence of Glu166 strongly enhances activity against nitrocefin but not ceftazidime, indicating it is indeed not required for deacylation of the adduct of the latter substrate. At high pH wild type BlaC was found to exist in two states, one of which converts ceftazidime much faster, resembling the open state previously reported for the BlaC mutant P167S. The pH-dependent switch between the closed and open states is caused by the loss at high pH of a low-barrier hydrogen bond, a proton shared between Asp172 and Asp179. These results illustrate how readily shifts in substrate specificity can occur as a consequence of subtle changes in protein structure.
Collapse
Affiliation(s)
- Jing Sun
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Aimee L Boyle
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Steffen Brünle
- Biophysical Structure Chemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Marcellus Ubbink
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands.
| |
Collapse
|
2
|
Galdadas I, Qu S, Oliveira ASF, Olehnovics E, Mack AR, Mojica MF, Agarwal PK, Tooke CL, Gervasio FL, Spencer J, Bonomo RA, Mulholland AJ, Haider S. Allosteric communication in class A β-lactamases occurs via cooperative coupling of loop dynamics. eLife 2021; 10:e66567. [PMID: 33755013 PMCID: PMC8060031 DOI: 10.7554/elife.66567] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 03/19/2021] [Indexed: 12/16/2022] Open
Abstract
Understanding allostery in enzymes and tools to identify it offer promising alternative strategies to inhibitor development. Through a combination of equilibrium and nonequilibrium molecular dynamics simulations, we identify allosteric effects and communication pathways in two prototypical class A β-lactamases, TEM-1 and KPC-2, which are important determinants of antibiotic resistance. The nonequilibrium simulations reveal pathways of communication operating over distances of 30 Å or more. Propagation of the signal occurs through cooperative coupling of loop dynamics. Notably, 50% or more of clinically relevant amino acid substitutions map onto the identified signal transduction pathways. This suggests that clinically important variation may affect, or be driven by, differences in allosteric behavior, providing a mechanism by which amino acid substitutions may affect the relationship between spectrum of activity, catalytic turnover, and potential allosteric behavior in this clinically important enzyme family. Simulations of the type presented here will help in identifying and analyzing such differences.
Collapse
Affiliation(s)
- Ioannis Galdadas
- University College London, Department of ChemistryLondonUnited Kingdom
| | - Shen Qu
- University College London School of Pharmacy, Pharmaceutical and Biological ChemistryLondonUnited Kingdom
| | - Ana Sofia F Oliveira
- University of Bristol, Centre for Computational Chemistry, School of ChemistryBristolUnited Kingdom
| | - Edgar Olehnovics
- University College London School of Pharmacy, Pharmaceutical and Biological ChemistryLondonUnited Kingdom
| | - Andrew R Mack
- Veterans Affairs Northeast Ohio Healthcare System, Research ServiceClevelandUnited States
- Case Western Reserve University, Department of Molecular Biology and MicrobiologyClevelandUnited States
| | - Maria F Mojica
- Veterans Affairs Northeast Ohio Healthcare System, Research ServiceClevelandUnited States
- Case Western Reserve University, Department of Infectious Diseases, School of MedicineClevelandUnited States
| | - Pratul K Agarwal
- Department of Physiological Sciences and High-Performance Computing Center, Oklahoma State UniversityStillwaterUnited States
| | - Catherine L Tooke
- University of Bristol, School of Cellular and Molecular MedicineBristolUnited Kingdom
| | - Francesco Luigi Gervasio
- University College London, Department of ChemistryLondonUnited Kingdom
- University College London, Institute of Structural and Molecular BiologyLondonUnited Kingdom
- University of Geneva, Pharmaceutical SciencesGenevaSwitzerland
| | - James Spencer
- University of Bristol, School of Cellular and Molecular MedicineBristolUnited Kingdom
| | - Robert A Bonomo
- Veterans Affairs Northeast Ohio Healthcare System, Research ServiceClevelandUnited States
- Case Western Reserve University, Department of Molecular Biology and MicrobiologyClevelandUnited States
- Case Western Reserve University, Department of Infectious Diseases, School of MedicineClevelandUnited States
- Case Western Reserve University, Department of BiochemistryClevelandUnited States
- Case Western Reserve University, Department of PharmacologyClevelandUnited States
- Case Western Reserve University, Department of Proteomics and BioinformaticsClevelandUnited States
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES)ClevelandUnited States
| | - Adrian J Mulholland
- University of Bristol, Centre for Computational Chemistry, School of ChemistryBristolUnited Kingdom
| | - Shozeb Haider
- University College London School of Pharmacy, Pharmaceutical and Biological ChemistryLondonUnited Kingdom
| |
Collapse
|
3
|
Soto D, Silva C, Ugalde C, Wong KY, Leung YC, So LY, Andresen M. Effect of Lactamase Inhibitors on the Biosensor Penp during the Measurement of Lactam Antibiotics Concentration. SENSORS (BASEL, SWITZERLAND) 2019; 19:s19051237. [PMID: 30870966 PMCID: PMC6427286 DOI: 10.3390/s19051237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 02/20/2019] [Accepted: 02/25/2019] [Indexed: 06/09/2023]
Abstract
PenP is a fluorescent biosensor of lactam antibiotics (LA). It is structurally derived from the mutant lactamase TEM-1 comprising the substitution E166C, where fluorescein is covalently linked to cysteine. The presence of LA in the medium produces a change in the intrinsic fluorescence level of the biosensor, and the integral of the fluorescence level over time correlates directly with the LA concentration. Previously, we have successfully used PenP to determine the concentration of lactam antibiotics in clinical samples. The use of lactamase inhibitors (LI) is a common strategy to enhance the effect of LA due to the inhibition of an important resistance mechanism of pathogenic microorganisms. Structurally, LI and LA share the common element of recognition of lactamases (the lactam ring), but they differ in the reversibility of the mechanism of interaction with said enzyme. Because the biological recognition domain of PenP is derived from a lactamase, LI is expected to interfere with the PenP detection capabilities. Surprisingly, this work provides evidence that the effect of LI is marginal in the determination of LA concentration mediated by PenP.
Collapse
Affiliation(s)
- Dagoberto Soto
- Departamento de Medicina Intensiva, Facultad de Medicina y Hospital Clínico, Pontificia Universidad Católica de Chile, Santiago 8330024, Chile.
| | - Camila Silva
- Departamento de Medicina Intensiva, Facultad de Medicina y Hospital Clínico, Pontificia Universidad Católica de Chile, Santiago 8330024, Chile.
| | - Cristian Ugalde
- Departamento de Medicina Intensiva, Facultad de Medicina y Hospital Clínico, Pontificia Universidad Católica de Chile, Santiago 8330024, Chile.
| | - Kwok-Yin Wong
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong.
| | - Yun-Chung Leung
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong.
| | - Lok-Yan So
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong.
| | - Max Andresen
- Departamento de Medicina Intensiva, Facultad de Medicina y Hospital Clínico, Pontificia Universidad Católica de Chile, Santiago 8330024, Chile.
| |
Collapse
|
4
|
Kumar G, Biswal S, Nathan S, Ghosh AS. Glutamate residues at positions 162 and 164 influence the beta-lactamase activity of SHV-14 obtained from Klebsiella pneumoniae. FEMS Microbiol Lett 2018; 365:4705895. [PMID: 29228168 DOI: 10.1093/femsle/fnx259] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 11/29/2017] [Indexed: 11/13/2022] Open
Abstract
Extensive production of SHV-14 beta-lactamase makes Klebsiella pneumoniae resistant to beta-lactams. The presence of omega-loop has been reported to influence the beta-lactamase activity, which is also present in SHV-14. Its omega-loop has three glutamates in nearly alternating positions 162, 164 and 167 but their concise role on the behaviour of SHV-14 is unknown. To uncover the influence of each glutamate on SHV-14, we replaced glutamates with alanine and estimated the effect of each mutation by assessing the change in beta-lactam sensitivities in the surrogate Escherichia coli cells and catalytic efficiencies for hydrolysis with the purified proteins. On expression, the clone of wild-type SHV-14 aggravated the resistance of host by 60-500 folds against penicillin and cephalosporin groups of antibiotics. However, the expression of mutated enzymes (especially E164A) substantially reduced the resistance level as compared to the wild type, and the results were in synchrony with the estimated enzymatic efficiencies of wild-type and mutated proteins. Therefore, with further support from the in silico analysis, we hypothesise that mutation at the glutamate residues in the omega-loop of SHV-14 can considerably modulate the beta-lactam sensitivity and hydrolysis, thus revealing the importance of such glutamates as the target for inhibitor design in future.
Collapse
Affiliation(s)
- Gaurav Kumar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal - 721302, India
| | - Sarmistha Biswal
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal - 721302, India
| | - Soshina Nathan
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal - 721302, India
| | - Anindya S Ghosh
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal - 721302, India
| |
Collapse
|
5
|
Fluorescent TEM-1 β-lactamase with wild-type activity as a rapid drug sensor for in vitro drug screening. Biosci Rep 2014; 34:BSR20140057. [PMID: 25074398 PMCID: PMC4155835 DOI: 10.1042/bsr20140057] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
We report the development of a novel fluorescent drug sensor from the bacterial drug target TEM-1 β-lactamase through the combined strategy of Val216→Cys216 mutation and fluorophore labelling for in vitro drug screening. The Val216 residue in TEM-1 is replaced with a cysteine residue, and the environment-sensitive fluorophore fluorescein-5-maleimide is specifically attached to the Cys216 residue in the V216C mutant for sensing drug binding at the active site. The labelled V216C mutant has wild-type catalytic activity and gives stronger fluorescence when β-lactam antibiotics bind to the active site. The labelled V216C mutant can differentiate between potent and impotent β-lactam antibiotics and can distinguish active-site binders from non-binders (including aggregates formed by small molecules in aqueous solution) by giving characteristic time-course fluorescence profiles. Mass spectrometric, molecular modelling and trypsin digestion results indicate that drug binding at the active site is likely to cause the fluorescein label to stay away from the active site and experience weaker fluorescence quenching by the residues around the active site, thus making the labelled V216C mutant to give stronger fluorescence in the drug-bound state. Given the ancestor's role of TEM-1 in the TEM family, the fluorescent TEM-1 drug sensor represents a good model to demonstrate the general combined strategy of Val216→Cys216 mutation and fluorophore labelling for fabricating tailor-made fluorescent drug sensors from other clinically significant TEM-type β-lactamase variants for in vitro drug screening.
Collapse
|
6
|
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]
|
7
|
Three factors that modulate the activity of class D β-lactamases and interfere with the post-translational carboxylation of Lys70. Biochem J 2011; 432:495-504. [PMID: 21108605 DOI: 10.1042/bj20101122] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The activity of class D β-lactamases is dependent on Lys70 carboxylation in the active site. Structural, kinetic and affinity studies show that this post-translational modification can be affected by the presence of a poor substrate such as moxalactam but also by the V117T substitution. Val117 is a strictly conserved hydrophobic residue located in the active site. In addition, inhibition of class D β-lactamases by chloride ions is due to a competition between the side chain carboxylate of the modified Lys70 and chloride ions. Determination of the individual kinetic constants shows that the deacylation of the acyl-enzyme is the rate-limiting step for the wild-type OXA-10 β-lactamase.
Collapse
|
8
|
Zou L, Cheong WL, Chung WH, Leung YC, Wong KY, Wong MK, Chan PH. A Switch-On Fluorescence Assay for Bacterial β-Lactamases with Amyloid Fibrils as Fluorescence Enhancer and Visual Tool. Chemistry 2010; 16:13367-71. [DOI: 10.1002/chem.201001633] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
9
|
Vandenameele J, Lejeune A, Di Paolo A, Brans A, Frère JM, Schmid FX, Matagne A. Folding of Class A β-Lactamases Is Rate-Limited by Peptide Bond Isomerization and Occurs via Parallel Pathways. Biochemistry 2010; 49:4264-75. [DOI: 10.1021/bi100369d] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Julie Vandenameele
- Laboratoire d’Enzymologie et Repliement des Protéines, Centre d’Ingénierie des Protéines, Université de Liège, Institut de Chimie B6, 4000 Liège (Sart Tilman), Belgium
| | - Annabelle Lejeune
- Laboratoire d’Enzymologie et Repliement des Protéines, Centre d’Ingénierie des Protéines, Université de Liège, Institut de Chimie B6, 4000 Liège (Sart Tilman), Belgium
| | - Alexandre Di Paolo
- Laboratoire d’Enzymologie et Repliement des Protéines, Centre d’Ingénierie des Protéines, Université de Liège, Institut de Chimie B6, 4000 Liège (Sart Tilman), Belgium
| | - Alain Brans
- Laboratoire d’Enzymologie et Repliement des Protéines, Centre d’Ingénierie des Protéines, Université de Liège, Institut de Chimie B6, 4000 Liège (Sart Tilman), Belgium
| | - Jean-Marie Frère
- Laboratoire d’Enzymologie et Repliement des Protéines, Centre d’Ingénierie des Protéines, Université de Liège, Institut de Chimie B6, 4000 Liège (Sart Tilman), Belgium
| | - Franz X. Schmid
- Laboratorium für Biochemie und Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, D-95440 Bayreuth, Germany
| | - André Matagne
- Laboratoire d’Enzymologie et Repliement des Protéines, Centre d’Ingénierie des Protéines, Université de Liège, Institut de Chimie B6, 4000 Liège (Sart Tilman), Belgium
| |
Collapse
|
10
|
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
|
11
|
Chan PH, So PK, Ma DL, Zhao Y, Lai TS, Chung WH, Chan KC, Yiu KF, Chan HW, Siu FM, Tsang CW, Leung YC, Wong KY. Fluorophore-Labeled β-Lactamase as a Biosensor for β-Lactam Antibiotics: A Study of the Biosensing Process. J Am Chem Soc 2008; 130:6351-61. [DOI: 10.1021/ja076111g] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pak-Ho Chan
- Department of Applied Biology and Chemical Technology, Central Laboratory of the Institute of Molecular Technology for Drug Discovery and Synthesis, and Department of Applied Mathematics, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, P.R. China, and Department of Chemistry, the University of Hong Kong, Hong Kong, P.R. China
| | - Pui-Kin So
- Department of Applied Biology and Chemical Technology, Central Laboratory of the Institute of Molecular Technology for Drug Discovery and Synthesis, and Department of Applied Mathematics, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, P.R. China, and Department of Chemistry, the University of Hong Kong, Hong Kong, P.R. China
| | - Dik-Lung Ma
- Department of Applied Biology and Chemical Technology, Central Laboratory of the Institute of Molecular Technology for Drug Discovery and Synthesis, and Department of Applied Mathematics, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, P.R. China, and Department of Chemistry, the University of Hong Kong, Hong Kong, P.R. China
| | - Yanxiang Zhao
- Department of Applied Biology and Chemical Technology, Central Laboratory of the Institute of Molecular Technology for Drug Discovery and Synthesis, and Department of Applied Mathematics, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, P.R. China, and Department of Chemistry, the University of Hong Kong, Hong Kong, P.R. China
| | - Tat-Shing Lai
- Department of Applied Biology and Chemical Technology, Central Laboratory of the Institute of Molecular Technology for Drug Discovery and Synthesis, and Department of Applied Mathematics, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, P.R. China, and Department of Chemistry, the University of Hong Kong, Hong Kong, P.R. China
| | - Wai-Hong Chung
- Department of Applied Biology and Chemical Technology, Central Laboratory of the Institute of Molecular Technology for Drug Discovery and Synthesis, and Department of Applied Mathematics, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, P.R. China, and Department of Chemistry, the University of Hong Kong, Hong Kong, P.R. China
| | - Kwok-Chu Chan
- Department of Applied Biology and Chemical Technology, Central Laboratory of the Institute of Molecular Technology for Drug Discovery and Synthesis, and Department of Applied Mathematics, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, P.R. China, and Department of Chemistry, the University of Hong Kong, Hong Kong, P.R. China
| | - Ka-Fai Yiu
- Department of Applied Biology and Chemical Technology, Central Laboratory of the Institute of Molecular Technology for Drug Discovery and Synthesis, and Department of Applied Mathematics, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, P.R. China, and Department of Chemistry, the University of Hong Kong, Hong Kong, P.R. China
| | - Hoi-Wan Chan
- Department of Applied Biology and Chemical Technology, Central Laboratory of the Institute of Molecular Technology for Drug Discovery and Synthesis, and Department of Applied Mathematics, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, P.R. China, and Department of Chemistry, the University of Hong Kong, Hong Kong, P.R. China
| | - Fung-Ming Siu
- Department of Applied Biology and Chemical Technology, Central Laboratory of the Institute of Molecular Technology for Drug Discovery and Synthesis, and Department of Applied Mathematics, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, P.R. China, and Department of Chemistry, the University of Hong Kong, Hong Kong, P.R. China
| | - Chun-Wai Tsang
- Department of Applied Biology and Chemical Technology, Central Laboratory of the Institute of Molecular Technology for Drug Discovery and Synthesis, and Department of Applied Mathematics, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, P.R. China, and Department of Chemistry, the University of Hong Kong, Hong Kong, P.R. China
| | - Yun-Chung Leung
- Department of Applied Biology and Chemical Technology, Central Laboratory of the Institute of Molecular Technology for Drug Discovery and Synthesis, and Department of Applied Mathematics, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, P.R. China, and Department of Chemistry, the University of Hong Kong, Hong Kong, P.R. China
| | - Kwok-Yin Wong
- Department of Applied Biology and Chemical Technology, Central Laboratory of the Institute of Molecular Technology for Drug Discovery and Synthesis, and Department of Applied Mathematics, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, P.R. China, and Department of Chemistry, the University of Hong Kong, Hong Kong, P.R. China
| |
Collapse
|
12
|
Tsang MW, Leung YC. Overexpression of the recombinant Enterobacter cloacae P99 AmpC beta-lactamase and its mutants based on a phi105 prophage system in Bacillus subtilis. Protein Expr Purif 2007; 55:75-83. [PMID: 17638579 DOI: 10.1016/j.pep.2007.06.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2007] [Revised: 05/31/2007] [Accepted: 06/06/2007] [Indexed: 10/23/2022]
Abstract
AmpC beta-lactamase is a bacterial enzyme with great clinical impact as it mediates beta-lactam antibiotic resistance in many Gram-negative bacteria. To facilitate the structure-function relationship studies on this clinically important enzyme, we developed new strategies for production of recombinant Enterobacter cloacae P99 AmpC beta-lactamase in Bacillus subtilis. With the utilization of a special thermo-inducible phi105 phage system, functionally active AmpC beta-lactamase was expressed in B. subtilis, either in an extracellular native form or an intracellular N-terminal (His)(6)-tagged form. A higher expression level was achieved when expressing the enzyme as the intracellular (His)(6)-tagged protein rather than as the extracellular native protein. In addition, from the approach of producing intracellular tagged protein, highly pure (>95%) (His)(6)-tagged beta-lactamase wild-type and mutants (Y150C and K315C) were obtained after a one-step nickel affinity chromatography with a yield of 28.5, 66, and 0.85 mg/L of culture, respectively. Furthermore, the Y150C and K315C mutants were characterized so as to investigate the roles of the conserved residues, Tyr150 and Lys315, in the AmpC beta-lactamase. Severe impairment in hydrolytic abilities and restored secondary structures of the Y150C and K315C mutants suggested the major contribution of these two residues in the catalytic reaction rather than the structural framework in the AmpC enzyme.
Collapse
Affiliation(s)
- Man-Wah Tsang
- Laboratory of the Institute of Molecular Technology for Drug Discovery and Synthesis, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | | |
Collapse
|
13
|
Chan PH, Chan KC, Liu HB, Chung WH, Leung YC, Wong KY. Fluorescein-labeled beta-lactamase mutant for high-throughput screening of bacterial beta-lactamases against beta-lactam antibiotics. Anal Chem 2007; 77:5268-76. [PMID: 16097768 DOI: 10.1021/ac0502605] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The increasing emergence of new bacterial beta-lactamases that can efficiently hydrolyze beta-lactam antibiotics to clinically inactive carboxylic acids has created an intractable problem in the treatment of bacterial infections, and it is highly desirable to develop a useful tool that can rapidly screen bacteria for beta-lactamases against a variety of antibiotic candidates in a high-throughput manner. This paper describes the use of a fluorescein-labeled beta-lactamase mutant (E166Cf) as a convenient fluorescent tool to screen beta-lactamases, including the Bacillus cereus beta-lactamase I (PenPC), B. cereus beta-lactamase II, Bacillus licheniformis PenP, Escherichia coli TEM-1, and Enterobacter cloacae P99 against various beta-lactam antibiotics (penicillin G, penicillin V, ampicillin, cefuroxime, cefoxitin, moxalactam, cephaloridine), using a 96-well microplate reader. The E166Cf mutant was constructed by replacing Glu166 on the flexible Omega-loop, which is close to the enzyme's active site, with a cysteine residue on a class A beta-lactamase (B. cereus PenPC) and subsequently labeling the mutant with thiol-reactive fluorescein-5-maleimide. Such modifications significantly impaired the hydrolytic activity of the E166Cf mutant compared to that of the wild-type enzyme. The fluorescence intensity of the E166Cf mutant increases in the presence of beta-lactam antibiotics. For antibiotics that are resistant to hydrolysis by the E166Cf mutant (cefuroxime, cefoxitin, moxalactam), the fluorescence signal slowly increases until it reaches a plateau. For antibiotics that can be slowly hydrolyzed by the E166Cf mutant (penicillin G, penicillin V, ampicillin), the fluorescence signal rapidly increases to the plateau and then declines after a prolonged incubation. The E166Cf mutant retains its characteristic pattern of fluorescence signals in the presence of both bacterial beta-lactamases and beta-lactamase-resistant antibiotics. In contrast, in the presence of both bacterial beta-lactamases and beta-lactamase-sensitive antibiotics, the fluorescence signals of the E166Cf mutant were decreased. The fluorescence signals from the E166Cf mutant allow an unambiguous differentiation of beta-lactamase-resistant antibiotics from beta-lactamase-sensitive ones in the screening of bacterial beta-lactamases against a panel of antibiotic candidates. This simple method may provide an alternative tool in choosing potent beta-lactam antibiotics for treatment of bacterial infections.
Collapse
Affiliation(s)
- Pak-Ho Chan
- Department of Applied Biology and Chemical Technology and Central Laboratory of the Institute of Molecular Technology for Drug Discovery and Synthesis, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | | | | | | | | | | |
Collapse
|
14
|
Hata M, Fujii Y, Tanaka Y, Ishikawa H, Ishii M, Neya S, Tsuda M, Hoshino T. Substrate deacylation mechanisms of serine-beta-lactamases. Biol Pharm Bull 2007; 29:2151-9. [PMID: 17077507 DOI: 10.1248/bpb.29.2151] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The substrate deacylation mechanisms of serine-beta-lactamases (classes A, C and D) were investigated by theoretical calculations. The deacylation of class A proceeds via four elementary reactions. The rate-determining process is the tetrahedral intermediate (TI) formation and the activation energy is 24.6 kcal/mol at the DFT level. The deacylation does not proceed only by Glu166, which acts as a general base, but Lys73 also participates in the reaction. The C3-carboxyl group of the substrate reduces the barrier height at the TI formation (substrate-assisted catalysis). In the case of class C, the deacylation consists of two elementary processes. The activation energy of the TI formation has been estimated to be 30.5 kcal/mol. Tyr150Oeta is stabilized in the deprotonated state in the acyl-enzyme complex and works as a general base. This situation can exist due to the interaction with two positively charged side chains of lysine (Lys67 and Lys315). The deacylation of class D also consists of two elementary reaction processes. The activation energy of the TI formation is ca. 30 kcal/mol. It is thought that the side chain of Lys70 is deprotonated and acts as a general base. When Lys70 is carbamylated, the activation energy is reduced to less than 20 kcal/mol. This suggests that the high hydrolysis activity of class D with carbamylated Lys70 is due to the reduction of activation energy for deacylation. From these results, it is concluded that the contribution of the lysine residue adjacent to the serine residue is indispensable for the enzymatic reactions by serine-beta-lactamases.
Collapse
Affiliation(s)
- Masayuki Hata
- Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Japan.
| | | | | | | | | | | | | | | |
Collapse
|
15
|
Ke YY, Lin TH. A theoretical study on the activation of Ser70 in the acylation mechanism of cephalosporin antibiotics. Biophys Chem 2005; 114:103-13. [PMID: 15829343 DOI: 10.1016/j.bpc.2004.11.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2004] [Revised: 11/15/2004] [Accepted: 11/15/2004] [Indexed: 11/28/2022]
Abstract
A computational study using some molecular modeling and quantum mechanical methods has been performed for determining the most favor activation process for Ser70 in the acylation mechanism for the cephalosporin antibiotics among the three proposed ones given in the literature. The computation is based on an X-ray structure of the B chain of the Bacillus licheniformis BS3 beta-lactamase-cefoxitin complex. The position of a catalytic water involved in one of the reaction mechanism is defined using the Grid20 and InsightII programs, while that of the truncated ligand is defined using the InsightII and FirstDiscovery programs. The geometry of structures of each reaction scheme is optimized at the HF/3-21 G level of theory, and then the single point energy for each reactive species in each reaction scheme is computed at the levels of HF/6-31 + G (3df, 2p) and B3LYP/6-31 + G (3df, 2p). The effect of solvent on each reaction scheme is also studied by comparing the calculation results for each reaction scheme either in gas phase or in solution using the HF/6-31 + G (3df, 2p) level of theory. A computation using the B3LYP/6-31 + G (3df, 2p) level of theory and the Polarized Continuum Model (PCM) and by treating water as a solvent is also conducted for each activation process. It is found that, energetically, the most favor activation process for Ser70 in the acylation mechanism is the one where a proton transfer is mediated by the catalytic water and the catalytic residues Glu166 and Ser70. This agrees with those observed in an ultrahigh resolution X-ray structure and a QM/MM theoretical study published recently on the same acylation process.
Collapse
Affiliation(s)
- Yi-Yu Ke
- Institute of Molecular Medicine and Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan
| | | |
Collapse
|
16
|
Liu HB, Chui KS, Chan CL, Tsang CW, Leung YC. An efficient heat-inducible Bacillus subtilis bacteriophage 105 expression and secretion system for the production of the Streptomyces clavuligerus beta-lactamase inhibitory protein (BLIP). J Biotechnol 2004; 108:207-17. [PMID: 15006422 DOI: 10.1016/j.jbiotec.2003.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2003] [Revised: 11/21/2003] [Accepted: 12/08/2003] [Indexed: 10/26/2022]
Abstract
The Streptomyces clavuligerus beta-lactamase inhibitory protein (BLIP) has been shown to be a potent inhibitor of class A beta-lactamases including the Escherichia coli TEM-1 beta-lactamase (Ki = 0.6 nM). A heat-inducible BLIP expression system was constructed based on a derivative of Bacillus subtilis phage phi105. The recombinant BLIP produced by this system was secreted to the culture medium, purified to homogeneity, and fully active. We have shown that the signal peptide of BLIP functions well in B. subtilis to secrete BLIP out of the cells, which facilitates purification. The absence of a His-tag also avoids the activity and structure of BLIP being altered. An unprecedented high yield of recoverable protein in culture supernatant (3.6mg of >95% pure BLIP/l culture) was achieved by a simple purification protocol. We have developed an efficient production process in which the culture time before heat-induction was 3-4h and the culture supernatant could be collected 5h after induction. This total time of 8-9h is considered to be very short compared to that of the native S. clavuligerus culturing (60-70h). We achieved a very efficient BLIP production rate of 0.8-0.9mg/l/h. Heterologous gene expression was tightly controlled and no production of BLIP was observed before heat-induction, suggesting that cell density can be further increased to improve enzyme yield.
Collapse
Affiliation(s)
- Hong-Bing Liu
- The Central Laboratory of the Institute of Molecular Technology for Drug Discovery and Synthesis and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | | | | | | | | |
Collapse
|
17
|
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
|
18
|
Chan PH, Liu HB, Chen YW, Chan KC, Tsang CW, Leung YC, Wong KY. Rational design of a novel fluorescent biosensor for beta-lactam antibiotics from a class A beta-lactamase. J Am Chem Soc 2004; 126:4074-5. [PMID: 15053574 DOI: 10.1021/ja038409m] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A rational design strategy was used to construct a sensitive "turn-on" biosensor for beta-lactam antibiotics and beta-lactamase inhibitors from a class A beta-lactamase mutant with suppressed hydrolytic activity. A fluorescein molecule was attached to the 166 position on the Omega-loop of the E166C mutant close to the active site of the beta-lactamase. Upon binding with antibiotics or inhibitors, the flexibility of the Omega-loop allows the fluorescein molecule to move out from the active site and be more exposed to solvent. This process is accompanied by an increase in the fluorescence of the labeled enzyme. The fluorescence intensity of the biosensor increases with the concentration of antibiotics or inhibitors, which can detect penicillin G at concentrations as low as 50 nM in water. This approach opens a possibility for converting highly active and nonallosteric enzymes into substrate-binding proteins for biosensing purposes.
Collapse
Affiliation(s)
- Pak-Ho Chan
- Department of Applied Biology and Chemical Technology and Central Laboratory of the Institute of Molecular Technology for Drug Discovery and Synthesis, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, P. R. China
| | | | | | | | | | | | | |
Collapse
|
19
|
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; 279:34665-73. [PMID: 15152012 PMCID: PMC3371256 DOI: 10.1074/jbc.m313143200] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Beta-lactamases and penicillin-binding proteins are bacterial enzymes involved in antibiotic resistance to beta-lactam antibiotics and biosynthetic assembly of cell wall, respectively. Members of these large families of enzymes all experience acylation by their respective substrates at an active site serine as the first step in their catalytic activities. A Ser-X-X-Lys sequence motif is seen in all these proteins, and crystal structures demonstrate that the side-chain functions of the serine and lysine are in contact with one another. Three independent methods were used in this report to address the question of the protonation state of this important lysine (Lys-73) in the TEM-1 beta-lactamase from Escherichia coli. These techniques included perturbation of the pK(a) of Lys-73 by the study of the gamma-thialysine-73 variant and the attendant kinetic analyses, investigation of the protonation state by titration of specifically labeled proteins by nuclear magnetic resonance, and by computational treatment using the thermodynamic integration method. All three methods indicated that the pK(a) of Lys-73 of this enzyme is attenuated to 8.0-8.5. It is argued herein that the unique ground-state ion pair of Glu-166 and Lys-73 of class A beta-lactamases has actually raised the pK(a) of the active site lysine to 8.0-8.5 from that of the parental penicillin-binding protein. Whereas we cannot rule out that Glu-166 might activate the active site water, which in turn promotes Ser-70 for the acylation event, such as proposed earlier, we would like to propose as a plausible alternative for the acylation step the possibility that the ion pair would reconfigure to the protonated Glu-166 and unprotonated Lys-73. As such, unprotonated Lys-73 could promote serine for acylation, a process that should be shared among all active-site serine beta-lactamases and penicillin-binding proteins.
Collapse
Affiliation(s)
- Dasantila Golemi-Kotra
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - Samy O. Meroueh
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - Choonkeun Kim
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - Sergei B. Vakulenko
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - Alexey Bulychev
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - Ann J. Stemmler
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - Timothy L. Stemmler
- Department of Biochemistry and Molecular Biology, Wayne State University, Detroit, Michigan 48202
- To whom correspondence may be addressed: Dept. of Biochemistry and Molecular Biology, Wayne State University, Detroit, MI 48202. Tel.: 313-577-5712; Fax: 313-577-2765;
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
- To whom correspondence may be addressed: Dept. of Chemistry and Biochemistry, University of Notre Dame, 423 Nieuwland Science Hall, Notre Dame, IN 46556. Tel.: 574-631-2933; Fax: 574-631-6652;
| |
Collapse
|
20
|
Fujii Y, Hata M, Hoshino T, Tsuda M. Catalytic Mechanism of Class A β-Lactamase: Role of Lysine 73 and C3-Carboxyl Group of the Substrate Pen G in the Deacylation Step. J Phys Chem B 2002. [DOI: 10.1021/jp021414c] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Yasuyuki Fujii
- Laboratory of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
| | - Masayuki Hata
- Laboratory of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
| | - Tyuji Hoshino
- Laboratory of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
| | - Minoru Tsuda
- Laboratory of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
| |
Collapse
|
21
|
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
|
22
|
Lietz EJ, Truher H, Kahn D, Hokenson MJ, Fink AL. Lysine-73 is involved in the acylation and deacylation of beta-lactamase. Biochemistry 2000; 39:4971-81. [PMID: 10819961 DOI: 10.1021/bi992681k] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Lysine 73 is a conserved active-site residue in the class A beta-lactamases, as well as other members of the serine penicillin-sensitive enzyme family; its role in catalysis remains controversial and uncertain. Mutation of Lys73 to alanine in the beta-lactamase from Bacillus licheniformis resulted in a substantial reduction in both turnover rate (k(cat)) and catalytic efficiency (k(cat)/K(m)), and a very significant shift in pK(1) to higher pH in the bell-shaped pH-rate profiles (k(cat)/K(m)) for several penicillin and cephalosporin substrates. The increase in pK(1) is consistent with the removal of the positive ammonium group of the lysine from the proximity of Glu166, to which the acid limb has been ascribed. The alkaline limb of the k(cat)/K(m) vs profiles is not shifted appreciably, as might have been expected if this limb reflected the ionization of Lys73 in the wild-type enzyme. The k(cat)/K(m) at the pH optimum for the mutant was down about 200-fold for penicillins and around 10(4) for cephalosporins, compared to the wild-type, suggesting significant differences in the mechanisms for catalysis of penicillins compared to cephalosporins. Burst kinetics were observed with several substrates assayed with K73A beta-lactamase, indicating an underlying branched-pathway kinetic scheme, and rate-limiting deacylation. FTIR analysis was used to determine whether acylation or deacylation was rate-limiting. In general, acylation was the rate-limiting step for cephalosporin substrates, whereas deacylation was rate-limiting for penicillin substrates. The results indicate that Lys73 plays an important role in both the acylation and deacylation steps of the catalytic mechanism. The effects of this mutation (K73A) indicate that Lys73 does not function as a general base in the catalytic mechanism of beta-lactamase. The existence of bell-shaped pH-rate profiles for the K73A variant suggests that Lys73 is not directly responsible for either limb in such plots. It is likely that both Glu166 and Lys73 are important to each other in terms of maintaining the optimum electrostatic environment for fully efficient catalytic activity to occur.
Collapse
Affiliation(s)
- E J Lietz
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
| | | | | | | | | |
Collapse
|
23
|
Vanwetswinkel S, Avalle B, Fastrez J. Selection of beta-lactamases and penicillin binding mutants from a library of phage displayed TEM-1 beta-lactamase randomly mutated in the active site omega-loop. J Mol Biol 2000; 295:527-40. [PMID: 10623544 DOI: 10.1006/jmbi.1999.3376] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A combinatorial library of mutants of the phage displayed TEM-1 lactamase was generated in the region encompassing residues 163 to 171 of the active site Omega-loop. Two in vitro selection protocols were designed to extract from the library phage-enzymes characterised by a fast acylation by benzyl-penicillin (PenG) to yield either stable or very unstable acyl-enzymes. The critical step of the selections was the kinetically controlled labelling of the phages by reaction with either a biotinylated penicillin derivative or a biotinylated penicillin sulfone, i.e. a beta-lactamase suicide substrate; the biotinylated phages were recovered by panning on immobilised streptavidin. As labelling with biotinylated suicide substrates tends to select enzymes that do not turnover, a counter-selection against penicillin binding mutants was introduced to extract the beta-lactamases. The selected phage-enzymes were characterised by sequencing to identify conserved residues and by kinetic analysis of the reaction with benzyl-penicillin. Several penicillin binding mutants, in which the essential Glu166 is replaced by Asn, were shown to be acylated very fast by PenG, the acylation being characterised by biphasic kinetics. These data are interpreted by a kinetic scheme in which the enzymes exist in two interconvertible conformations. The rate constant of the conformational change suggests that it involves an isomerisation of the peptide bond between residues 166 and 167 and controls a conformation of the Omega-loop compatible with fast acylation of the active site serine residue.
Collapse
Affiliation(s)
- S Vanwetswinkel
- Université Catholique de Louvain, Laboratoire de Biochimie Physique et des Biopolymères, Place L. Pasteur, 1 Bte 1B, Louvain-la-Neuve, B1348, Belgium
| | | | | |
Collapse
|
24
|
Therrien C, Sanschagrin F, Palzkill T, Levesque RC. Roles of amino acids 161 to 179 in the PSE-4 omega loop in substrate specificity and in resistance to ceftazidime. Antimicrob Agents Chemother 1998; 42:2576-83. [PMID: 9756758 PMCID: PMC105900 DOI: 10.1128/aac.42.10.2576] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The PSE-4 enzyme is a prototype carbenicillin-hydrolyzing enzyme exhibiting high activity against penicillins and early cephalosporins. To understand the mechanism that modulates substrate profiles and to verify the ability of PSE-4 to extend its substrate specificity toward expanded-spectrum cephalosporins, we used random replacement mutagenesis to generate six random libraries from amino acids 162 to 179 in the Omega loop. This region is known from studies with TEM-1 to be implicated in substrate specificity. It was found that the mechanism modulating ceftazidime hydrolysis in PSE-4 was different from that in TEM-1. The specificity of class 2c carbenicillin-hydrolyzing enzymes could not be assigned to the Omega loop of PSE-4. Analysis of the percentage of functional enzymes revealed that the hydrolysis of ampicillin was more affected than hydrolysis of carbenicillin by amino acid substitutions at positions 162 to 164 and 165 to 167.
Collapse
Affiliation(s)
- C Therrien
- Microbiologie Moléculaire et Génie des Protéines, Sciences de la Vie et de la Santé, Faculté de Médecine, Université Laval, Ste-Foy, Québec, Canada G1K 7P4
| | | | | | | |
Collapse
|
25
|
Davis JJ, Green ML, Allen O. Hill H, Leung YC, Sadler PJ, Sloan J, Xavier AV, Chi Tsang S. The immobilisation of proteins in carbon nanotubes. Inorganica Chim Acta 1998. [DOI: 10.1016/s0020-1693(97)05926-4] [Citation(s) in RCA: 144] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
26
|
Wu L, Buist A, den Hertog J, Zhang ZY. Comparative kinetic analysis and substrate specificity of the tandem catalytic domains of the receptor-like protein-tyrosine phosphatase alpha. J Biol Chem 1997; 272:6994-7002. [PMID: 9054389 DOI: 10.1074/jbc.272.11.6994] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The catalytic activity and substrate specificity of protein-tyrosine phosphatase alpha (PTPalpha) is primarily controlled by the membrane proximal catalytic domain (D1). The membrane distal (D2) domain of PTPalpha by itself is a genuine PTPase, possessing catalytic activity comparable to that of D1 using aryl phosphates as substrates. Surprisingly, kcat and kcat/Km for the D2-catalyzed hydrolysis of phosphotyrosine-containing peptides are several orders of magnitude reduced in comparison with those of D1. Substitution of the putative general acid/base Glu-690 in D2 by an Asp, which is invariably found in the WPD motifs in all cytoplasmic PTPases and all the D1 domains of receptor-like PTPases, only increases the kcat for D2 by 4-fold. Thus the much reduced D2 activity toward peptide substrates may be due to structural differences in the active sites other than the general acid/base. Alternatively, the D2 domain may have a functional active site with a highly stringent substrate specificity. PTPalpha display modest peptide substrate selectivity and are sensitive to charges adjacent to phosphotyrosine. In the sequence context of DADEpYLIPQQG (where pY stands for phosphotyrosine), the minimal sizes recognized by PTPalpha are either ADEpYLI or DADEpY-NH2.
Collapse
Affiliation(s)
- L Wu
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | | | | | | |
Collapse
|
27
|
Guillaume G, Vanhove M, Lamotte-Brasseur J, Ledent P, Jamin M, Joris B, Frère JM. Site-directed mutagenesis of glutamate 166 in two beta-lactamases. Kinetic and molecular modeling studies. J Biol Chem 1997; 272:5438-44. [PMID: 9038144 DOI: 10.1074/jbc.272.9.5438] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The catalytic pathway of class A beta-lactamases involves an acyl-enzyme intermediate where the substrate is ester-linked to the Ser-70 residue. Glu-166 and Lys-73 have been proposed as candidates for the role of general base in the activation of the serine OH group. The replacement of Glu-166 by an asparagine in the TEM-1 and by a histidine in the Streptomyces albus G beta-lactamases yielded enzymes forming stable acyl-enzymes with beta-lactam antibiotics. Although acylation of the modified proteins by benzylpenicillin remained relatively fast, it was significantly impaired when compared to that observed with the wild-type enzyme. Moreover, the E166N substitution resulted in a spectacular modification of the substrate profile much larger than that described for other mutations of Omega-loop residues. Molecular modeling studies indicate that the displacement of the catalytic water molecule can be related to this observation. These results confirm the crucial roles of Glu-166 and of the "catalytic" water molecule in both the acylation and the deacylation processes.
Collapse
Affiliation(s)
- G Guillaume
- Centre d'Ingénierie des Protéines and Laboratoire d'Enzymologie, Université de Liège, Institut de Chimie B6, Sart-Tilman, B-4000 Liège, Belgium
| | | | | | | | | | | | | |
Collapse
|
28
|
Avalle B, Vanwetswinkel S, Fastrez J. In vitro selection for catalytic turnover from a library of β-lactamase mutants and penicillin-binding proteins. Bioorg Med Chem Lett 1997. [DOI: 10.1016/s0960-894x(97)00040-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
29
|
Strynadka NC, Martin R, Jensen SE, Gold M, Jones JB. Structure-based design of a potent transition state analogue for TEM-1 beta-lactamase. NATURE STRUCTURAL BIOLOGY 1996; 3:688-95. [PMID: 8756327 DOI: 10.1038/nsb0896-688] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The structure of the plasmid-mediated beta-lactamase TEM-1 has been solved in complex with a designed boronic acid inhibitor (1R)-1-acetamido-2-(3-carboxyphenyl)ethane boronic acid at 1.7 A resolution. The boronate inhibitor was designed based on the crystallographic coordinates of the acyl-enzyme intermediate of TEM-1 bound to the substrate penicillin G. The boronate-TEM-1 complex is highly ordered and defines a novel transition state analogue of the deacylation step in the beta-lactamase reaction pathway. The design principles of this highly effective inhibitor (Ki = 110 nM) and the resulting structural and mechanistic implications are presented.
Collapse
Affiliation(s)
- N C Strynadka
- Department of Biochemistry, University of Alberta, Edmonton, Canada
| | | | | | | | | |
Collapse
|
30
|
Damblon C, Raquet X, Lian LY, Lamotte-Brasseur J, Fonze E, Charlier P, Roberts GC, Frère JM. 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 1996; 93:1747-52. [PMID: 8700829 PMCID: PMC39852 DOI: 10.1073/pnas.93.5.1747] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Beta-Lactamases are widespread in the bacterial world, where they are responsible for resistance to penicillins, cephalosporins, and related compounds, currently the most widely used antibacterial agents. Detailed structural and mechanistic understanding of these enzymes can be expected to guide the design of new antibacterial compounds resistant to their action. A number of high-resolution structures are available for class A beta-lactamases, whose catalytic mechanism involves the acylation of a serine residue at the active site. The identity of the general base which participates in the activation of this serine residue during catalysis has been the subject of controversy, both a lysine residue and a glutamic acid residue having been proposed as candidates for this role. We have used the pH dependence of chemical modification of epsilon-amino groups by 2,4,6,-trinitrobenzenesulfonate and the pH dependence of the epsilon-methylene 1H and 13C chemical shifts (in enzyme selectively labeled with [epsilon-13C]lysine) to estimate the pKa of the relevant lysine residue, lysine-73, of TEM-1 beta-lactamase. Both methods show that the pKa of this residue is > 10, making it very unlikely that this residue could act as a proton acceptor in catalysis. An alternative mechanism in which this role is performed by glutamate-166 through an intervening water molecule is described.
Collapse
Affiliation(s)
- C Damblon
- Centre d'Ingénierie des Protéines, Institut de Chimie, Université de Liège, Belgium
| | | | | | | | | | | | | | | |
Collapse
|
31
|
Knox JR. Extended-spectrum and inhibitor-resistant TEM-type beta-lactamases: mutations, specificity, and three-dimensional structure. Antimicrob Agents Chemother 1995; 39:2593-601. [PMID: 8592985 PMCID: PMC162995 DOI: 10.1128/aac.39.12.2593] [Citation(s) in RCA: 244] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Affiliation(s)
- J R Knox
- Department of Molecular and Cell Biology, University of Connecticut, Storrs 06269-3125, USA.
| |
Collapse
|
32
|
Galleni M, Lamotte-Brasseur J, Raquet X, Dubus A, Monnaie D, Knox JR, Frère JM. The enigmatic catalytic mechanism of active-site serine beta-lactamases. Biochem Pharmacol 1995; 49:1171-8. [PMID: 7763298 DOI: 10.1016/0006-2952(94)00502-d] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- M Galleni
- Centre d'Ingénierie des Protéines, Université de Liège, Belgium
| | | | | | | | | | | | | |
Collapse
|
33
|
Leung YC, Errington J. Characterization of an insertion in the phage phi 105 genome that blocks host Bacillus subtilis lysis and provides strong expression of heterologous genes. Gene 1995; 154:1-6. [PMID: 7867934 DOI: 10.1016/0378-1119(94)00874-r] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A defective prophage vector, phi 105MU331, for high-level protein overproduction in Bacillus subtilis, was derived by random insertion of a lacZ reporter gene. The site of insertion not only provided efficient inducible transcription of heterologous genes, but also prevented lysis of the host cell. The region of the insertion in phi 105MU331 lies close to the right cohesive end of phi 105. DNA sequence analysis revealed that this region of phi 105 somewhat resembles the lysis cassette of various phages, including lambda. The site of insertion lies in a possible 'holin' gene, which could explain the block in host cell lysis. Dual promoters apparently responsible for the strong inducible transcription lie in an untranslated region just upstream from the putative holin gene. This region is probably equivalent to the site of the major late promoter and antiterminator of the lambdoid phages. The sequence features could, thus, account for the useful properties of the phi 105MU331 vector system.
Collapse
Affiliation(s)
- Y C Leung
- Sir William Dunn School of Pathology, University of Oxford, UK
| | | |
Collapse
|
34
|
Matagne A, Frère JM. Contribution of mutant analysis to the understanding of enzyme catalysis: the case of class A beta-lactamases. BIOCHIMICA ET BIOPHYSICA ACTA 1995; 1246:109-27. [PMID: 7819278 DOI: 10.1016/0167-4838(94)00177-i] [Citation(s) in RCA: 92] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Class A beta-lactamases represent a family of well studied enzymes. They are responsible for many antibiotic resistance phenomena and thus for numerous failures in clinical chemotherapy. Despite the facts that five structures are known at high resolution and that detailed analyses of enzymes modified by site-directed mutagenesis have been performed, their exact catalytic mechanism remains controversial. This review attempts to summarize and to discuss the many available data.
Collapse
Affiliation(s)
- A Matagne
- Laboratoire d'Enzymologie et Centre d'Ingénierie des Protéines, Université de Liège, Belgium
| | | |
Collapse
|