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Opening of a cryptic pocket in β-lactamase increases penicillinase activity. Proc Natl Acad Sci U S A 2021; 118:2106473118. [PMID: 34799442 PMCID: PMC8617505 DOI: 10.1073/pnas.2106473118] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/06/2021] [Indexed: 11/18/2022] Open
Abstract
A protein is a shape-shifter, but it is currently unclear which of the many structures a protein can adopt are relevant for its function. Here, we examine conformations that contain a “cryptic” pocket (i.e., a pocket absent in ligand-free structures). Cryptic pockets have potential utility in drug discovery efforts because they provide a means to target “undruggable” proteins (i.e., proteins lacking known pockets) or enhance rather than inhibit protein function. In this study, we use a combination of thiol-labeling and kinetic assays, NMR, and molecular dynamic simulations to identify the function of the Ω-loop cryptic pocket in β-lactamase enzymes. We find that an open pocket population is beneficial for hydrolysis of the substrate benzylpenicillin. Understanding the functional role of protein-excited states has important implications in protein design and drug discovery. However, because these states are difficult to find and study, it is still unclear if excited states simply result from thermal fluctuations and generally detract from function or if these states can actually enhance protein function. To investigate this question, we consider excited states in β-lactamases and particularly a subset of states containing a cryptic pocket which forms under the Ω-loop. Given the known importance of the Ω-loop and the presence of this pocket in at least two homologs, we hypothesized that these excited states enhance enzyme activity. Using thiol-labeling assays to probe Ω-loop pocket dynamics and kinetic assays to probe activity, we find that while this pocket is not completely conserved across β-lactamase homologs, those with the Ω-loop pocket have a higher activity against the substrate benzylpenicillin. We also find that this is true for TEM β-lactamase variants with greater open Ω-loop pocket populations. We further investigate the open population using a combination of NMR chemical exchange saturation transfer experiments and molecular dynamics simulations. To test our understanding of the Ω-loop pocket’s functional role, we designed mutations to enhance/suppress pocket opening and observed that benzylpenicillin activity is proportional to the probability of pocket opening in our designed variants. The work described here suggests that excited states containing cryptic pockets can be advantageous for function and may be favored by natural selection, increasing the potential utility of such cryptic pockets as drug targets.
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2
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Furey IM, Mehta SC, Sankaran B, Hu L, Prasad BVV, Palzkill T. Local interactions with the Glu166 base and the conformation of an active site loop play key roles in carbapenem hydrolysis by the KPC-2 β-lactamase. J Biol Chem 2021; 296:100799. [PMID: 34022225 PMCID: PMC8189571 DOI: 10.1016/j.jbc.2021.100799] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/06/2021] [Accepted: 05/17/2021] [Indexed: 01/05/2023] Open
Abstract
The Klebsiella pneumoniae carbapenemase-2 (KPC-2) is a common source of antibiotic resistance in Gram-negative bacterial infections. KPC-2 is a class A β-lactamase that exhibits a broad substrate profile and hydrolyzes most β-lactam antibiotics including carbapenems owing to rapid deacylation of the covalent acyl-enzyme intermediate. However, the features that allow KPC-2 to deacylate substrates more rapidly than non-carbapenemase enzymes are not clear. The active-site residues in KPC-2 are largely conserved in sequence and structure compared with non-carbapenemases, suggesting that subtle alterations may collectively facilitate hydrolysis of carbapenems. We utilized a nonbiased genetic approach to identify mutants deficient in carbapenem hydrolysis but competent for ampicillin hydrolysis. Subsequent pre–steady-state enzyme kinetics analyses showed that the substitutions slow the rate of deacylation of carbapenems. Structure determination via X-ray diffraction indicated that a F72Y mutant forms a hydrogen bond between the tyrosine hydroxyl group and Glu166, which may lower basicity and impair the activation of the catalytic water for deacylation, whereas several mutants impact the structure of the Q214-R220 active site loop. A T215P substitution lowers the deacylation rate and drastically alters the conformation of the loop, thereby disrupting interactions between the enzyme and the carbapenem acyl-enzyme intermediate. Thus, the environment of the Glu166 general base and the precise placement and conformational stability of the Q214-R220 loop are critical for efficient deacylation of carbapenems by the KPC-2 enzyme. Therefore, the design of carbapenem antibiotics that interact with Glu166 or alter the Q214-R220 loop conformation may disrupt enzyme function and overcome resistance.
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Affiliation(s)
- Ian M Furey
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Shrenik C Mehta
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Banumathi Sankaran
- Department of Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Liya Hu
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston Texas, USA
| | - B V Venkataram Prasad
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston Texas, USA
| | - Timothy Palzkill
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston Texas, USA.
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3
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Stojanoski V, Hu L, Sankaran B, Wang F, Tao P, Prasad BVV, Palzkill T. Mechanistic Basis of OXA-48-like β-Lactamases' Hydrolysis of Carbapenems. ACS Infect Dis 2021; 7:445-460. [PMID: 33492952 DOI: 10.1021/acsinfecdis.0c00798] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Carbapenem-hydrolyzing class D β-lactamases (CHDLs) are an important source of resistance to these last resort β-lactam antibiotics. OXA-48 is a member of a group of CHDLs named OXA-48-like enzymes. On the basis of sequence similarity, OXA-163 can be classified as an OXA-48-like enzyme, but it has altered substrate specificity. Compared to OXA-48, it shows impaired activity for carbapenems but displays an enhanced hydrolysis of oxyimino-cephalosporins. Here, we address the mechanistic and structural basis for carbapenem hydrolysis by OXA-48-like enzymes. Pre-steady-state kinetic analysis indicates that the rate-limiting step for OXA-48 and OXA-163 hydrolysis of carbapenems is deacylation and that the greatly reduced carbapenemase activity of OXA-163 compared to that of OXA-48 is due entirely to a slower deacylation reaction. Furthermore, our structural data indicate that the positioning of the β5-β6 loop is necessary for carbapenem hydrolysis by OXA-48. A major difference between the OXA-48 and OXA-163 complexes with carbapenems is that the 214-RIEP-217 deletion in OXA-163 creates a large opening in the active site that is absent in the OXA-48/carbapenem structures. We propose that the larger active site results in less constraint on the conformation of the 6α-hydroxyethyl group in the acyl-enzyme. The acyl-enzyme intermediate assumes multiple conformations, most of which are incompatible with rapid deacylation. Consistent with this hypothesis, molecular dynamics simulations indicate that the most stable complex is formed between OXA-48 and imipenem, which correlates with the OXA-48 hydrolysis of imipenem being the fastest observed. Furthermore, the OXA-163 complexes with imipenem and meropenem are the least stable and show significant conformational fluctuations, which correlates with the slow hydrolysis of these substrates.
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Affiliation(s)
| | | | - Banumathi Sankaran
- Department of Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States,
| | - Feng Wang
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas 75205, United States
| | - Peng Tao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas 75205, United States
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4
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Mehta SC, Furey IM, Pemberton OA, Boragine DM, Chen Y, Palzkill T. KPC-2 β-lactamase enables carbapenem antibiotic resistance through fast deacylation of the covalent intermediate. J Biol Chem 2021; 296:100155. [PMID: 33273017 PMCID: PMC7895804 DOI: 10.1074/jbc.ra120.015050] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 11/24/2020] [Accepted: 12/03/2020] [Indexed: 01/23/2023] Open
Abstract
Serine active-site β-lactamases hydrolyze β-lactam antibiotics through the formation of a covalent acyl-enzyme intermediate followed by deacylation via an activated water molecule. Carbapenem antibiotics are poorly hydrolyzed by most β-lactamases owing to slow hydrolysis of the acyl-enzyme intermediate. However, the emergence of the KPC-2 carbapenemase has resulted in widespread resistance to these drugs, suggesting it operates more efficiently. Here, we investigated the unusual features of KPC-2 that enable this resistance. We show that KPC-2 has a 20,000-fold increased deacylation rate compared with the common TEM-1 β-lactamase. Furthermore, kinetic analysis of active site alanine mutants indicates that carbapenem hydrolysis is a concerted effort involving multiple residues. Substitution of Asn170 greatly decreases the deacylation rate, but this residue is conserved in both KPC-2 and non-carbapenemase β-lactamases, suggesting it promotes carbapenem hydrolysis only in the context of KPC-2. X-ray structure determination of the N170A enzyme in complex with hydrolyzed imipenem suggests Asn170 may prevent the inactivation of the deacylating water by the 6α-hydroxyethyl substituent of carbapenems. In addition, the Thr235 residue, which interacts with the C3 carboxylate of carbapenems, also contributes strongly to the deacylation reaction. In contrast, mutation of the Arg220 and Thr237 residues decreases the acylation rate and, paradoxically, improves binding affinity for carbapenems. Thus, the role of these residues may be ground state destabilization of the enzyme-substrate complex or, alternatively, to ensure proper alignment of the substrate with key catalytic residues to facilitate acylation. These findings suggest modifications of the carbapenem scaffold to avoid hydrolysis by KPC-2 β-lactamase.
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Affiliation(s)
- Shrenik C Mehta
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Ian M Furey
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Orville A Pemberton
- Department of Molecular Medicine, University of South Florida Morsani College of Medicine, Tampa, Florida, USA
| | - David M Boragine
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Yu Chen
- Department of Molecular Medicine, University of South Florida Morsani College of Medicine, Tampa, Florida, USA
| | - Timothy Palzkill
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA.
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5
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Soeung V, Lu S, Hu L, Judge A, Sankaran B, Prasad BVV, Palzkill T. A drug-resistant β-lactamase variant changes the conformation of its active-site proton shuttle to alter substrate specificity and inhibitor potency. J Biol Chem 2020; 295:18239-18255. [PMID: 33109613 DOI: 10.1074/jbc.ra120.016103] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/22/2020] [Indexed: 11/06/2022] Open
Abstract
Lys234 is one of the residues present in class A β-lactamases that is under selective pressure due to antibiotic use. Located adjacent to proton shuttle residue Ser130, it is suggested to play a role in proton transfer during catalysis of the antibiotics. The mechanism underpinning how substitutions in this position modulate inhibitor efficiency and substrate specificity leading to drug resistance is unclear. The K234R substitution identified in several inhibitor-resistant β-lactamase variants is associated with decreased potency of the inhibitor clavulanic acid, which is used in combination with amoxicillin to overcome β-lactamase-mediated antibiotic resistance. Here we show that for CTX-M-14 β-lactamase, whereas Lys234 is required for hydrolysis of cephalosporins such as cefotaxime, either lysine or arginine is sufficient for hydrolysis of ampicillin. Further, by determining the acylation and deacylation rates for cefotaxime hydrolysis, we show that both rates are fast, and neither is rate-limiting. The K234R substitution causes a 1500-fold decrease in the cefotaxime acylation rate but a 5-fold increase in kcat for ampicillin, suggesting that the K234R enzyme is a good penicillinase but a poor cephalosporinase due to slow acylation. Structural results suggest that the slow acylation by the K234R enzyme is due to a conformational change in Ser130, and this change also leads to decreased inhibition potency of clavulanic acid. Because other inhibitor resistance mutations also act through changes at Ser130 and such changes drastically reduce cephalosporin but not penicillin hydrolysis, we suggest that clavulanic acid paired with an oxyimino-cephalosporin rather than penicillin would impede the evolution of resistance.
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Affiliation(s)
- Victoria Soeung
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Shuo Lu
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Liya Hu
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Allison Judge
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Banumathi Sankaran
- Department of Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - B V Venkataram Prasad
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Timothy Palzkill
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA.
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6
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Palacios AR, Rossi MA, Mahler GS, Vila AJ. Metallo-β-Lactamase Inhibitors Inspired on Snapshots from the Catalytic Mechanism. Biomolecules 2020; 10:E854. [PMID: 32503337 PMCID: PMC7356002 DOI: 10.3390/biom10060854] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 05/31/2020] [Accepted: 06/01/2020] [Indexed: 02/06/2023] Open
Abstract
β-Lactam antibiotics are the most widely prescribed antibacterial drugs due to their low toxicity and broad spectrum. Their action is counteracted by different resistance mechanisms developed by bacteria. Among them, the most common strategy is the expression of β-lactamases, enzymes that hydrolyze the amide bond present in all β-lactam compounds. There are several inhibitors against serine-β-lactamases (SBLs). Metallo-β-lactamases (MBLs) are Zn(II)-dependent enzymes able to hydrolyze most β-lactam antibiotics, and no clinically useful inhibitors against them have yet been approved. Despite their large structural diversity, MBLs have a common catalytic mechanism with similar reaction species. Here, we describe a number of MBL inhibitors that mimic different species formed during the hydrolysis process: substrate, transition state, intermediate, or product. Recent advances in the development of boron-based and thiol-based inhibitors are discussed in the light of the mechanism of MBLs. We also discuss the use of chelators as a possible strategy, since Zn(II) ions are essential for substrate binding and catalysis.
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Affiliation(s)
- Antonela R. Palacios
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Ocampo and Esmeralda, S2002LRK Rosario, Argentina; (A.R.P.); (M.-A.-R.)
| | - María-Agustina Rossi
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Ocampo and Esmeralda, S2002LRK Rosario, Argentina; (A.R.P.); (M.-A.-R.)
| | - Graciela S. Mahler
- Laboratorio de Química Farmacéutica, Facultad de Química, Universidad de la Republica (UdelaR), Montevideo 11800, Uruguay;
| | - Alejandro J. Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Ocampo and Esmeralda, S2002LRK Rosario, Argentina; (A.R.P.); (M.-A.-R.)
- Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, S2002LRK Rosario, Argentina
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7
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Kabra A, Rumpa E, Li Y. Modulation of conformational equilibrium by phosphorylation underlies the activation of deubiquitinase A. J Biol Chem 2020; 295:3945-3951. [PMID: 32071088 DOI: 10.1074/jbc.ac119.010808] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 02/16/2020] [Indexed: 01/20/2023] Open
Abstract
Deubiquitinases deconjugate ubiquitin modifications from target proteins and are involved in many cellular processes in eukaryotes. The functions of deubiquitinases are regulated by post-translational modifications, mainly phosphorylation and ubiquitination. Post-translational modifications can result in subtle changes in structural and dynamic properties, which are difficult to identify but functionally important. In this work, we used NMR spectroscopy to characterize the conformational properties of the human deubiquitinase A (DUBA), a negative regulator of type I interferon. DUBA activity is regulated by phosphorylation at a single serine residue, Ser-177. We found that the catalytic rate constant of DUBA is enhanced by phosphorylation. By comparing NMR and enzyme kinetics data among different forms of DUBA with low and high activities, we concluded that a two-state equilibrium that was present only in phosphorylated DUBA is important for DUBA activity. Our results highlight the importance of defining conformational dynamics in understanding the mechanism of DUBA activation.
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Affiliation(s)
- Ashish Kabra
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40208
| | - Efsita Rumpa
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40208
| | - Ying Li
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40208
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8
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Chow C, Xu H, Blanchard JS. Kinetic characterization of hydrolysis of nitrocefin, cefoxitin, and meropenem by β-lactamase from Mycobacterium tuberculosis. Biochemistry 2013; 52:4097-104. [PMID: 23672214 DOI: 10.1021/bi400177y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The constitutively expressed, chromosomally encoded β-lactamase (BlaC) is the enzyme responsible for the intrinsic resistance to β-lactam antibiotics in Mycobacterium tuberculosis. Previous studies from this laboratory have shown that the enzyme exhibits an extended-spectrum phenotype, with very high levels of penicillinase and cephalosporinase activity, as well as weak carbapenemase activity [Tremblay, L. W., et al. (2008) Biochemistry 47, 5312-5316]. In this report, we have determined the pH dependence of the kinetic parameters, revealing that the maximal velocity depends on the ionization state of two groups: a general base exhibiting a pK value of 4.5 and a general acid exhibiting a pK value of 7.8. Having defined a region where the kinetic parameters are pH-independent (pH 6.5), we determined solvent kinetic isotope effects (SKIEs) for three substrates whose kcat values differ by 5.5 orders of magnitude. Nitrocefin is a highly activated, chromogenic cephalosporin derivative that exhibits steady-state solvent kinetic isotope effects of 1.4 on both V and V/K. Cefoxitin is a slower cephalosporin derivative that exhibits a large SKIE on V of 3.9 but a small SKIE of 1.8 on V/K in steady-state experiments. Pre-steady-state, stopped-flow experiments with cefoxitin revealed a burst of β-lactam ring opening with associated SKIE values of 1.6 on the acylation step and 3.4 on the deacylation step. Meropenem is an extremely slow substrate for BlaC and exhibits burst kinetics in the steady-state experiments. SKIE determinations with meropenem revealed large SKIEs on both the acylation and deacylation steps of 3.8 and 4.0, respectively. Proton inventories in all cases were linear, indicating the participation of a single solvent-derived proton in the chemical step responsible for the SKIE. The rate-limiting steps for β-lactam hydrolysis of these substrates are analyzed, and the chemical steps responsible for the observed SKIE are discussed.
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Affiliation(s)
- Carmen Chow
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
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9
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Tsutakawa SE, Shin DS, Mol CD, Izumi T, Arvai AS, Mantha AK, Szczesny B, Ivanov IN, Hosfield DJ, Maiti B, Pique ME, Frankel KA, Hitomi K, Cunningham RP, Mitra S, Tainer JA. Conserved structural chemistry for incision activity in structurally non-homologous apurinic/apyrimidinic endonuclease APE1 and endonuclease IV DNA repair enzymes. J Biol Chem 2013; 288:8445-8455. [PMID: 23355472 DOI: 10.1074/jbc.m112.422774] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Non-coding apurinic/apyrimidinic (AP) sites in DNA form spontaneously and as DNA base excision repair intermediates are the most common toxic and mutagenic in vivo DNA lesion. For repair, AP sites must be processed by 5' AP endonucleases in initial stages of base repair. Human APE1 and bacterial Nfo represent the two conserved 5' AP endonuclease families in the biosphere; they both recognize AP sites and incise the phosphodiester backbone 5' to the lesion, yet they lack similar structures and metal ion requirements. Here, we determined and analyzed crystal structures of a 2.4 Å resolution APE1-DNA product complex with Mg(2+) and a 0.92 Å Nfo with three metal ions. Structural and biochemical comparisons of these two evolutionarily distinct enzymes characterize key APE1 catalytic residues that are potentially functionally similar to Nfo active site components, as further tested and supported by computational analyses. We observe a magnesium-water cluster in the APE1 active site, with only Glu-96 forming the direct protein coordination to the Mg(2+). Despite differences in structure and metal requirements of APE1 and Nfo, comparison of their active site structures surprisingly reveals strong geometric conservation of the catalytic reaction, with APE1 catalytic side chains positioned analogously to Nfo metal positions, suggesting surprising functional equivalence between Nfo metal ions and APE1 residues. The finding that APE1 residues are positioned to substitute for Nfo metal ions is supported by the impact of mutations on activity. Collectively, the results illuminate the activities of residues, metal ions, and active site features for abasic site endonucleases.
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Affiliation(s)
| | - David S Shin
- Scripps Research Institute, La Jolla, California 92037
| | | | - Tadahide Izumi
- University of Kentucky, Lexington, Kentucky 40536; University of Texas Medical Branch, Galveston, Texas 77555
| | | | - Anil K Mantha
- University of Texas Medical Branch, Galveston, Texas 77555
| | | | | | | | | | - Mike E Pique
- Scripps Research Institute, La Jolla, California 92037
| | | | - Kenichi Hitomi
- Lawrence Berkeley National Laboratory, Berkeley, California 94720; Scripps Research Institute, La Jolla, California 92037; Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | | | - Sankar Mitra
- University of Texas Medical Branch, Galveston, Texas 77555
| | - John A Tainer
- Lawrence Berkeley National Laboratory, Berkeley, California 94720; Scripps Research Institute, La Jolla, California 92037.
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10
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Mourão MA, Srividhya J, McSharry PE, Crampin EJ, Schnell S. A graphical user interface for a method to infer kinetics and network architecture (MIKANA). PLoS One 2011; 6:e27534. [PMID: 22096591 PMCID: PMC3214083 DOI: 10.1371/journal.pone.0027534] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Accepted: 10/19/2011] [Indexed: 11/18/2022] Open
Abstract
One of the main challenges in the biomedical sciences is the determination of reaction mechanisms that constitute a biochemical pathway. During the last decades, advances have been made in building complex diagrams showing the static interactions of proteins. The challenge for systems biologists is to build realistic models of the dynamical behavior of reactants, intermediates and products. For this purpose, several methods have been recently proposed to deduce the reaction mechanisms or to estimate the kinetic parameters of the elementary reactions that constitute the pathway. One such method is MIKANA: Method to Infer Kinetics And Network Architecture. MIKANA is a computational method to infer both reaction mechanisms and estimate the kinetic parameters of biochemical pathways from time course data. To make it available to the scientific community, we developed a Graphical User Interface (GUI) for MIKANA. Among other features, the GUI validates and processes an input time course data, displays the inferred reactions, generates the differential equations for the chemical species in the pathway and plots the prediction curves on top of the input time course data. We also added a new feature to MIKANA that allows the user to exclude a priori known reactions from the inferred mechanism. This addition improves the performance of the method. In this article, we illustrate the GUI for MIKANA with three examples: an irreversible Michaelis–Menten reaction mechanism; the interaction map of chemical species of the muscle glycolytic pathway; and the glycolytic pathway of Lactococcus lactis. We also describe the code and methods in sufficient detail to allow researchers to further develop the code or reproduce the experiments described. The code for MIKANA is open source, free for academic and non-academic use and is available for download (Information S1).
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Affiliation(s)
- Márcio A. Mourão
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Jeyaraman Srividhya
- The Biocomplexity Institute, Department of Physics, Indiana University, Bloomington, Indiana, United States of America
| | - Patrick E. McSharry
- Smith School of Enterprise and the Environment, University of Oxford, Oxford, United Kingdom
- Mathematical Institute, University of Oxford, Oxford, United Kingdom
| | - Edmund J. Crampin
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
- Department of Engineering Science, University of Auckland, Auckland, New Zealand
| | - Santiago Schnell
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- Center for Computational Medicine & Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- Brehm Center for Diabetes Research, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- * E-mail:
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11
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Srividhya J, Mourão MA, Crampin EJ, Schnell S. Enzyme catalyzed reactions: from experiment to computational mechanism reconstruction. Comput Biol Chem 2009; 34:11-8. [PMID: 19945917 DOI: 10.1016/j.compbiolchem.2009.10.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2009] [Revised: 10/23/2009] [Accepted: 10/23/2009] [Indexed: 11/30/2022]
Abstract
The traditional experimental practice in enzyme kinetics involves the measurement of substrate or product concentrations as a function of time. Advances in computing have produced novel approaches for modeling enzyme catalyzed reactions from time course data. One example of such an approach is the selection of appropriate chemical reactions that best fit the data. A common limitation of this approach resides in the number of chemical species considered. The number of possible chemical reactions grows exponentially with the number of chemical species, which makes difficult to select reactions that uniquely describe the data and diminishes the efficiency of the methods. In addition, a method's performance is also dependent on several quantitative and qualitative properties of the time course data, of which we know very little. This information is important to experimentalists as it could allow them to setup their experiments in ways that optimize the network reconstruction. We have previously described a method for inferring reaction mechanisms and kinetic rate parameters from time course data. Here, we address the limitations in the number of chemical reactions by allowing the introduction of information about chemical interactions. We also address the unknown properties of the input data by determining experimental data properties that maximize our method's performance. We investigate the following properties: initial substrate-enzyme concentration ratios; initial substrate-enzyme concentration variation ranges; number of data points; number of different experiments (time courses); and noise. We test the method using data generated in silico from the Michaelis-Menten and the Hartley-Kilby reaction mechanisms. Our results demonstrate the importance of experimental design for time course assays that has not been considered in experimental protocols. These considerations can have far reaching implications for the computational mechanism reconstruction process.
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Affiliation(s)
- Jeyaraman Srividhya
- Institute for Mathematics and Its Applications, University of Minnesota, Minneapolis, MN 55455, USA
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12
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Schlee S, Deuss M, Bruning M, Ivens A, Schwab T, Hellmann N, Mayans O, Sterner R. Activation of anthranilate phosphoribosyltransferase from Sulfolobus solfataricus by removal of magnesium inhibition and acceleration of product release . Biochemistry 2009; 48:5199-209. [PMID: 19385665 DOI: 10.1021/bi802335s] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Anthranilate phosphoribosyltransferase from the hyperthermophilic archaeon Sulfolobus solfataricus (ssAnPRT) is encoded by the sstrpD gene and catalyzes the reaction of anthranilate (AA) with a complex of Mg(2+) and 5'-phosphoribosyl-alpha1-pyrophosphate (Mg.PRPP) to N-(5'-phosphoribosyl)-anthranilate (PRA) and pyrophosphate (PP(i)) within tryptophan biosynthesis. The ssAnPRT enzyme is highly thermostable (half-life at 85 degrees C = 35 min) but only marginally active at ambient temperatures (turnover number at 37 degrees C = 0.33 s(-1)). To understand the reason for the poor catalytic proficiency of ssAnPRT, we have isolated from an sstrpD library the activated ssAnPRT-D83G + F149S double mutant by metabolic complementation of an auxotrophic Escherichia coli strain. Whereas the activity of purified wild-type ssAnPRT is strongly reduced in the presence of high concentrations of Mg(2+) ions, this inhibition is no longer observed in the double mutant and the ssAnPRT-D83G single mutant. The comparison of the crystal structures of activated and wild-type ssAnPRT shows that the D83G mutation alters the binding mode of the substrate Mg.PRPP. Analysis of PRPP and Mg(2+)-dependent enzymatic activity indicates that this leads to a decreased affinity for a second Mg(2+) ion and thus reduces the concentration of enzymes with the inhibitory Mg(2).PRPP complex bound to the active site. Moreover, the turnover number of the double mutant ssAnPRT-D83G + F149S is elevated 40-fold compared to the wild-type enzyme, which can be attributed to an accelerated release of the product PRA. This effect appears to be mainly caused by an increased conformational flexibility induced by the F149S mutation, a hypothesis which is supported by the reduced thermal stability of the ssAnPRT-F149S single mutant.
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Affiliation(s)
- Sandra Schlee
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Germany
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13
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Dal Peraro M, Llarrull LI, Rothlisberger U, Vila AJ, Carloni P. Water-Assisted Reaction Mechanism of Monozinc β-Lactamases. J Am Chem Soc 2004; 126:12661-8. [PMID: 15453800 DOI: 10.1021/ja048071b] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hybrid Car-Parrinello QM/MM calculations are used to investigate the reaction mechanism of hydrolysis of a common beta-lactam substrate (cefotaxime) by the monozinc beta-lactamase from Bacillus cereus (BcII). The calculations suggest a fundamental role for an active site water in the catalytic mechanism. This water molecule binds the zinc ion in the first step of the reaction, expanding the zinc coordination number and providing a proton donor adequately oriented for the second step. The free energy barriers of the two reaction steps are similar and consistent with the available experimental data. The conserved hydrogen bond network in the active site, defined by Asp120, Cys221, and His263, not only contributes to orient the nucleophile (as already proposed), but it also guides the second catalytic water molecule to the zinc ion after the substrate is bound. The hydrolysis reaction in water has a relatively high free energy barrier, which is consistent with the stability of cefotaxime in water solution. The modeled Michaelis complexes for other substrates are also characterized by the presence of an ordered water molecule in the same position, suggesting that this mechanism might be general for the hydrolysis of different beta-lactam substrates.
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Affiliation(s)
- Matteo Dal Peraro
- International School for Advanced Studies, SISSA-ISAS, INFM-Democritos Center, via Beirut 4, 34014 Trieste, Italy
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14
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Dal Peraro M, Vila AJ, Carloni P. Substrate binding to mononuclear metallo-β-lactamase from Bacillus cereus. Proteins 2003; 54:412-23. [PMID: 14747990 DOI: 10.1002/prot.10554] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Structure and dynamics of substrate binding (cefotaxime) to the catalytic pocket of the mononuclear zinc-beta-lactamase from Bacillus cereus are investigated by molecular dynamics simulations. The calculations, which are based on the hydrogen-bond pattern recently proposed by Dal Peraro et al. (J Biol Inorg Chem 2002; 7:704-712), are carried out for both the free and the complexed enzyme. In the resting state, active site pattern and temperature B-factors are in agreement with crystallographic data. In the complexed form, cefotaxime is accommodated into a stable orientation in the catalytic pocket within the nanosecond timescale, interacting with the enzyme zinc-bound hydroxide and the surrounding loops. The beta-lactam ring remains stable and very close to the hydroxide nucleophile agent, giving a stable representation of the productive enzyme-substrate complex.
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Affiliation(s)
- Matteo Dal Peraro
- International School for Advanced Studies, SISSA and INFM-DEMOCRITOS, Trieste, Italy
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15
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Taibi-Tronche P, Massova I, Vakulenko SB, Lerner SA, Mobashery S. Evidence for Structural Elasticity of Class A β-Lactamases in the Course of Catalytic Turnover of the Novel Cephalosporin Cefepime. J Am Chem Soc 1996. [DOI: 10.1021/ja9529753] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pascale Taibi-Tronche
- Contribution from the Departments of Chemistry, Medicine, and Biochemistry, Wayne State University, Detroit, Michigan 48202
| | - Irina Massova
- Contribution from the Departments of Chemistry, Medicine, and Biochemistry, Wayne State University, Detroit, Michigan 48202
| | - Sergei B. Vakulenko
- Contribution from the Departments of Chemistry, Medicine, and Biochemistry, Wayne State University, Detroit, Michigan 48202
| | - Stephen A. Lerner
- Contribution from the Departments of Chemistry, Medicine, and Biochemistry, Wayne State University, Detroit, Michigan 48202
| | - Shahriar Mobashery
- Contribution from the Departments of Chemistry, Medicine, and Biochemistry, Wayne State University, Detroit, Michigan 48202
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16
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Tan AK, Fink AL. Identification of the site of covalent attachment of nafcillin, a reversible suicide inhibitor of beta-lactamase. Biochem J 1992; 281 ( Pt 1):191-6. [PMID: 1731755 PMCID: PMC1130660 DOI: 10.1042/bj2810191] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Nafcillin was shown to reversibly inhibit beta-lactamase from Staphylococcus aureus PC1 with characteristics indicative of a type A inhibitor [Citri, Samuni & Zyk (1976) Proc. Natl. Acad. Sci. U.S.A. 73, 1048-1052]. At nafcillin concentrations above 80 mM, complete inactivation occurred within 200 s. Upon removal of the excess nafcillin the inhibited enzyme was re-activated completely, with a rate constant of 2.0 x 10(-3) s-1 (25 degrees C). The inhibited enzyme was shown to be in the form of a covalent acyl-enzyme intermediate. Digestion by pepsin and trypsin yielded a single nafcillin-labelled peptide fragment which was isolated, sequenced and shown to be: Ala-Tyr-Ala-Ser-Thr-Ser-Lys. This sequence corresponds to the region surrounding the active-site serine residue, Ser-70, indicating that the inhibitor is covalently attached to the same residue as productive substrates.
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Affiliation(s)
- A K Tan
- Department of Chemistry and Biochemistry, University of California, Santa Cruz 95064
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17
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Company M, Benitez MJ, Jiménez JS. Degradation of beta-lactam antibiotics in the presence of Zn2+ and 2-amino-2-hydroxymethylpropane-1,3-diol (Tris). A hypothetical non-enzymic model of beta-lactamases. Int J Biol Macromol 1991; 13:225-30. [PMID: 1777429 DOI: 10.1016/0141-8130(91)90077-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The system composed of 2-amino-2-hydroxymethylpropane-1,3-diol (Tris) and Zn2+ catalyses the degradation of cephalosporins. The beta-lactam opening fits to a first-order process, with a constant directly proportional to the zinc ion concentration. The pH and Tris concentration dependency displayed by the first-order constant, as well as the nature of the degradation products point to a mechanism that can be considered as an extension of that proposed for the benzylpenicillin degradation. The mechanism proposed here, and the values of the kinetic constants calculated, as compared with those of beta-lactamases, lead to the conclusion that the Tris-Zn2+ system simulates the catalytic action of the serine beta-lactamases rather than the action of the Zn(2+)-dependent type of enzymes.
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Affiliation(s)
- M Company
- Departamento de Quimica Fisica Aplicada, Universidad Autónoma de Madrid, Spain
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18
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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: 3.4] [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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19
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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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20
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Pratt RF, McConnell TS, Murphy SJ. Accumulation of acyl-enzyme intermediates during turnover of penicillins by the class A beta-lactamase of Staphylococcus aureus PC1. Biochem J 1988; 254:919-22. [PMID: 3264153 PMCID: PMC1135173 DOI: 10.1042/bj2540919] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The interaction of dansylpenicillin with the class A Staphylococcus aureus PCI beta-lactamase yielded an accumulating intermediate with fluorescence enhanced beyond that of the substrate. Acid quenching of the reaction mixture yielded a denatured enzyme with 1 molar equivalent of dansyl group covalently bound to it. A similar quenching experiment with the PC1 beta-lactamase and [14C]benzylpenicillin yielded an enzyme with 1 molar equivalent of 14C covalently bound. These data indicate that in turnover of S-type penicillins by the PC1 beta-lactamase deacylation is rate-determining. This has not indicate previously been demonstrated for a class A beta-lactamase.
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Affiliation(s)
- R F Pratt
- Department of Chemistry, Wesleyan University, Middletown, CT 06457
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21
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Martin MT, Waley SG. Kinetic characterization of the acyl-enzyme mechanism for beta-lactamase I. Biochem J 1988; 254:923-5. [PMID: 3143353 PMCID: PMC1135174 DOI: 10.1042/bj2540923] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
beta-Lactamase I catalyses the hydrolysis of penicillins by an acyl-enzyme mechanism. A procedure was developed for determining the rate constants for the acylation and deacylation steps for the good substrates benzylpenicillin and phenoxymethylpenicillin; this depends on determining the fraction of enzyme that is present as acyl-enzyme in the steady state.
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Affiliation(s)
- M T Martin
- Sir William Dunn School of Pathology, University of Oxford, U.K
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22
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Abstract
The cryoenzymology of several different beta-lactamases has been investigated. Particular attention has been paid to the experimental pitfalls of the technique. These include such factors as false bursts at the start of the reaction, instability of the enzymes during turnover, and Km values so high that little of the enzyme is present as a complex. Many of the difficulties in cryoenzymology stem from the use of organic cryosolvents. A novel "salt" cryosolvent has been tested: ammonium acetate solutions can be used down to about -60 degrees C. The enzymes examined are readily soluble, and stable, in this solvent. Nevertheless, out of 17 beta-lactamase beta-lactam systems, only 4 proved suitable for detailed investigation. In two of these, the hydrolysis of nitrocefin or 7-(thienyl-2-acetamido)-3-[[2-[[4- (dimethylamino)phenyl]azo]pyridinio]-methyl]cephem-4-carboxylic acid (PADAC), by beta-lactamase I from Bacillus cereus, substrate was converted into product at a slow enough rate (at -60 or -55 degrees C, respectively) for it to be possible to do successive scans during the course of the reaction. The spectra were those of substrate and product, and no intermediate was detected. The results argue against the accumulation of intermediate acyl-enzyme. The hydrolysis of PADAC by the P99 beta-lactamase from Enterobacter cloacae again showed spectra characteristic of substrate and product, and there was, moreover, a break in the Arrhenius plot; it is possible that a conformational change is (at least partially) rate-determining. The hydrolysis of dinitrophenylpenicillin by the P99 beta-lactamase did show features suggesting the accumulation of acyl-enzyme.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- S J Cartwright
- Sir William Dunn School of Pathology, University of Oxford, U.K
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23
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Little C, Emanuel EL, Gagnon J, Waley SG. Carboxy groups as essential residues in beta-lactamases. Biochem J 1986; 240:215-9. [PMID: 3493768 PMCID: PMC1147395 DOI: 10.1042/bj2400215] [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: 01/06/2023]
Abstract
Beta-lactamases are divided into classes A, B and C on the basis of their amino acid sequences. Beta-Lactamases were incubated at pH 4.0 with the carboxy-group reagent 1-(3-dimethylaminopropyl)-3-ethylcarbodi-imide plus a coloured nucleophile and the extents of inactivation and nucleophile incorporation were monitored. Two class A enzymes (from Bacillus cereus and Bacillus licheniformis) and two class C enzymes (from Enterobacter cloacae P99 and Pseudomonas aeruginosa) were examined. All four enzymes were inactivated, with total inactivation corresponding to the incorporation of approx. 2-3 mol of nucleophile/mol of enzyme. In the case of beta-lactamase I from Bacillus cereus, some 53% of the incorporated nucleophile was located on glutamic acid-168 in the amino acid sequence.
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24
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Bicknell R, Schäffer A, Waley SG, Auld DS. Changes in the coordination geometry of the active-site metal during catalysis of benzylpenicillin hydrolysis by Bacillus cereus beta-lactamase II. Biochemistry 1986; 25:7208-15. [PMID: 3099831 DOI: 10.1021/bi00370a066] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Rapid-scanning stopped-flow spectroscopy (425-700 nm) has been used to study spectral changes in cobalt(II)-substituted Bacillus cereus beta-lactamase II during the binding and hydrolysis of benzylpenicillin. The experiments were carried out in aqueous solution over a temperature range of 3-20 degrees C. Three metallointermediates have been characterized by their visible absorption spectra. Two of them have visible absorption spectra identical with the intermediates ES1 and ES2 previously observed at subzero temperatures in a mixed aqueous/organic solvent [Bicknell, R., & Waley, S.G. (1985) Biochemistry 24, 6876-6887]. In addition, the branched kinetic pathway observed with the zinc(II) and cobalt(II) beta-lactamase II at subzero temperatures has been shown to occur with the cobalt(II)-substituted enzyme in aqueous solution at above-zero temperatures; thus, at pH 6.0 and 3 degrees C, the rate and equilibrium constants are readily determined for the reaction scheme: (Formula: see text). A third transient intermediate (called ES*) was found to precede ES1 in the pre-steady-state time period. The identity of the intermediates formed in aqueous solution with those previously observed in the cryostudy confirms that the mechanism is not changed either by the presence of an organic cosolvent or by subzero temperatures. Further characterization of ES1 and the steady-state intermediate ES2 at subzero temperatures, where their lifetime may be extended for up to several hours, has involved circular and magnetic circular dichroic studies. The magnetic circular dichroic spectra identify changes in the coordination sphere of the active-site metal during catalysis.(ABSTRACT TRUNCATED AT 250 WORDS)
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25
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Crompton IE, Waley SG. The determination of specificity constants in enzyme-catalysed reactions. Biochem J 1986; 239:221-4. [PMID: 3800980 PMCID: PMC1147263 DOI: 10.1042/bj2390221] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A convenient and accurate procedure for determining the kinetic parameter Vmax./Km is described. This avoids the error in the usual method of taking the observed first-order rate constant of an enzymic reaction at low substrate concentration as Vmax./Km. A series of reactions is used in which the initial concentration of substrate is below Km (e.g. from 5% to 50% of Km). Measurements are taken over the same extent of reaction (e.g. 70%) for each member of the series, and treated as if the kinetics were truly first-order. The reciprocal of the observed first-order rate constant is then plotted against the initial concentration of substrate: the reciprocal of the ordinate intercept is Vmax./Km. The procedure, as well as being applicable to simple reactions, is shown to be valid when there is competitive inhibition by the product, or when the reaction is reversible, or when there is competitive or mixed inhibition. The hydrolysis of cephalosporin C by a beta-lactamase from Pseudomonas aeruginosa is used to illustrate the method.
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