1
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Garsevanyan S, Barlow M. The Klebsiella pneumoniae carbapenemase (KPC) β-Lactamase Has Evolved in Response to Ceftazidime Avibactam. Antibiotics (Basel) 2023; 13:40. [PMID: 38247599 PMCID: PMC10812414 DOI: 10.3390/antibiotics13010040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 12/23/2023] [Accepted: 12/29/2023] [Indexed: 01/23/2024] Open
Abstract
Klebsiella pneumoniae carbapenemase KPC is an important resistance gene that has disseminated globally in response to carbapenem use. It is now being implicated as a resistance determinant in Ceftazidime Avibactam (CAZ-AVI) resistance. Given that CAZ-AVI is a last-resort antibiotic, it is critical to understand how resistance to this drug is evolving. In particular, we were interested in determining the evolutionary response of KPC to CAZ-AVI consumption. Through phylogenetic reconstruction, we identified the variable sites under positive selection in the KPC gene that are correlated with Ceftazidime Avibactam (CAZ-AVI) resistance. Our approach was to use a phylogeny to identify multiple independent occurrences of mutations at variable sites and a literature review to correlate CAZ-AVI resistance with the mutations we identified. We found the following sites that are under positive selection: P104, W105, A120, R164, L169, A172, D179, V240, Y241, T243, Y264, and H274. The sites that correlate with CAZ-AVI resistance are R164, L169, A172, D179, V240, Y241, T243, and H274. Overall, we found that there is evidence of positive selection in KPC and that CAZ-AVI is the major selective pressure.
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Affiliation(s)
| | - Miriam Barlow
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California Merced, Merced, CA 95343, USA;
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2
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Oelschlaeger P, Kaadan H, Dhungana R. Strategies to Name Metallo-β-Lactamases and Number Their Amino Acid Residues. Antibiotics (Basel) 2023; 12:1746. [PMID: 38136780 PMCID: PMC10740994 DOI: 10.3390/antibiotics12121746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/12/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Metallo-β-lactamases (MBLs), also known as class B β-lactamases (BBLs), are Zn(II)-containing enzymes able to inactivate a broad range of β-lactams, the most commonly used antibiotics, including life-saving carbapenems. They have been known for about six decades, yet they have only gained much attention as a clinical problem for about three decades. The naming conventions of these enzymes have changed over time and followed various strategies, sometimes leading to confusion. We are summarizing the naming strategies of the currently known MBLs. These enzymes are quite diverse on the amino acid sequence level but structurally similar. Problems trying to describe conserved residues, such as Zn(II) ligands and other catalytically important residues, which have different numbers in different sequences, have led to the establishment of a standard numbering scheme for BBLs. While well intended, the standard numbering scheme is not trivial and has not been applied consistently. We revisit this standard numbering scheme and suggest some strategies for how its implementation could be made more accessible to researchers. Standard numbering facilitates the comparison of different enzymes as well as their interaction with novel antibiotics and BBL inhibitors.
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Affiliation(s)
- Peter Oelschlaeger
- Department of Biotechnology and Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, CA 91766, USA; (H.K.)
| | - Heba Kaadan
- Department of Biotechnology and Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, CA 91766, USA; (H.K.)
| | - Rinku Dhungana
- Department of Biotechnology and Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, CA 91766, USA; (H.K.)
- Department of Biological Sciences, Kenneth P. Dietrich School of Arts & Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
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3
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Žagar D, Zore A, Torkar KG. The occurrence of antibiotic-resistant bacteria on the clothes of nursery teachers in daycare centres. J Appl Microbiol 2022; 132:4517-4530. [PMID: 35267237 PMCID: PMC9314099 DOI: 10.1111/jam.15520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 02/28/2022] [Accepted: 03/05/2022] [Indexed: 11/28/2022]
Abstract
AIMS Childcare facilities act as microenvironments that facilitate and promote the selection, spread, and transmission of antibiotic-resistant microorganisms in the community. We focused on the study of antimicrobial resistance and genetic predispositions for β-lactamase production in bacterial isolates from nursery teachers' clothing. METHODS AND RESULTS Antimicrobial resistance of bacterial strains belonging to Enterobacteriaceae, Enterococcus, Staphylococcus spp., Pseudomonas spp. and Bacillus spp. isolated from 80 samples of nursery teachers' clothing was determined. The selected ESβL genes were found in 30 (44.1%) of 68 strains examined. The CTX-M type ESβL determinants were detected in 15.4%, 71.5%, and 42.5% of the Enterobacteriaceae, Pseudomonas, and Bacillus isolates, respectively. The OXA-type coding genes were detected only in strains of the genera Pseudomonas (57.1%) and Bacillus (48.6%). Thus, most B. cereus strains were sensitive to the recommended antibiotics used to treat infections caused by these bacteria. Methicillin resistance was phenotypically confirmed in 27 (14.6%) of 185 staphylococcal isolates. Four isolates (2.2%) were identified as MRSA. Vancomycin resistance was not observed in any of the staphylococcal and enterococci strains. CONCLUSIONS This study has shown that potential pathogens have been isolated from the clothing of nursery teachers, posing a risk of transmission to children. These clothes should be maintained and properly laundered to avoid cross-contamination and the spread of multidrug-resistant (MDR) bacteria in childcare centres. SIGNIFICANCE AND IMPACT OF THE STUDY This study provides insight into the route of transmission of MDR microorganisms through the clothing of nursery teachers, to which greater importance should be given in the future. Proper procedures for the cleaning and use of clothing in daycare centres should be clarified and standardised.
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Affiliation(s)
- Dominika Žagar
- University of Ljubljana, Faculty of Health Sciences, Zdravstvena pot 5, SI-1000, Ljubljana, Slovenia
| | - Anamarija Zore
- University of Ljubljana, Faculty of Health Sciences, Zdravstvena pot 5, SI-1000, Ljubljana, Slovenia
| | - Karmen Godič Torkar
- University of Ljubljana, Faculty of Health Sciences, Zdravstvena pot 5, SI-1000, Ljubljana, Slovenia
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4
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Au HW, Tsang MW, So PK, Wong KY, Leung YC. Thermostable β-Lactamase Mutant with Its Active Site Conjugated with Fluorescein for Efficient β-Lactam Antibiotic Detection. ACS OMEGA 2019; 4:20493-20502. [PMID: 31858033 PMCID: PMC6906784 DOI: 10.1021/acsomega.9b02211] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 11/14/2019] [Indexed: 05/09/2023]
Abstract
Monitoring the β-lactam antibiotic level has been an important task in food industry and clinical practice. Here, we report the development of a fluorescent PenP β-lactamase, PenP-E166Cf/N170Q, for efficient β-lactam antibiotic detection. It was constructed by covalently attaching fluorescein onto the active-site entrance of a thermostable E166Cf/N170Q mutant of a Bacillus licheniformis PenP β-lactamase. It gave a fluorescence turn-on signal toward various β-lactam antibiotics, where the fluorescence enhancement was attributed to the acyl-enzyme complex formed between PenP-E166Cf/N170Q and the β-lactam antibiotic. It demonstrated enhanced signal stability over its parental PenP-E166Cf because of the suppressed hydrolytic activity by the N170Q mutation. Compared with our previously constructed PenPC-E166Cf biosensor, PenP-E166Cf/N170Q was more thermostable and advanced in detecting β-lactams in terms of response time, signal stability, and detection limit. Positive fluorescence signals generated by E166Cf/N170Q in response to the penicillin-containing milk and mouse serum illustrated the feasibility of the biosensor for antibiotic detection in real samples. Taken together, our findings suggest the potential application of PenP-E166Cf/N170Q in biosensing β-lactam antibiotics.
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Affiliation(s)
- Ho-Wah Au
- Department
of Applied Biology and Chemical Technology, State Key
Laboratory of Chemical Biology and Drug Discovery and Lo Ka Chung Research Centre for
Natural Anti-Cancer Drug Development, The
Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Man-Wah Tsang
- Department
of Applied Biology and Chemical Technology, State Key
Laboratory of Chemical Biology and Drug Discovery and Lo Ka Chung Research Centre for
Natural Anti-Cancer Drug Development, The
Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Pui-Kin So
- Department
of Applied Biology and Chemical Technology, State Key
Laboratory of Chemical Biology and Drug Discovery and Lo Ka Chung Research Centre for
Natural Anti-Cancer Drug Development, The
Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Kwok-Yin Wong
- Department
of Applied Biology and Chemical Technology, State Key
Laboratory of Chemical Biology and Drug Discovery and Lo Ka Chung Research Centre for
Natural Anti-Cancer Drug Development, The
Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
- E-mail: (K.-Y.W.)
| | - Yun-Chung Leung
- Department
of Applied Biology and Chemical Technology, State Key
Laboratory of Chemical Biology and Drug Discovery and Lo Ka Chung Research Centre for
Natural Anti-Cancer Drug Development, The
Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
- E-mail: (Y.-C.L.)
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5
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Law KH, Tsang MW, Wong YK, Tsang MS, Lau PY, Wong KY, Ho KP, Leung YC. Efficient production of secretory Streptomyces clavuligerus β-lactamase inhibitory protein (BLIP) in Pichia pastoris. AMB Express 2018; 8:64. [PMID: 29679312 PMCID: PMC5910447 DOI: 10.1186/s13568-018-0586-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 04/05/2018] [Indexed: 11/10/2022] Open
Abstract
β-Lactamase inhibitory protein (BLIP), a low molecular weight protein from Streptomyces clavuligerus, has a wide range of potential applications in the fields of biotechnology and pharmaceutical industry because of its tight interaction with and potent inhibition on clinically important class A β-lactamases. To meet the demands for considerable amount of highly pure BLIP, this study aimed at developing an efficient expression system in eukaryotic Pichia pastoris (a methylotrophic yeast) for production of BLIP. With methanol induction, recombinant BLIP was overexpressed in P. pastoris X-33 and secreted into the culture medium. A high yield of ~ 300 mg/L culture secretory BLIP recovered from the culture supernatant without purification was found to be > 90% purity. The recombinant BLIP was fully active and showed an inhibition constant (Ki) for TEM-1 β-lactamase (0.55 ± 0.07 nM) comparable to that of the native S. clavuligerus-expressed BLIP (0.5 nM). Yeast-produced BLIP in combination with ampicillin effectively inhibited the growth of β-lactamase-producing Gram-positive Bacillus. Our approach of expressing secretory BLIP in P. pastoris gave 71- to 1200-fold more BLIP with high purity than the other conventional methods, allowing efficient production of large amount of highly pure BLIP, which merits fundamental science studies, drug development and biotechnological applications.
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6
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Antimicrobial susceptibility and characterization of metallo-β-lactamases, extended-spectrum β-lactamases, and carbapenemases of Bacillus cereus isolates. Microb Pathog 2018; 118:140-145. [PMID: 29551437 DOI: 10.1016/j.micpath.2018.03.026] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 02/06/2018] [Accepted: 03/15/2018] [Indexed: 11/22/2022]
Abstract
The susceptibility of 66 clinical and environmental B. cereus isolates were tested to selected antimicrobials by a broth microdilution method. All strains were resistant to β-lactams and susceptible to gentamicin and imipenem. Sixty-five (98.5%) isolates were susceptible to meropenem and ciprofloxacin and 74.2% to azithromycin. Significant differences in MIC values between environmental and clinical isolates were not demonstrated (p > 0.05). According to the disc diffusion method, 80.3%-98.5% of the strains were resistant to one or more of four cephalosporins. The presence of genes for B. cereus β-lactamases BCI, BCII, BCIII, extended-spectrum β-lactamases from the CTX and TEM family and the carbapenemases belonging to IMP and VIM family was studied. BlaII genes were expressed in all isolates; the PCR products for blaIII were also detected in two strains, but none of them was positive for blaI. The amplicon of the family blaCTX-M, mostly M-1 and M-15, was confirmed among 68.2% of the isolates, while were blaVIM-like genes determined in 21.2% of the samples.
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7
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Brown JR, Livesay DR. Flexibility Correlation between Active Site Regions Is Conserved across Four AmpC β-Lactamase Enzymes. PLoS One 2015; 10:e0125832. [PMID: 26018804 PMCID: PMC4446314 DOI: 10.1371/journal.pone.0125832] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 03/26/2015] [Indexed: 11/24/2022] Open
Abstract
β-lactamases are bacterial enzymes that confer resistance to β-lactam antibiotics, such as penicillins and cephalosporins. There are four classes of β-lactamase enzymes, each with characteristic sequence and structure properties. Enzymes from class A are the most common and have been well characterized across the family; however, less is known about how physicochemical properties vary across the C and D families. In this report, we compare the dynamical properties of four AmpC (class C) β-lactamases using our distance constraint model (DCM). The DCM reliably predicts thermodynamic and mechanical properties in an integrated way. As a consequence, quantitative stability/flexibility relationships (QSFR) can be determined and compared across the whole family. The DCM calculates a large number of QSFR metrics. Perhaps the most useful is the flexibility index (FI), which quantifies flexibility along the enzyme backbone. As typically observed in other systems, FI is well conserved across the four AmpC enzymes. Cooperativity correlation (CC), which quantifies intramolecular couplings within structure, is rarely conserved across protein families; however, it is in AmpC. In particular, the bulk of each structure is composed of a large rigid cluster, punctuated by three flexibly correlated regions located at the active site. These regions include several catalytic residues and the Ω-loop. This evolutionary conservation combined with active their site location strongly suggests that these coupled dynamical modes are important for proper functioning of the enzyme.
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Affiliation(s)
- Jenna R. Brown
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28262, United States of America
| | - Dennis R. Livesay
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28262, United States of America
- * E-mail:
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8
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Bovine intestinal bacteria inactivate and degrade ceftiofur and ceftriaxone with multiple beta-lactamases. Antimicrob Agents Chemother 2011; 55:4990-8. [PMID: 21876048 DOI: 10.1128/aac.00008-11] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The veterinary cephalosporin drug ceftiofur is rapidly degraded in the bovine intestinal tract. A cylinder-plate assay was used to detect microbiologically active ceftiofur, and high-performance liquid chromatography-mass spectrometry analysis was used to quantify the amount of ceftiofur remaining after incubation with bovine intestinal anaerobic bacteria, which were isolated from colon contents or feces from 8 cattle. Ninety-six percent of the isolates were able to inactivate ceftiofur to some degree, and 54% actually degraded the drug. None of 9 fungal isolates inactivated or degraded ceftiofur. Facultative and obligate anaerobic bacterial species that inactivated or degraded ceftiofur were identified with Vitek and Biolog systems, respectively. A subset of ceftiofur degraders also degraded the chemically similar drug ceftriaxone. Most of the species of bacteria that degraded ceftiofur belonged to the genera Bacillus and Bacteroides. PCR analysis of bacterial DNA detected specific β-lactamase genes. Bacillus cereus and B. mycoides isolates produced extended-spectrum β-lactamases and metallo-β-lactamases. Seven isolates of Bacteroides spp. produced multiple β-lactamases, including possibly CepA, and metallo-β-lactamases. Isolates of Eubacterium biforme, Bifidobacterium breve, and several Clostridium spp. also produced ceftiofur-degrading β-lactamases. An agar gel overlay technique on isoelectric focusing separations of bacterial lysates showed that β-lactamase enzymes were sufficient to degrade ceftiofur. These results suggest that ceftiofur is inactivated nonenzymatically and degraded enzymatically by multiple β-lactamases from bacteria in the large intestines of cattle.
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9
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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.
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Affiliation(s)
- Nuno T Antunes
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
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10
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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
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11
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Okazaki S, Suzuki A, Komeda H, Yamaguchi S, Asano Y, Yamane T. Crystal structure and functional characterization of a D-stereospecific amino acid amidase from Ochrobactrum anthropi SV3, a new member of the penicillin-recognizing proteins. J Mol Biol 2006; 368:79-91. [PMID: 17331533 DOI: 10.1016/j.jmb.2006.10.070] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2006] [Revised: 10/19/2006] [Accepted: 10/20/2006] [Indexed: 11/28/2022]
Abstract
D-amino acid amidase (DAA) from Ochrobactrum anthropi SV3, which catalyzes the stereospecific hydrolysis of D-amino acid amides to yield the D-amino acid and ammonia, has attracted increasing attention as a catalyst for the stereospecific production of D-amino acids. In order to clarify the structure-function relationships of DAA, the crystal structures of native DAA, and of the D-phenylalanine/DAA complex, were determined at 2.1 and at 2.4 A resolution, respectively. Both crystals contain six subunits (A-F) in the asymmetric unit. The fold of DAA is similar to that of the penicillin-recognizing proteins, especially D-alanyl-D-alanine-carboxypeptidase from Streptomyces R61, and class C beta-lactamase from Enterobacter cloacae strain GC1. The catalytic residues of DAA and the nucleophilic water molecule for deacylation were assigned based on these structures. DAA has a flexible Omega-loop, similar to class C beta-lactamase. DAA forms a pseudo acyl-enzyme intermediate between Ser60 O(gamma) and the carbonyl moiety of d-phenylalanine in subunits A, B, C, D, and E, but not in subunit F. The difference between subunit F and the other subunits (A, B, C, D and E) might be attributed to the order/disorder structure of the Omega-loop: the structure of this loop cannot assigned in subunit F. Deacylation of subunit F may be facilitated by the relative movement of deprotonated His307 toward Tyr149. His307 N(epsilon2) extracts the proton from Tyr149 O(eta), then Tyr149 O(eta) attacks a nucleophilic water molecule as a general base. Gln214 on the Omega-loop is essential for forming a network of water molecules that contains the nucleophilic water needed for deacylation. Although peptidase activity is found in almost all penicillin-recognizing proteins, DAA lacks peptidase activity. The lack of transpeptidase and carboxypeptidase activities may be attributed to steric hindrance of the substrate-binding pocket by a loop comprised of residues 278-290 and the Omega-loop.
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Affiliation(s)
- Seiji Okazaki
- Department of Biotechnology, School of Engineering, Nagoya University, Chikusa, Nagoya 464-8603, Japan
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12
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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.
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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;
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13
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Goldberg SD, Iannuccilli W, Nguyen T, Ju J, Cornish VW. Identification of residues critical for catalysis in a class C beta-lactamase by combinatorial scanning mutagenesis. Protein Sci 2003; 12:1633-45. [PMID: 12876313 PMCID: PMC2323950 DOI: 10.1110/ps.0302903] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Despite their clinical importance, the mechanism of action of the class C beta-lactamases is poorly understood. In contrast to the class A and class D beta-lactamases, which contain a glutamate residue and a carbamylated lysine in their respective active sites that are thought to serve as general base catalysts for beta-lactam hydrolysis, the mechanism of activation of the serine and water nucleophiles in the class C enzymes is unclear. To probe for residues involved in catalysis, the class C beta-lactamase from Enterobacter cloacae P99 was studied by combinatorial scanning mutagenesis at 122 positions in and around the active site. Over 1000 P99 variants were screened for activity in a high-throughput in vivo antibiotic resistance assay and sequenced by 96-capillary electrophoresis to identify residues that are important for catalysis. P99 mutants showing reduced capability to convey antibiotic resistance were purified and characterized in vitro. The screen identified an active-site hydrogen-bonding network that is key to catalysis. A second cluster of residues was identified that likely plays a structural role in the enzyme. Otherwise, residues not directly contacting the substrate showed tolerance to substitution. The study lends support to the notion that the class C beta-lactamases do not have a single residue that acts as the catalytic general base. Rather, catalysis is affected by a hydrogen-bonding network in the active site, suggesting a possible charge relay system.
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Affiliation(s)
- Shalom D Goldberg
- Department of Chemistry, Columbia University, 3000 Broadway, New York, NY 10027, USA
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14
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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.
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Affiliation(s)
- George Minasov
- Department of Molecular Pharmacology & Biological Chemistry, Northwestern University, 303 East Chicago Avenue, Chicago, Illinois 60611-3008, USA
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15
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Alvarez-Idaboy J, González-Jonte R, Hernández-Laguna A, Smeyers Y. Reaction mechanism of the acyl-enzyme formation in β-lactam hydrolysis by means of quantum chemical modeling. ACTA ACUST UNITED AC 2000. [DOI: 10.1016/s0166-1280(00)00351-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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16
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Abstract
Bacillus cereus is a causative agent in both gastrointestinal and in nongastrointestinal infections. Enterotoxins, emetic toxin (cereulide), hemolysins, and phoshpolipase C as well as many enzymes such as beta-lactamases, proteases and collagenases are known as potential virulence factors of B. cereus. A special surface structure of B. cereus cells, the S-layer, has a significant role in the adhesion to host cells, in phagocytosis and in increased radiation resistance. Interest in B. cereus has been growing lately because it seems that B. cereus-related diseases, in particular food poisonings, are growing in number.
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Affiliation(s)
- A Kotiranta
- Institute of Dentistry, P.O. Box 41, FIN-00014, University of Helsinki, Helsinki, Finland
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17
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Laurent F, Poirel L, Naas T, Chaibi EB, Labia R, Boiron P, Nordmann P. Biochemical-genetic analysis and distribution of FAR-1, a class A beta-lactamase from Nocardia farcinica. Antimicrob Agents Chemother 1999; 43:1644-50. [PMID: 10390216 PMCID: PMC89337 DOI: 10.1128/aac.43.7.1644] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/1998] [Accepted: 04/23/1999] [Indexed: 11/20/2022] Open
Abstract
From genomic DNA of the clinical isolate Nocardia farcinica VIC, a 1. 6-kb Sau3AI fragment was cloned and expressed in Escherichia coli JM109. The recombinant strain expressed a beta-lactamase (pI, 4.6), FAR-1, which conferred high levels of resistance to amoxicillin, piperacillin, ticarcillin, and cephalothin. The hydrolysis constants (kcat, Km, Ki, and 50% inhibitory concentration) confirmed the MIC results and showed that FAR-1 activity is inhibited by clavulanic acid and at a low level by tazobactam and sulbactam. Moreover, FAR-1 beta-lactamase hydrolyzes aztreonam (at a low level) without significant activity against ceftazidime, cefotaxime and imipenem. FAR-1 mature protein of molecular mass ca 32 kDa, has less than 60% amino acid identity with any other class A beta-lactamases, being most closely related to PEN-A from Burkholderia cepacia (52%). A blaFAR-1-like gene was found in all studied N. farcinica strains, underlining the constitutive origin of this gene.
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Affiliation(s)
- F Laurent
- Service de Bactériologie-Virologie, Hôpital de Bicêtre, Assistance Publique-Hôpitaux de Paris, Faculté de Médecine Paris-Sud, 94275 Le Kremlin-Bicêtre Cédex, France
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18
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Fournier B, Roy PH, Lagrange PH, Philippon A. Chromosomal beta-lactamase genes of Klebsiella oxytoca are divided into two main groups, blaOXY-1 and blaOXY-2. Antimicrob Agents Chemother 1996; 40:454-9. [PMID: 8834897 PMCID: PMC163133 DOI: 10.1128/aac.40.2.454] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The chromosomally encoded beta-lactamase gene (blaOXY-2) of the wild-type Klebsiella oxytoca SL911 was cloned and sequenced. Its nucleotide sequence similarity with the previously sequenced K. oxytoca beta-lactamase gene (blaOXY-1) (Y. Arakawa, M. Ohta, N. Kido, M. Mori, H. Ito, T. Komatsu, Y. Fujii, and N. Kato, Antimicrob. Agents Chemother. 33:63-70, 1989) is 87.3%, and its amino acid similarity is 89.7%. This group of K. oxytoca beta-lactamases is related to chromosomal beta-lactamases of Citrobacter diversus, Proteus vulgaris, and Yersinia enterocolitica and to the plasmid-mediated extended-spectrum beta-lactamases MEN-1 and Toho-1. By colony hybridization with 86 strains susceptible and resistant to aztreonam, isolated in six countries, K. oxytoca beta-lactamase genes hybridized with either a specific blaOXY-1 DNA probe (668 bp) or a blaOXY-2 DNA probe (723 bp). Thus, beta-lactamase genes could be divided into two groups: blaOXY-1 (47% of the strains) and blaOXY-2 (53% of the strains). A study of isoelectric points confirmed the great variability reported in the literature. However, the two beta-lactamase groups were each represented by four different pIs: for OXY-2, 5.2, 5.7, 6.4, and 6.8, with the 5.2 form representing 59% of all OXY-2 enzymes, and for OXY-1, 7.1, 7.5, 8.2, and 8.8, with the 7.5 form representing 88% of all OXY-1 enzymes.
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Affiliation(s)
- B Fournier
- Laboratoire de Microbiologie, Université Paris VII, France
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19
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Zhang MY, Lövgren A. Cloning and sequencing of a beta-lactamase-encoding gene from the insect pathogen Bacillus thuringiensis. Gene 1995; 158:83-6. [PMID: 7789815 DOI: 10.1016/0378-1119(95)00089-o] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A beta-lactamase (Bla)-encoding gene (bla) from Bacillus thuringiensis (Bt) was cloned and the nucleotide (nt) sequence was determined. Both the nt sequence and deduced amino acid sequences reveal that the Bt Bla is very similar to that of B. cereus and other group A Bla. The transcription start point was also determined. Comparison of the upstream region of Bt bla with that of other genes suggested the presence of three sequence elements that might be involved in promoter function: the -10 (TCGGTGAT) and -35 (TTAT) sequences, an A+T-rich region (5'TACTAGCTATAATTTTTTAGT) and an inverted repeat sequence (5'-GAGATAGAGGC[GCTACTATCTC).
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Affiliation(s)
- M Y Zhang
- Department of Microbiology, Stockholm University, Sweden
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20
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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.
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Affiliation(s)
- A Matagne
- Laboratoire d'Enzymologie et Centre d'Ingénierie des Protéines, Université de Liège, Belgium
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21
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Somerville JE, Goshorn SC, Fell HP, Darveau RP. Bacterial aspects associated with the expression of a single-chain antibody fragment in Escherichia coli. Appl Microbiol Biotechnol 1994; 42:595-603. [PMID: 7765735 DOI: 10.1007/s002530050299] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The bacterial expression of a single-chain antibody fragment, designated L6 sFv, was examined. Periplasmic targeting resulted in the production of a correctly folded protein that bound tumor antigen. However, immediately after induction at either 30 degrees C or 37 degrees C there was a significant loss in bacterial viability, which was followed by a loss in absorbance. The loss in absorbance correlated with cell lysis and release of the L6 sFv into the culture supernatant. The kinetics of appearance of L6 sFv in the supernatant paralleled that of periplasmic beta-lactamase and confirmed an initial loss of cell-wall integrity prior to cell lysis. Bacteria incubated at 30 degrees C produced approximately threefold more correctly folded antibody fragment because of an increase in the number of cells/A660 at the lower incubation temperature. More than 95% of the L6 sFv, made at either incubation temperature, was incorrectly folded. Osmotic-shock procedures did not release L6 sFv. However, in situ subtilisin susceptibility experiments with bacterial spheroplasts confirmed a periplasmic location. French press disruption resulted in the release of correctly but not incorrectly folded material. Membrane fractionation revealed that the incorrectly folded L6 sFv remained associated with both the inner and outer membrane. These results demonstrate that, in this system, antibody fragment expression resulted initially in cell death, which was followed by release of protein into the culture supernatant and eventually cell lysis. It is also suggested that membrane association in the periplasmic space may impede proper folding.
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Affiliation(s)
- J E Somerville
- Inflammation Department, Bristol-Myers Squibb Pharmaceutical Research Institute, Seattle, WA 98121
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22
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Bacterial aspects associated with the expression of a single-chain antibody fragment in Escherichia coli. Appl Microbiol Biotechnol 1994. [DOI: 10.1007/bf00173926] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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23
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Farmer TH, Page JW, Payne DJ, Knowles DJ. Kinetic and physical studies of beta-lactamase inhibition by a novel penem, BRL 42715. Biochem J 1994; 303 ( Pt 3):825-30. [PMID: 7980451 PMCID: PMC1137621 DOI: 10.1042/bj3030825] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The interactions of Staphylococcus aureus, Bacillus cereus I, TEM, Klebsiella pneumoniae K1 and Enterobacter cloacae P99 beta-lactamases with the novel penem inhibitor BRL 42715 were investigated kinetically and, in some cases, by electrospray mass spectrometry (e.s.m.s.). All the beta-lactamases were rapidly inactivated by BRL 42715, with second-order rate constants ranging from 0.17 to 6.4 microM-1.s-1. The initial stoichiometry of beta-lactamase inhibition was essentially 1:1, with the exception of the K1 enzyme. In this instance about 20 molecules of BRL 42715 were hydrolysed before the enzyme was completely inhibited. Inhibited beta-lactamases did not readily regain activity in the absence of BRL 42715, the half-lives for regeneration of free enzyme ranging from 5 min for the K1 beta-lactamase to over 2 days for the staphylococcal enzyme. Recovery of activity was incomplete for TEM-1, K1 and P99 beta-lactamases, suggesting partitioning of the inhibited enzymes to give a permanently (or at least very stable) inactivated species. Examination of the interactions of the penem with TEM, B. cereus I and P99 beta-lactamases by e.s.m.s. also showed rapid and stoichiometric binding of the inhibitor. In all cases a mass increase of 264 Da over the native enzyme was observed, corresponding to the molecular mass of BRL 42715, showing that no fragmentation of the penem occurred on reaction with the beta-lactamases.
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Affiliation(s)
- T H Farmer
- Microbial Metabolism and Biochemistry Department, SmithKline Beecham Pharmaceuticals, Surrey, U.K
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24
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Escobar WA, Tan AK, Lewis ER, Fink AL. Site-directed mutagenesis of glutamate-166 in beta-lactamase leads to a branched path mechanism. Biochemistry 1994; 33:7619-26. [PMID: 7912106 DOI: 10.1021/bi00190a015] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Glutamate-166 of the Bacillus licheniformis beta-lactamase was specifically mutated to aspartate and cysteine in order to probe the function of this residue in catalysis. In both cases, a large decrease in activity (kcat/Km was 3.5 x 10(-5) smaller for E166C and 1 x 10(-3) smaller for E166D than for the wild-type) was observed, although the kinetics for the two mutants were very different. The pH-rate profiles for E166D and E166C reflected the ionization characteristics of the new residue at site 166. This result indicates that the ionization of Glu-166 is responsible for the acidic limb of the kcat/Km-pH profiles, and suggests that the function of Glu-166 is that of a general base catalyst. The kinetics of the E166C mutant were investigated in detail. An initial burst was observed, whose amplitude was stoichiometric with the enzyme concentration, suggesting rate-limiting deacylation of the acyl-enzyme intermediate. However, further study revealed that in the presence of 0.5 M sodium sulfate, which stabilizes the native conformational state, the magnitude of the burst corresponded to 2 equiv of enzyme. This observation, in conjunction with the limited effect of the mutation on Km, indicated that the mutation resulted in a change in the kinetic mechanism from the linear, acyl-enzyme pathway to one with a branch leading to an inactive form of the acyl-enzyme.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- W A Escobar
- Department of Chemistry and Biochemistry, University of California, Santa Cruz 95064
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25
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Leung YC, Robinson CV, Aplin RT, Waley SG. Site-directed mutagenesis of beta-lactamase I: role of Glu-166. Biochem J 1994; 299 ( Pt 3):671-8. [PMID: 7910734 PMCID: PMC1138073 DOI: 10.1042/bj2990671] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Two Glu-166 mutants of beta-lactamase I from Bacillus cereus 569/H were constructed: one with a lengthened side chain (E166Cmc, the S-carboxymethylcysteine mutant) and the other with the side chain shortened and made non-polar (E166A). Their kinetic properties were studied and compared with those of the wild-type and the E166D mutant (with a shortened side chain) previously made by Gibson, Christensen and Waley (1990) (Biochem. J. 272, 613-619). Surprisingly, with good penicillin substrates, Km, kcat. and kcat./Km of the two conservative mutants (E166Cmc and E166D) are similar to those of the non-conservative mutant E166A. Their kcat. values are 3000-fold lower than that of the wild-type enzyme, showing that Glu-166 is a very important residue. The acylenzyme intermediate of E166A and a good substrate, penicillin V, was trapped by acid-quench and observed by electrospray ionization mass spectrometry, suggesting that Glu-166 is more important in catalysing the deacylation step than the acylation step. The beta-lactamase I E166A mutant is about 200-fold more active than the Bacillus licheniformis E166A mutant with nitrocefin or 6 beta-furylacryloyl-amidopenicillanic acid as substrate. This suggested that other groups in the active site of the beta-lactamase I mutant may activate the catalytic water molecule for deacylation.
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Affiliation(s)
- Y C Leung
- Sir William Dunn School of Pathology, University of Oxford, U.K
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26
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Payne DJ, Skett PW, Aplin RT, Robinson CV, Knowles DJ. beta-Lactamase ragged ends detected by electrospray mass spectrometry correlates poorly with multiple banding on isoelectric focusing. BIOLOGICAL MASS SPECTROMETRY 1994; 23:159-64. [PMID: 8148407 DOI: 10.1002/bms.1200230307] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Purified preparations of TEM-2, P99, Bacillus cereus I and B. cereus II beta-lactamases were examined by electrospray (ES) mass spectrometry. The ES mass spectra of the B. cereus enzymes revealed the presence of four to five components of different mass, corresponding to the loss of different numbers of N-terminal amino acids (ragged ends). The ES mass spectra of both TEM-2 and P99 consisted of a single component with no evidence of ragged ends. All four beta-lactamase preparations were visualized on isoelectric focusing (IEF) gels stained with nitrocefin to investigate a possible correlation between IEF patterns and ragged ends. Multiple banding patterns were seen with each beta-lactamase preparation. Although these may correlate with the presence of ragged ends in the two B. cereus preparations, the satellite bands seen with P99 and TEM-2 were not associated with differences detected by ES mass spectrometry. In this study we have shown for the first time that beta-lactamase satellite bands seen on IEF are not always associated with ragged ends. Furthermore, we have illustrated the use of ES mass spectrometry to characterize the extent of ragged end formation in protein samples. This is of particular significance if the sample is required for detailed biochemical or crystallography experiments.
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Affiliation(s)
- D J Payne
- SmithKline Beecham Pharmaceuticals, Betchworth, Surrey, UK
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27
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Nukaga M, Tanimoto K, Tsukamoto K, Imajo S, Ishiguro M, Sawai T. A survey of a functional amino acid of class C beta-lactamase corresponding to Glu166 of class A beta-lactamases. FEBS Lett 1993; 332:93-8. [PMID: 8104827 DOI: 10.1016/0014-5793(93)80491-c] [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: 01/28/2023]
Abstract
The class C beta-lactamase of Citrobacter freundii GN346 is a typical cephalosporinase comprising 361 amino acids. The aspartic acid at position 217 and glutamic acid at position 219 in this beta-lactamase were, respectively, previously shown not to be the counterpart of Glu166 (ABL166) in class A beta-lactamases, even though sequence alignment of class A and C enzymes strongly suggested this possibility [(1990) FEBS Lett. 264, 211-214; (1990) J. Bacteriol. 172, 4348-4351]. We tried again to assign candidates for the counterpart of Glu166 through sequence alignment based on other criteria, the glutamic acids at positions 195 and 205 in the class C beta-lactamase being selected. To investigate this possibility, these two glutamic acids were changed to glutamine, lysine or alanine, respectively. All the mutant enzymes showed more than 50% of the activity of the wild-type enzyme, indicating that the possibility was ruled out. These results strongly suggested the possibility that the class C beta-lactamase lacks a functional acidic residue corresponding to Glu166 in class A enzymes.
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Affiliation(s)
- M Nukaga
- Division of Microbial Chemistry, Faculty of Pharmaceutical Sciences, Chiba University, Japan
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28
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Gibson RM, Errington J. A novel Bacillus subtilis expression vector based on bacteriophage phi 105. Gene X 1992; 121:137-42. [PMID: 1427087 DOI: 10.1016/0378-1119(92)90172-l] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
We have developed a novel expression vector based on the bacteriophage phi 105, and employed it for the production of mutant beta-lactamases in Bacillus subtilis. Expression of the beta-lactamase-encoding gene was low when cloned into the prophage under the control of its own promoter. However, expression was considerably elevated when the gene was inserted into the phage genome in the same orientation as phage transcription. A defective phi 105 vector was constructed with a deletion removing a region needed for cell lysis, and with a mutation in the immunity repressor, rendering it temperature sensitive. Production of beta-lactamase could then be induced by a shift in temperature and without concomitant cell lysis, facilitating purification of the protein from the culture supernatant. This phage has considerable potential for development as a vector for controllable production of heterologous proteins in B. subtilis.
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Affiliation(s)
- R M Gibson
- Sir William Dunn School of Pathology, University of Oxford, UK
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29
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Pratt RF, Krishnaraj R, Xu H. Effect of side-chain amide thionation on turnover of beta-lactam substrates by beta-lactamases. Further evidence on the question of side-chain hydrogen-bonding in catalysis. Biochem J 1992; 286 ( Pt 3):857-62. [PMID: 1417747 PMCID: PMC1132983 DOI: 10.1042/bj2860857] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Two side-chain-thionated beta-lactams, a penicillin and a cephalosporin, have been prepared and found to be not significantly poorer as substrates of typical serine (classes A and C) beta-lactamases than are their oxo analogues. This result is interpreted to mean that any hydrogen-bonding site on these enzymes for the beta-lactam side-chain amide carbonyl group must be flexible and is more likely to be a passive rather than active or essential feature of the active site. Previously, data from crystal structures and site-directed mutagenesis had suggested that the side chain of Asn-132 of class-A beta-lactamases, a component of the conserved SDN loop, forms a hydrogen bond with the side-chain carbonyl of the beta-lactam substrate and may provide significant transition-state stabilization during catalysis. The thionocephalosporin was also equally as good as its oxo analogue as a substrate of the class-B beta-lactamase II of Bacillus cereus and not significantly less effective as an inhibitor of the Streptomyces R61 DD-peptidase; a tight hydrogen-bond donor site for the beta-lactam side-chain amide is apparently not present in these enzymes either.
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Affiliation(s)
- R F Pratt
- Department of Chemistry, Wesleyan University, Middletown, CT 06459
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30
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Fluit A, Visser M. Nucleic acid analysis of antibiotic resistance. Int J Antimicrob Agents 1992; 1:205-21. [DOI: 10.1016/0924-8579(92)90031-l] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/25/1992] [Indexed: 11/30/2022]
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31
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Palzkill T, Botstein D. Probing beta-lactamase structure and function using random replacement mutagenesis. Proteins 1992; 14:29-44. [PMID: 1329081 DOI: 10.1002/prot.340140106] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A new analytical mutagenesis technique is described that involves randomizing the DNA sequence of a short stretch of a gene (3-6 codons) and determining the percentage of all possible random sequences that produce a functional protein. A low percentage of functional random sequences in a complete library of random substitutions indicates that the region mutagenized is important for the structure and/or function of the protein. Repeating the mutagenesis over many regions throughout a protein gives a global perspective of which amino acid sequences in a protein are critical. We applied this method to 66 codons of the gene encoding TEM-1 beta-lactamase in 19 separate experiments. We found that TEM-1 beta-lactamase is extremely tolerant of amino acid substitutions: on average, 44% of all mutants with random substitutions function and 20% of the substitutions are expressed, secreted, and fold well enough to function at levels similar to those for the wild-type enzyme. We also found a few exceptional regions where only a few random sequences function. Examination of the X-ray structures of homologous beta-lactamases indicates that the regions most sensitive to substitution are in the vicinity of the active site pocket or buried in the hydrophobic core of the protein. DNA sequence analysis of functional random sequences has been used to obtain more detailed information about the amino acid sequence requirements for several regions and this information has been compared to sequence conservation among several related beta-lactamases.
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Affiliation(s)
- T Palzkill
- Department of Genetics, School of Medicine, Stanford University, California 94305
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32
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Barthélémy M, Péduzzi J, Bernard H, Tancrède C, Labia R. Close amino acid sequence relationship between the new plasmid-mediated extended-spectrum beta-lactamase MEN-1 and chromosomally encoded enzymes of Klebsiella oxytoca. BIOCHIMICA ET BIOPHYSICA ACTA 1992; 1122:15-22. [PMID: 1633193 DOI: 10.1016/0167-4838(92)90121-s] [Citation(s) in RCA: 108] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Isolated from an Escherichia coli strain MEN-1 is a plasmid-mediated beta-lactamase that confers resistance to methoxy imino third-generation cephalosporins. The protein purified to homogeneity was digested by trypsin, chymotrypsin and endoproteinase Asp-N. Amino acid sequence determinations of the resulting peptides gave rise to the alignment of the 263 residues of the beta-lactamase. From amino acid sequence comparison MEN-1 was found to share more than 72% identity with the chromosomally mediated beta-lactamases of Klebsiella oxytoca. Therefore, MEN-1 is the first transferable extended-spectrum beta-lactamase which is not directly derived from the widespread TEMs or SHV-1 penicillinases with which it presents less than 39% identity.
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Affiliation(s)
- M Barthélémy
- Muséum National Histoire Naturelle, CNRS URA 401, Paris, France
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33
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Bourguignon-Bellefroid C, Joris B, Van Beeumen J, Ghuysen JM, Frère JM. Point mutations of two arginine residues in the Streptomyces R61 DD-peptidase. Biochem J 1992; 283 ( Pt 1):123-8. [PMID: 1567359 PMCID: PMC1131003 DOI: 10.1042/bj2830123] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Incubation of the exocellular DD-carboxypeptidase/transpeptidase of Streptomyces R61 with phenylglyoxal resulted in a time-dependent decrease in the enzyme activity. This inactivation was demonstrated to be due to modification of the Arg-99 side chain. In consequence, the role of that residue was investigated by site-directed mutagenesis. Mutation of Arg-99 into leucine appeared to be highly detrimental to enzyme stability, reflecting a determining structural role for this residue. The conserved Arg-103 residue was also substituted by using site-directed mutagenesis. The modification to a serine residue yielded a stable enzyme, the catalytic properties of which were similar to those of the wild-type enzyme. Thus Arg-103, although strictly conserved or replaced by a lysine residue in most of the active-site penicillin-recognizing proteins, did not appear to fulfil any essential role in either the enzyme activity or structure.
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34
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Jelsch C, Lenfant F, Masson JM, Samama JP. Beta-lactamase TEM1 of E. coli. Crystal structure determination at 2.5 A resolution. FEBS Lett 1992; 299:135-42. [PMID: 1544485 DOI: 10.1016/0014-5793(92)80232-6] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The crystal structure of beta-lactamase TEM1 from E. coli has been solved to 2.5 A resolution by X-ray diffraction methods and refined to a crystallographic R-factor of 22.7%. The structure was determined by multiple isomorphous replacement using four heavy atom derivatives. The solution from molecular replacement, using a polyalanine model constructed from the C alpha coordinates of S. Aureus PCl enzyme, provided a set of phases used for heavy atom derivatives analysis. The E. coli beta-lactamase TEM1 is made up of two domains whose topology is similar to that of the PCl enzyme. However, global superposition of the two proteins shows significant differences.
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Affiliation(s)
- C Jelsch
- Laboratoire de Cristallographie Biologique, IBMC du CNRS, Strasbourg, France
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35
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Escobar WA, Tan AK, Fink AL. Site-directed mutagenesis of beta-lactamase leading to accumulation of a catalytic intermediate. Biochemistry 1991; 30:10783-7. [PMID: 1681903 DOI: 10.1021/bi00108a025] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Site-specific mutation of Glu-166 to Ala in beta-lactamase causes a millionfold reduction in catalytic activity toward both penicillin and cephalosporin substrates and results in the stoichiometric accumulation of a normally transient acyl-enzyme intermediate. Kinetic analysis indicated that substitution of Glu-166 by Ala leads to negligible effect on the acylation half of the reaction but effectively eliminates the deacylation reaction. Such differential effects on the rates of formation and breakdown of an enzyme-substrate intermediate have not been previously reported. Thus, unlike the situation for most transfer enzymes, e.g., the serine proteases, acylation and deacylation in beta-lactamase catalysis are not "mirror" images and must involve different mechanisms. The results suggest an explanation for the different catalytic activities between the beta-lactamases and the penicillin-binding proteins involved in bacterial cell-wall synthesis.
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Affiliation(s)
- W A Escobar
- Department of Chemistry and Biochemistry, University of California, Santa Cruz 95064
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36
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Replacement of lysine 234 affects transition state stabilization in the active site of beta-lactamase TEM1. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(19)47357-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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37
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Ambler RP, Coulson AF, Frère JM, Ghuysen JM, Joris B, Forsman M, Levesque RC, Tiraby G, Waley SG. A standard numbering scheme for the class A beta-lactamases. Biochem J 1991; 276 ( Pt 1):269-70. [PMID: 2039479 PMCID: PMC1151176 DOI: 10.1042/bj2760269] [Citation(s) in RCA: 860] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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38
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Mottl H, Terpstra P, Keck W. Penicillin-binding protein 4 ofEscherichia colishows a novel type of primary structure among penicillin-interacting proteins. FEMS Microbiol Lett 1991. [DOI: 10.1111/j.1574-6968.1991.tb04445.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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39
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Herzberg O. Refined crystal structure of beta-lactamase from Staphylococcus aureus PC1 at 2.0 A resolution. J Mol Biol 1991; 217:701-19. [PMID: 2005620 DOI: 10.1016/0022-2836(91)90527-d] [Citation(s) in RCA: 184] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The crystal structure of a class A beta-lactamase from Staphylococcus aureus PC1 has been refined at 2.0 A resolution. The resulting crystallographic R-factor (R = sigma h parallel Fo[-]Fc parallel/sigma h[Fo], where [Fo] and [Fc] are the observed and calculated structure factor amplitudes, respectively), is 0.163 for the 17,547 reflections with I greater than or equal to 2 sigma (I) within the 8.0 A to 2.0 A resolution range. The molecule consists of two closely associated domains. One domain is formed by a five-stranded antiparallel beta-sheet with three helices packing against a face of the sheet. The second domain is formed mostly by helices that pack against the second face of the sheet. The active site is located in the interface between the two domains, and many of the residues that form it are conserved in all known sequences of class A beta-lactamases. Similar to the serine proteases, an oxyanion hole is implicated in catalysis. It is formed by two main-chain nitrogen atoms, that of the catalytic seryl residue, Ser70, and that of Gln237 on an edge beta-strand of the major beta-sheet. Ser70 is interacting with another conserved seryl residue, Ser130, located between the two ammonium groups of the functionally important lysine residues, Lys73 and Lys234. Such intricate interactions point to a possible catalytic role for this second seryl residue. Another key catalytic residue is Glu166. There are several unusual structural features associated with the active site. (1) A cis peptide bond has been identified between the catalytic Glu166 and Ile167. (2) Ala69 and Leu220 have strained phi, psi dihedral angles making close contacts that restrict the conformation of the active site beta-strand involved in the formation of the oxyanion hole. (3) A buried aspartate residue, the conserved Asp233, is located next to the active site Lys234. It is interacting with another buried aspartyl residue, Asp246. An internal solvent molecule is also involved, but the rest of its interactions with the protein indicate it is not a cation. (4) Another conserved aspartyl residue that is desolvated is Asp131, adjacent to Ser130. Its charge is stabilized by interactions with four main-chain nitrogen atoms. (5) An internal cavity underneath the active site depression is filled with six solvent molecules. This, and an adjacent cavity occupied by three solvent molecules partially separate the omega-loop associated with the active site from the rest of the protein.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- O Herzberg
- Center for Advanced Research in Biotechnology, Maryland Biotechnology Institute, University of Maryland, Rockville 20850
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40
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Adachi H, Ohta T, Matsuzawa H. Site-directed mutants, at position 166, of RTEM-1 beta-lactamase that form a stable acyl-enzyme intermediate with penicillin. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)49972-3] [Citation(s) in RCA: 108] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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41
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Inactivation of the RTEM-1 cysteine beta-lactamase by iodoacetate. The nature of active-site functional groups and comparisons with the native enzyme. Biochem J 1991; 273(Pt 1):85-91. [PMID: 1989590 PMCID: PMC1149883 DOI: 10.1042/bj2730085] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The pH-rate profile for inactivation of the RTEM-1 cysteine beta-lactamase by iodoacetate supports previous evidence [Knap & Pratt (1989) Proteins Struct. Funct. Genet. 6, 316-323] for the activation of the active-site thiol group by adjacent functional groups. The enhanced reactivity of iodoacetate, with respect to that of iodoacetamide, suggests the influence of a positive charge in the active site. The reactivity of iodoacetate is not affected by dissociation of an active-site functional group of pKa 6.7, which increases the reactivity of neutral reagents, probably because of a compensation phenomenon; it is, however, lost on dissociation of an acid of pKa 8.1. It is concluded that the active cysteine beta-lactamase has four functional groups at the active site, one nucleophilic thiolate of Cys-70, one neutral acid (most probably the carboxy group of Glu-166, from the crystal structures) and two cationic residues (most probably Lys-73 and Lys-234). A comparison of these results with the pH-dependence of reactivity of the native RTEM-2 beta-lactamase suggests that the active form of the latter enzyme is also monocationic, although the nucleophile (Ser-70) is likely to be neutral in this case and the carboxylic acid dissociated. A mechanism of class A beta-lactamase catalysis is discussed where the Glu-166 carboxylate acts as a general base/acid catalyst and Lys-73 is principally required for electrostatic stabilization of the anionic tetrahedral intermediate.
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42
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Site-directed mutagenesis of beta-lactamase I. Single and double mutants of Glu-166 and Lys-73. Biochem J 1990; 272:613-9. [PMID: 1980064 PMCID: PMC1149752 DOI: 10.1042/bj2720613] [Citation(s) in RCA: 120] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Two single mutants and the corresponding double mutant of beta-lactamase I from Bacillus cereus 569/H were constructed and their kinetics investigated. The mutants have Lys-73 replaced by arginine (K73R), or Glu-166 replaced by aspartic acid (E166D), or both (K73R + E166D). All four rate constants in the acyl-enzyme mechanism were determined for the E166D mutant by the methods described by Christensen, Martin & Waley [(1990) Biochem. J. 266, 853-861]. Both the rate constants for acylation and deacylation for the hydrolysis of benzylpenicillin were decreased about 2000-fold in this mutant. In the K73R mutant, and in the double mutant, the rate constants for acylation were decreased about 100-fold and 10,000-fold respectively. All three mutants also had lowered values for the rate constants for the formation and dissociation of the non-covalent enzyme-substrate complex. The specificities of the mutants did not differ greatly from those of wild-type beta-lactamase, but the hydrolysis of cephalosporin C by the K73R mutant gave 'burst' kinetics.
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43
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Jacob F, Joris B, Lepage S, Dusart J, Frère JM. Role of the conserved amino acids of the 'SDN' loop (Ser130, Asp131 and Asn132) in a class A beta-lactamase studied by site-directed mutagenesis. Biochem J 1990; 271:399-406. [PMID: 2173561 PMCID: PMC1149568 DOI: 10.1042/bj2710399] [Citation(s) in RCA: 89] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Ser130, Asp131 and Asn132 ('SDN') are highly conserved residues in class A beta-lactamases forming one wall of the active-site cavity. All three residues of the SDN loop in Streptomyces albus G beta-lactamase were modified by site-directed mutagenesis. The mutant proteins were expressed in Streptomyces lividans, purified from culture supernatants and their kinetic parameters were determined for several substrates. Ser130 was substituted by Asn, Ala and Gly. The first modification yielded an almost totally inactive protein, whereas the smaller-side-chain mutants (A and G) retained some activity, but were less stable than the wild-type enzyme. Ser130 might thus be involved in maintaining the structure of the active-site cavity. Mutations of Asp131 into Glu and Gly proved to be highly detrimental to enzyme stability, reflecting significant structural perturbations. Mutation of Asn132 into Ala resulted in a dramatically decreased enzymic activity (more than 100-fold) especially toward cephalosporin substrates, kcat. being the most affected parameter, which would indicate a role of Asn132 in transition-state stabilization rather than in ground-state binding. Comparison of the N132A and the previously described N132S mutant enzymes underline the importance of an H-bond-forming residue at position 132 for the catalytic process.
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Affiliation(s)
- F Jacob
- Laboratoire d'Enzymologie, Université de Liège, Belgium
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44
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Tsukamoto K, Ohno R, Sawai T. Extension of the substrate spectrum by an amino acid substitution at residue 219 in the Citrobacter freundii cephalosporinase. J Bacteriol 1990; 172:4348-51. [PMID: 2115867 PMCID: PMC213260 DOI: 10.1128/jb.172.8.4348-4351.1990] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The cephalosporinase of Citrobacter freundii GN346 is a class C beta-lactamase, consisting of 361 amino acids and exhibiting the substrate profile of a typical cephalosporinase. On the conversion of a conserved glutamic acid at residue 219 to lysine, the substrate spectrum of the cephalosporinase was extended to oxyimino cephalosporins, aztreonam and carbenicillin, which are essentially undesirable substrates for the enzyme. Escherichia coli cells carrying the mutant gene showed higher resistance levels to cefuroxime, aztreonam, and carbenicillin, but a lower resistance level to cefoxitin, than cells carrying the wild gene. The kcat values of the purified mutant enzyme for ceftazidime, cefuroxime, and cefmenoxime were 77,100, and 300 times those of the wild enzyme, respectively. The relative Vmax values of the mutant enzyme for aztreonam and carbenicillin were determined to be 11 and 23 times those of the wild enzyme, respectively, but the value of the mutant enzyme for cefoxitin was only one-third that of the wild enzyme.
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Affiliation(s)
- K Tsukamoto
- Division of Microbial Chemistry, Faculty of Pharmaceutical Sciences, Chiba University, Japan
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45
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Ellerby LM, Escobar WA, Fink AL, Mitchinson C, Wells JA. The role of lysine-234 in beta-lactamase catalysis probed by site-directed mutagenesis. Biochemistry 1990; 29:5797-806. [PMID: 1974463 DOI: 10.1021/bi00476a022] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Lys-234 has been postulated to participate in beta-lactamase catalysis by acting as an electrostatic anchor for the C3 carboxylate of penicillins [Herzberg, O., & Moult, J. (1987) Science 236, 694-701]. To test this hypothesis, site-directed mutagenesis was used to convert the Lys-234 in Bacillus licheniformis beta-lactamase into Glu-234 or Ala-234. The wild-type, Glu-234, and Ala-234 beta-lactamases have been expressed in Bacillus subtilis and purified to homogeneity. The wild-type, K234E, and K234A enzymes have virtually identical circular dichroism and fluorescence spectra, similar thermal stabilities at neutral pH, and the same susceptibilities to proteolysis, indicating the lack of significant structural perturbation caused by the mutation. At acidic and basic pH the mutant enzymes have the same native circular dichroism as the wild-type enzyme but the thermal stability is significantly different. The mutations cause perturbations of the pK values of the ionizing groups responsible for the pH dependence of the catalytic reaction in both the free enzyme and the E.S complex. As expected, conversion of Lys-234 to Ala or Glu decreased substrate binding (Km) by 1-2 orders of magnitude for several penicillin and cephalosporin substrates at neutral and higher pH. However, at low pH, Km is essentially the same for the K234E and K234A enzymes as for the wild-type enzyme. Furthermore, decreases of 2-3 orders of magnitude in kcat were also observed, indicating substantial effects on the transition-state binding, as well as on ground-state binding. Surprisingly, changing the C3 carboxylate of phenoxymethylpenicillin to a hydroxymethyl group led to little difference in kinetic properties with the K234E or K234A enzyme. The results of this investigation indicate the Lys-234 is an important active-site residue involved in both ground-state and transition-state binding.
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Affiliation(s)
- L M Ellerby
- Department of Chemistry, University of California, Santa Cruz 95064
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46
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Tsukamoto K, Kikura R, Ohno R, Sawai T. Substitution of aspartic acid-217 of Citrobacter freundii cephalosporinase and properties of the mutant enzymes. FEBS Lett 1990; 264:211-4. [PMID: 1972682 DOI: 10.1016/0014-5793(90)80250-m] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
On the assumption that Asp-217 of a Citrobacter freundii cephalosporinase forms a salt-bridge with the conserved Lys-67, Asp-217 was changed to glutamic acid, threonine or lysine. The mutant enzymes retained about the same level of activity as that of the wild-type enzyme, and the participation of Asp-217 in the salt-bridge was ruled out. However, the mutations resulted in an increase in hydrolytic activity toward oxyimino-cephalosporins such as cefuroxime, cefmenoxime and ceftazidime, suggesting a possible mechanism of the bacterial resistance to the novel beta-lactams by a single mutation in cephalosporinases.
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Affiliation(s)
- K Tsukamoto
- Division of Microbial Chemistry, Faculty of Pharmaceutical Sciences, Chiba University, Japan
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47
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Christensen H, Martin MT, Waley SG. Beta-lactamases as fully efficient enzymes. Determination of all the rate constants in the acyl-enzyme mechanism. Biochem J 1990; 266:853-61. [PMID: 2158301 PMCID: PMC1131217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2023]
Abstract
The rate constants for both acylation and deacylation of beta-lactamase PC1 from Staphylococcus aureus and the RTEM beta-lactamase from Escherichia coli were determined by the acid-quench method [Martin & Waley (1988) Biochem. J. 254, 923-925] with several good substrates, and, for a wider range of substrates, of beta-lactamase I from Bacillus cereus. The values of the acylation and deacylation rate constants for benzylpenicillin were approximately the same (i.e. differing by no more than 2-fold) for each enzyme. The variation of kcat./Km for benzylpenicillin with the viscosity of the medium was used to obtain values for all four rate constants in the acyl-enzyme mechanism for all three enzymes. The reaction is partly diffusion-controlled, and the rate constant for the dissociation of the enzyme-substrate complex has approximately the same value as the rate constants for acylation and deacylation. Thus all three first-order rate constants have comparable values. Here there is no single rate-determining step for beta-lactamase action. This is taken to be a sign of a fully efficient enzyme.
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Affiliation(s)
- H Christensen
- Sir William Dunn School of Pathology, University of Oxford, U.K
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48
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Tsukamoto K, Tachibana K, Yamazaki N, Ishii Y, Ujiie K, Nishida N, Sawai T. Role of lysine-67 in the active site of class C beta-lactamase from Citrobacter freundii GN346. EUROPEAN JOURNAL OF BIOCHEMISTRY 1990; 188:15-22. [PMID: 1969344 DOI: 10.1111/j.1432-1033.1990.tb15365.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Citrobacter freundii GN346 produces a class C beta-lactamase exhibiting the substrate profile of a typical cephalosporinase. The structural and promoter regions of the cephalosporinase gene, comprising 1408 nucleotides, were completely sequenced. The amino acid sequence of the mature enzyme, comprising 361 amino acids, and its molecular mass, 39,878 Da, were determined. The active site was confirmed to be Ser-64. The amino acid sequence of the enzyme differs from that of the cephalosporinase of C. freundii OS60 by nine residues. The nucleotide sequence of the promoter region suggests a possible attenuator structure. Lys-67, one of the most conserved residues found in class A and C beta-lactamases and penicillin-binding proteins, was converted into arginine, threonine or glutamic acid through site-directed mutagenesis. The Glu-67 enzyme had lost the catalytic activity and the Thr-67 enzyme only showed a trace of activity. The Arg-67 enzyme, which retained a significant amount of the activity, was purified. The Km values of the Arg-67 enzyme for cephalothin, cephaloridine and benzylpenicillin are 13-19 times those of the wild-type enzyme; the kcat values for the three substrates are 37%, 3%, and 36% those of the wild-type enzyme, respectively.
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Affiliation(s)
- K Tsukamoto
- Division of Microbial Chemistry, Faculty of Pharmaceutical Sciences, Chiba University, Japan
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49
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Moews PC, Knox JR, Dideberg O, Charlier P, Frère JM. Beta-lactamase of Bacillus licheniformis 749/C at 2 A resolution. Proteins 1990; 7:156-71. [PMID: 2326252 DOI: 10.1002/prot.340070205] [Citation(s) in RCA: 153] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Two crystal forms (A and B) of the 29,500 Da Class A beta-lactamase (penicillinase) from Bacillus licheniformis 749/C have been examined crystallographically. The structure of B-form crystals has been solved to 2 A resolution, the starting model for which was a 3.5 A structure obtained from A-form crystals. The beta-lactamase has an alpha + beta structure with 11 helices and 5 beta-strands seen also in a penicillin target DD-peptidase of Streptomyces R61. Atomic parameters of the two molecules in the asymmetric unit were refined by simulated annealing at 2.0 A resolution. The R factor is 0.208 for the 27,330 data greater than 3 sigma (F), with water molecules excluded from the model. The catalytic Ser-70 is at the N-terminus of a helix and is within hydrogen bonding distance of conserved Lys-73. Also interacting with the Lys-73 are Asn-132 and the conserved Glu-166, which is on a potentially flexible helix-containing loop. The structure suggests the binding of beta-lactam substrates is facilitated by interactions with Lys-234, Thr-235, and Ala-237 in a conserved beta-strand peptide, which is antiparallel to the beta-lactam's acylamido linkage; an exposed cavity near Asn-170 exists for acylamido substituents. The reactive double bond of clavulanate-type inhibitors may interact with Arg-244 on the fourth beta-strand. A very similar binding site architecture is seen in the DD-peptidase.
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Affiliation(s)
- P C Moews
- Department of Molecular and Cell Biology, University of Connecticut, Storrs 06269
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50
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Matagne A, Misselyn-Bauduin AM, Joris B, Erpicum T, Granier B, Frère JM. The diversity of the catalytic properties of class A beta-lactamases. Biochem J 1990; 265:131-46. [PMID: 2302162 PMCID: PMC1136623 DOI: 10.1042/bj2650131] [Citation(s) in RCA: 153] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The catalytic properties of four class A beta-lactamases were studied with 24 different substrates. They exhibit a wide range of variation. Similarly, the amino acid sequences are also quite different. However, no relationships were found between the sequence similarities and the substrate profiles. Lags and bursts were observed with various compounds containing a large sterically hindered side chain. As a group, the enzymes could be distinguished from the class C beta-lactamases on the basis of the kappa cat. values for several substrates, particularly oxacillin, cloxacillin and carbenicillin. Surprisingly, that distinction was impossible with the kappa cat./Km values, which represent the rates of acylation of the active-site serine residue by the beta-lactam. For several cephalosporin substrates (e.g. cefuroxime and cefotaxime) class A enzymes consistently exhibited higher kappa cat. values than class C enzymes, thus belying the usual distinction between 'penicillinases' and 'cephalosporinases'. The problem of the repartition of class A beta-lactamases into sub-classes is discussed.
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Affiliation(s)
- A Matagne
- Université de Liège, Institute de Chimie, Belgium
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