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Alonso SDV, González Flecha FL. Fifty years of biophysics in Argentina. Biophys Rev 2023; 15:431-438. [PMID: 37681102 PMCID: PMC10480372 DOI: 10.1007/s12551-023-01114-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 08/10/2023] [Indexed: 09/09/2023] Open
Abstract
In 1972, a group of young Argentinean scientists nucleated in the so-called Membrane Club constituted the Biophysical Society of Argentina (SAB). Over the years, this Society has grown and embraced new areas of research and emerging technologies. In this commentary, we provide an overview of the early stages of biophysics development in Argentina and highlight some of the notable achievements made during the past five decades. The SAB Annual Meetings have been a platform for intense scientific discussions, and the Society has fostered numerous international connections, becoming a hallmark of SAB activities over these 50 years. Initially centered on membrane biophysics, SAB focus has since expanded to encompass diverse fields such as molecular, cellular, and systems biophysics.
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Affiliation(s)
- Silvia del V. Alonso
- Laboratorio de Bio-Nanotecnología, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Argentina
- Grupo de Biología Estructural y Biotecnología (GBEyB), IMBICE (CONICET CCT-La Plata), La Plata, Argentina
| | - F. Luis González Flecha
- Laboratorio de Biofísica Molecular, Instituto de Química y Fisicoquímica Biológicas, Universidad de Buenos Aires – CONICET, Buenos Aires, Argentina
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2
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Bahr G, González LJ, Vila AJ. Metallo-β-lactamases in the Age of Multidrug Resistance: From Structure and Mechanism to Evolution, Dissemination, and Inhibitor Design. Chem Rev 2021; 121:7957-8094. [PMID: 34129337 PMCID: PMC9062786 DOI: 10.1021/acs.chemrev.1c00138] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Antimicrobial resistance is one of the major problems in current practical medicine. The spread of genes coding for resistance determinants among bacteria challenges the use of approved antibiotics, narrowing the options for treatment. Resistance to carbapenems, last resort antibiotics, is a major concern. Metallo-β-lactamases (MBLs) hydrolyze carbapenems, penicillins, and cephalosporins, becoming central to this problem. These enzymes diverge with respect to serine-β-lactamases by exhibiting a different fold, active site, and catalytic features. Elucidating their catalytic mechanism has been a big challenge in the field that has limited the development of useful inhibitors. This review covers exhaustively the details of the active-site chemistries, the diversity of MBL alleles, the catalytic mechanism against different substrates, and how this information has helped developing inhibitors. We also discuss here different aspects critical to understand the success of MBLs in conferring resistance: the molecular determinants of their dissemination, their cell physiology, from the biogenesis to the processing involved in the transit to the periplasm, and the uptake of the Zn(II) ions upon metal starvation conditions, such as those encountered during an infection. In this regard, the chemical, biochemical and microbiological aspects provide an integrative view of the current knowledge of MBLs.
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Affiliation(s)
- Guillermo Bahr
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Lisandro J. González
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Alejandro J. Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
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3
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González JM. Visualizing the superfamily of metallo-β-lactamases through sequence similarity network neighborhood connectivity analysis. Heliyon 2021; 7:e05867. [PMID: 33426353 PMCID: PMC7785958 DOI: 10.1016/j.heliyon.2020.e05867] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 11/19/2020] [Accepted: 12/23/2020] [Indexed: 12/13/2022] Open
Abstract
Protein sequence similarity networks (SSNs) constitute a convenient approach to analyze large polypeptide sequence datasets, and have been successfully applied to study a number of protein families over the past decade. SSN analysis is herein combined with traditional cladistic and phenetic phylogenetic analysis (respectively based on multiple sequence alignments and all-against-all three-dimensional protein structure comparisons) in order to assist the ancestral reconstruction and integrative revision of the superfamily of metallo-β-lactamases (MBLs). It is shown that only 198 out of 15,292 representative nodes contain at least one experimentally obtained protein structure in the Protein Data Bank or a manually annotated SwissProt entry, that is to say, only 1.3 % of the superfamily has been functionally and/or structurally characterized. Besides, neighborhood connectivity coloring, which measures local network interconnectivity, is introduced for detection of protein families within SSN clusters. This approach provides a clear picture of how many families remain unexplored in the superfamily, while most MBL research is heavily biased towards a few families. Further research is suggested in order to determine the SSN topological properties, which will be instrumental for the improvement of automated sequence annotation methods.
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4
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Park YS, Kim TY, Park H, Lee JH, Nguyen DQ, Hong MK, Lee SH, Kang LW. Structural Study of Metal Binding and Coordination in Ancient Metallo-β-Lactamase PNGM-1 Variants. Int J Mol Sci 2020; 21:ijms21144926. [PMID: 32664695 PMCID: PMC7404133 DOI: 10.3390/ijms21144926] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/08/2020] [Accepted: 07/08/2020] [Indexed: 01/16/2023] Open
Abstract
The increasing incidence of community- and hospital-acquired infections with multidrug-resistant (MDR) bacteria poses a critical threat to public health and the healthcare system. Although β-lactam antibiotics are effective against most bacterial infections, some bacteria are resistant to β-lactam antibiotics by producing β-lactamases. Among β-lactamases, metallo-β-lactamases (MBLs) are especially worrisome as only a few inhibitors have been developed against them. In MBLs, the metal ions play an important role as they coordinate a catalytic water molecule that hydrolyzes β-lactam rings. We determined the crystal structures of different variants of PNGM-1, an ancient MBL with additional tRNase Z activity. The variants were generated by site-directed mutagenesis targeting metal-coordinating residues. In PNGM-1, both zinc ions are coordinated by six coordination partners in an octahedral geometry, and the zinc-centered octahedrons share a common face. Structures of the PNGM-1 variants confirm that the substitution of a metal-coordinating residue causes the loss of metal binding and β-lactamase activity. Compared with PNGM-1, subclass B3 MBLs lack one metal-coordinating residue, leading to a shift in the metal-coordination geometry from an octahedral to tetrahedral geometry. Our results imply that a subtle change in the metal-binding site of MBLs can markedly change their metal-coordination geometry and catalytic activity.
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Affiliation(s)
- Yoon Sik Park
- Department of Biological Sciences, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea; (Y.S.P.); (H.P.); (D.Q.N.); (M.-K.H.)
| | - Tae Yeong Kim
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, 116 Myongjiro, Yongin, Gyeonggido 17058, Korea; (T.Y.K.); (J.H.L.)
| | - Hyunjae Park
- Department of Biological Sciences, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea; (Y.S.P.); (H.P.); (D.Q.N.); (M.-K.H.)
| | - Jung Hun Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, 116 Myongjiro, Yongin, Gyeonggido 17058, Korea; (T.Y.K.); (J.H.L.)
| | - Diem Quynh Nguyen
- Department of Biological Sciences, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea; (Y.S.P.); (H.P.); (D.Q.N.); (M.-K.H.)
| | - Myoung-Ki Hong
- Department of Biological Sciences, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea; (Y.S.P.); (H.P.); (D.Q.N.); (M.-K.H.)
| | - Sang Hee Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, 116 Myongjiro, Yongin, Gyeonggido 17058, Korea; (T.Y.K.); (J.H.L.)
- Correspondence: (S.H.L.); (L.-W.K.); Tel.: +82-31-330-6195 (S.H.L.); +82-2-450-4090 (L.-W.K.)
| | - Lin-Woo Kang
- Department of Biological Sciences, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea; (Y.S.P.); (H.P.); (D.Q.N.); (M.-K.H.)
- Correspondence: (S.H.L.); (L.-W.K.); Tel.: +82-31-330-6195 (S.H.L.); +82-2-450-4090 (L.-W.K.)
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5
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Behzadi P, García-Perdomo HA, Karpiński TM, Issakhanian L. Metallo-ß-lactamases: a review. Mol Biol Rep 2020; 47:6281-6294. [DOI: 10.1007/s11033-020-05651-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 07/08/2020] [Indexed: 01/09/2023]
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6
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Fullington S, Cheng Z, Thomas C, Miller C, Yang K, Ju LC, Bergstrom A, Shurina BA, Bretz SL, Page RC, Tierney DL, Crowder MW. An integrated biophysical approach to discovering mechanisms of NDM-1 inhibition for several thiol-containing drugs. J Biol Inorg Chem 2020; 25:717-727. [PMID: 32500360 DOI: 10.1007/s00775-020-01794-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 05/18/2020] [Indexed: 12/29/2022]
Abstract
Due to the rapid proliferation of antibiotic-resistant pathogenic bacteria, known as carbapenem-resistant enterobacteriaceae, the efficacy of β-lactam antibiotics is threatened. β-lactam antibiotics constitute over 50% of the available antibiotic arsenal. Recent efforts have been focused on developing inhibitors to these enzymes. In an effort to understand the mechanism of inhibition(s) of four FDA-approved thiol-containing drugs that were previously reported to be inhibitors of New Delhi metallo-β-lactamase (NDM-1), various biochemical and spectroscopic techniques were used. Isothermal titration calorimetry demonstrated the binding affinity to NDM-1 corresponds to the reported IC50 values of the inhibitors. Equilibrium dialyses and metal analyses demonstrated that all of these inhibitors formed ternary complexes with ZnZn-NDM-1. Spectroscopic studies on CoCo-NDM-1 revealed two distinct binding modes for the thiol-containing compounds. These findings validate the need to further investigate the mechanism of inhibition of MBL inhibitors. Further research to identify inhibition capabilities beyond reported IC50 values is necessary for understanding the binding modes of these identified compounds and to provide the necessary foundation for developing clinically relevant MBL inhibitors.
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Affiliation(s)
- Sarah Fullington
- Department of Chemistry and Biochemistry, 160 Hughes Laboratories, Miami University, 651 E. High Street, Oxford, OH, 45056, USA
| | - Zishuo Cheng
- Department of Chemistry and Biochemistry, 160 Hughes Laboratories, Miami University, 651 E. High Street, Oxford, OH, 45056, USA
| | - Caitlyn Thomas
- Department of Chemistry and Biochemistry, 160 Hughes Laboratories, Miami University, 651 E. High Street, Oxford, OH, 45056, USA
| | - Callie Miller
- Department of Chemistry and Biochemistry, 160 Hughes Laboratories, Miami University, 651 E. High Street, Oxford, OH, 45056, USA
| | - Kundi Yang
- Department of Chemistry and Biochemistry, 160 Hughes Laboratories, Miami University, 651 E. High Street, Oxford, OH, 45056, USA
| | - Lin-Cheng Ju
- Department of Chemistry and Biochemistry, 160 Hughes Laboratories, Miami University, 651 E. High Street, Oxford, OH, 45056, USA
| | - Alexander Bergstrom
- Department of Chemistry and Biochemistry, 160 Hughes Laboratories, Miami University, 651 E. High Street, Oxford, OH, 45056, USA
| | - Ben A Shurina
- Department of Chemistry and Biochemistry, 160 Hughes Laboratories, Miami University, 651 E. High Street, Oxford, OH, 45056, USA
| | - Stacey Lowery Bretz
- Department of Chemistry and Biochemistry, 160 Hughes Laboratories, Miami University, 651 E. High Street, Oxford, OH, 45056, USA
| | - Richard C Page
- Department of Chemistry and Biochemistry, 160 Hughes Laboratories, Miami University, 651 E. High Street, Oxford, OH, 45056, USA.
| | - David L Tierney
- Department of Chemistry and Biochemistry, 160 Hughes Laboratories, Miami University, 651 E. High Street, Oxford, OH, 45056, USA.
| | - Michael W Crowder
- Department of Chemistry and Biochemistry, 160 Hughes Laboratories, Miami University, 651 E. High Street, Oxford, OH, 45056, USA.
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7
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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: 38] [Impact Index Per Article: 9.5] [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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8
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Tooke CL, Hinchliffe P, Bragginton EC, Colenso CK, Hirvonen VHA, Takebayashi Y, Spencer J. β-Lactamases and β-Lactamase Inhibitors in the 21st Century. J Mol Biol 2019; 431:3472-3500. [PMID: 30959050 PMCID: PMC6723624 DOI: 10.1016/j.jmb.2019.04.002] [Citation(s) in RCA: 437] [Impact Index Per Article: 87.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 03/27/2019] [Accepted: 04/01/2019] [Indexed: 12/31/2022]
Abstract
The β-lactams retain a central place in the antibacterial armamentarium. In Gram-negative bacteria, β-lactamase enzymes that hydrolyze the amide bond of the four-membered β-lactam ring are the primary resistance mechanism, with multiple enzymes disseminating on mobile genetic elements across opportunistic pathogens such as Enterobacteriaceae (e.g., Escherichia coli) and non-fermenting organisms (e.g., Pseudomonas aeruginosa). β-Lactamases divide into four classes; the active-site serine β-lactamases (classes A, C and D) and the zinc-dependent or metallo-β-lactamases (MBLs; class B). Here we review recent advances in mechanistic understanding of each class, focusing upon how growing numbers of crystal structures, in particular for β-lactam complexes, and methods such as neutron diffraction and molecular simulations, have improved understanding of the biochemistry of β-lactam breakdown. A second focus is β-lactamase interactions with carbapenems, as carbapenem-resistant bacteria are of grave clinical concern and carbapenem-hydrolyzing enzymes such as KPC (class A) NDM (class B) and OXA-48 (class D) are proliferating worldwide. An overview is provided of the changing landscape of β-lactamase inhibitors, exemplified by the introduction to the clinic of combinations of β-lactams with diazabicyclooctanone and cyclic boronate serine β-lactamase inhibitors, and of progress and strategies toward clinically useful MBL inhibitors. Despite the long history of β-lactamase research, we contend that issues including continuing unresolved questions around mechanism; opportunities afforded by new technologies such as serial femtosecond crystallography; the need for new inhibitors, particularly for MBLs; the likely impact of new β-lactam:inhibitor combinations and the continuing clinical importance of β-lactams mean that this remains a rewarding research area.
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Affiliation(s)
- Catherine L Tooke
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Philip Hinchliffe
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Eilis C Bragginton
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Charlotte K Colenso
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Viivi H A Hirvonen
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Yuiko Takebayashi
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom.
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9
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The Reaction Mechanism of Metallo-β-Lactamases Is Tuned by the Conformation of an Active-Site Mobile Loop. Antimicrob Agents Chemother 2018; 63:AAC.01754-18. [PMID: 30348667 DOI: 10.1128/aac.01754-18] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 10/01/2018] [Indexed: 12/31/2022] Open
Abstract
Carbapenems are "last resort" β-lactam antibiotics used to treat serious and life-threatening health care-associated infections caused by multidrug-resistant Gram-negative bacteria. Unfortunately, the worldwide spread of genes coding for carbapenemases among these bacteria is threatening these life-saving drugs. Metallo-β-lactamases (MβLs) are the largest family of carbapenemases. These are Zn(II)-dependent hydrolases that are active against almost all β-lactam antibiotics. Their catalytic mechanism and the features driving substrate specificity have been matter of intense debate. The active sites of MβLs are flanked by two loops, one of which, loop L3, was shown to adopt different conformations upon substrate or inhibitor binding, and thus are expected to play a role in substrate recognition. However, the sequence heterogeneity observed in this loop in different MβLs has limited the generalizations about its role. Here, we report the engineering of different loops within the scaffold of the clinically relevant carbapenemase NDM-1. We found that the loop sequence dictates its conformation in the unbound form of the enzyme, eliciting different degrees of active-site exposure. However, these structural changes have a minor impact on the substrate profile. Instead, we report that the loop conformation determines the protonation rate of key reaction intermediates accumulated during the hydrolysis of different β-lactams in all MβLs. This study demonstrates the existence of a direct link between the conformation of this loop and the mechanistic features of the enzyme, bringing to light an unexplored function of active-site loops on MβLs.
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10
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Cheng Z, VanPelt J, Bergstrom A, Bethel C, Katko A, Miller C, Mason K, Cumming E, Zhang H, Kimble RL, Fullington S, Bretz SL, Nix JC, Bonomo RA, Tierney DL, Page RC, Crowder MW. A Noncanonical Metal Center Drives the Activity of the Sediminispirochaeta smaragdinae Metallo-β-lactamase SPS-1. Biochemistry 2018; 57:5218-5229. [PMID: 30106565 PMCID: PMC6314204 DOI: 10.1021/acs.biochem.8b00728] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
In an effort to evaluate whether a recently reported putative metallo-β-lactamase (MβL) contains a novel MβL active site, SPS-1 from Sediminispirochaeta smaragdinae was overexpressed, purified, and characterized using spectroscopic and crystallographic studies. Metal analyses demonstrate that recombinant SPS-1 binds nearly 2 equiv of Zn(II), and steady-state kinetic studies show that the enzyme hydrolyzes carbapenems and certain cephalosporins but not β-lactam substrates with bulky substituents at the 6/7 position. Spectroscopic studies of Co(II)-substituted SPS-1 suggest a novel metal center in SPS-1, with a reduced level of spin coupling between the metal ions and a novel Zn1 metal binding site. This site was confirmed with a crystal structure of the enzyme. The structure shows a Zn2 site that is similar to that in NDM-1 and other subclass B1 MβLs; however, the Zn1 metal ion is coordinated by two histidine residues and a water molecule, which is held in position by a hydrogen bond network. The Zn1 metal is displaced nearly 1 Å from the position reported in other MβLs. The structure also shows extended helices above the active site, which create a binding pocket that precludes the binding of substrates with large, bulky substituents at the 6/7 position of β-lactam antibiotics. This study reveals a novel metal binding site in MβLs and suggests that the targeting of metal binding sites in MβLs with inhibitors is now more challenging with the identification of this new MβL.
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Affiliation(s)
- Zishuo Cheng
- Department of Chemistry and Biochemistry, 651 E. High Street, 160 Hughes Laboratories, Miami University, Oxford, OH 45056
| | - Jamie VanPelt
- Department of Chemistry and Biochemistry, 651 E. High Street, 160 Hughes Laboratories, Miami University, Oxford, OH 45056
| | - Alexander Bergstrom
- Department of Chemistry and Biochemistry, 651 E. High Street, 160 Hughes Laboratories, Miami University, Oxford, OH 45056
| | - Christopher Bethel
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH 44106
| | - Andrew Katko
- Department of Chemistry and Biochemistry, 651 E. High Street, 160 Hughes Laboratories, Miami University, Oxford, OH 45056
| | - Callie Miller
- Department of Chemistry and Biochemistry, 651 E. High Street, 160 Hughes Laboratories, Miami University, Oxford, OH 45056
| | - Kelly Mason
- Department of Chemistry and Biochemistry, 651 E. High Street, 160 Hughes Laboratories, Miami University, Oxford, OH 45056
| | - Erin Cumming
- Department of Chemistry and Biochemistry, 651 E. High Street, 160 Hughes Laboratories, Miami University, Oxford, OH 45056
| | - Huan Zhang
- Department of Chemistry and Biochemistry, 651 E. High Street, 160 Hughes Laboratories, Miami University, Oxford, OH 45056
| | - Robert L. Kimble
- Department of Chemistry and Biochemistry, 651 E. High Street, 160 Hughes Laboratories, Miami University, Oxford, OH 45056
| | - Sarah Fullington
- Department of Chemistry and Biochemistry, 651 E. High Street, 160 Hughes Laboratories, Miami University, Oxford, OH 45056
| | - Stacey Lowery Bretz
- Department of Chemistry and Biochemistry, 651 E. High Street, 160 Hughes Laboratories, Miami University, Oxford, OH 45056
| | - Jay C. Nix
- Molecular Biology Consortium, Beamline 4.2.2, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Robert A. Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH 44106
- Departments of Medicine, Pharmacology, Molecular Biology and Microbiology, Biochemistry, Proteomics and Bioinformatics, and the CWRU-Cleveland VAMC Center of Antimicrobial Resistance and Epidemiology, Cleveland, OH 44106
| | - David L. Tierney
- Department of Chemistry and Biochemistry, 651 E. High Street, 160 Hughes Laboratories, Miami University, Oxford, OH 45056
| | - Richard C. Page
- Department of Chemistry and Biochemistry, 651 E. High Street, 160 Hughes Laboratories, Miami University, Oxford, OH 45056
| | - Michael W Crowder
- Department of Chemistry and Biochemistry, 651 E. High Street, 160 Hughes Laboratories, Miami University, Oxford, OH 45056
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11
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Cheng Z, Thomas PW, Ju L, Bergstrom A, Mason K, Clayton D, Miller C, Bethel CR, VanPelt J, Tierney DL, Page RC, Bonomo RA, Fast W, Crowder MW. Evolution of New Delhi metallo-β-lactamase (NDM) in the clinic: Effects of NDM mutations on stability, zinc affinity, and mono-zinc activity. J Biol Chem 2018; 293:12606-12618. [PMID: 29909397 PMCID: PMC6093243 DOI: 10.1074/jbc.ra118.003835] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 06/07/2018] [Indexed: 11/06/2022] Open
Abstract
Infections by carbapenem-resistant Enterobacteriaceae are difficult to manage owing to broad antibiotic resistance profiles and because of the inability of clinically used β-lactamase inhibitors to counter the activity of metallo-β-lactamases often harbored by these pathogens. Of particular importance is New Delhi metallo-β-lactamase (NDM), which requires a di-nuclear zinc ion cluster for catalytic activity. Here, we compare the structures and functions of clinical NDM variants 1-17. The impact of NDM variants on structure is probed by comparing melting temperature and refolding efficiency and also by spectroscopy (UV-visible, 1H NMR, and EPR) of di-cobalt metalloforms. The impact of NDM variants on function is probed by determining the minimum inhibitory concentrations of various antibiotics, pre-steady-state and steady-state kinetics, inhibitor binding, and zinc dependence of resistance and activity. We observed only minor differences among the fully loaded di-zinc enzymes, but most NDM variants had more distinguishable selective advantages in experiments that mimicked zinc scarcity imposed by typical host defenses. Most NDM variants exhibited improved thermostability (up to ∼10 °C increased Tm ) and improved zinc affinity (up to ∼10-fold decreased Kd, Zn2). We also provide first evidence that some NDM variants have evolved the ability to function as mono-zinc enzymes with high catalytic efficiency (NDM-15, ampicillin: kcat/Km = 5 × 106 m-1 s-1). These findings reveal the molecular mechanisms that NDM variants have evolved to overcome the combined selective pressures of β-lactam antibiotics and zinc deprivation.
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Affiliation(s)
- Zishuo Cheng
- From the Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056
| | - Pei W Thomas
- the Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, and the LaMontagne Center of Infectious Disease, University of Texas, Austin, Texas 78712
| | - Lincheng Ju
- the Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China
| | - Alexander Bergstrom
- From the Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056
| | - Kelly Mason
- From the Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056
| | - Delaney Clayton
- From the Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056
| | - Callie Miller
- From the Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056
| | - Christopher R Bethel
- the Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, and
| | - Jamie VanPelt
- From the Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056
| | - David L Tierney
- From the Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056,
| | - Richard C Page
- From the Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056,
| | - Robert A Bonomo
- the Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, and
- the Departments of Medicine, Pharmacology, Molecular Biology and Microbiology, Biochemistry, Proteomics, and Bioinformatics, Case Western Reserve University (CWRU)-Cleveland Veterans Administration Medical Center (VAMC) Center of Antimicrobial Resistance and Epidemiology (CARES), Cleveland, Ohio 44106
| | - Walter Fast
- the Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, and the LaMontagne Center of Infectious Disease, University of Texas, Austin, Texas 78712,
| | - Michael W Crowder
- From the Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056,
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12
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Bergstrom A, Katko A, Adkins Z, Hill J, Cheng Z, Burnett M, Yang H, Aitha M, Mehaffey MR, Brodbelt JS, Tehrani KHME, Martin NI, Bonomo RA, Page RC, Tierney DL, Fast W, Wright GD, Crowder MW. Probing the Interaction of Aspergillomarasmine A with Metallo-β-lactamases NDM-1, VIM-2, and IMP-7. ACS Infect Dis 2018; 4:135-145. [PMID: 29091730 DOI: 10.1021/acsinfecdis.7b00106] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Metallo-β-lactamases (MBLs) are a growing threat to the continued efficacy of β-lactam antibiotics. Recently, aspergillomarasmine A (AMA) was identified as an MBL inhibitor, but the mode of inhibition was not fully characterized. Equilibrium dialysis and metal analysis studies revealed that 2 equiv of AMA effectively removes 1 equiv of Zn(II) from MBLs NDM-1, VIM-2, and IMP-7 when the MBL is at micromolar concentrations. Conversely, 1H NMR studies revealed that 2 equiv of AMA remove 2 equiv of Co(II) from Co(II)-substituted NDM-1, VIM-2, and IMP-7 when the MBL/AMA are at millimolar concentrations. Our findings reveal that AMA inhibits the MBLs by removal of the active site metal ions required for β-lactam hydrolysis among the most clinically significant MBLs.
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Affiliation(s)
- Alexander Bergstrom
- Department of Chemistry
and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, United States
| | - Andrew Katko
- Department of Chemistry
and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, United States
| | - Zach Adkins
- Department of Chemistry
and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, United States
| | - Jessica Hill
- Department of Chemistry
and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, United States
| | - Zishuo Cheng
- Department of Chemistry
and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, United States
| | - Mia Burnett
- Department of Chemistry
and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, United States
| | - Hao Yang
- Department of Chemistry
and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, United States
| | - Mahesh Aitha
- Department of Chemistry
and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, United States
| | - M. Rachel Mehaffey
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Kamaleddin H. M. E. Tehrani
- Department of Chemical Biology and Drug
Discovery Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Nathaniel I. Martin
- Department of Chemical Biology and Drug
Discovery Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Robert A. Bonomo
- Research
Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, 10701 East Boulevard, Cleveland, Ohio 44106, United States
| | - Richard C. Page
- Department of Chemistry
and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, United States
| | - David L. Tierney
- Department of Chemistry
and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, United States
| | - Walter Fast
- Division of Chemical Biology and Medicinal Chemistry,
College of Pharmacy, University of Texas, 107 W. Dean Keeton, Austin, Texas 78712, United States
| | - Gerard D. Wright
- Michael
G DeGroote Institute for Infectious Disease and Department of Biochemistry
and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S4L8, Canada
| | - Michael W. Crowder
- Department of Chemistry
and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, United States
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13
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A general reaction mechanism for carbapenem hydrolysis by mononuclear and binuclear metallo-β-lactamases. Nat Commun 2017; 8:538. [PMID: 28912448 PMCID: PMC5599593 DOI: 10.1038/s41467-017-00601-9] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 07/12/2017] [Indexed: 12/16/2022] Open
Abstract
Carbapenem-resistant Enterobacteriaceae threaten human health, since carbapenems are last resort drugs for infections by such organisms. Metallo-β-lactamases (MβLs) are the main mechanism of resistance against carbapenems. Clinically approved inhibitors of MBLs are currently unavailable as design has been limited by the incomplete knowledge of their mechanism. Here, we report a biochemical and biophysical study of carbapenem hydrolysis by the B1 enzymes NDM-1 and BcII in the bi-Zn(II) form, the mono-Zn(II) B2 Sfh-I and the mono-Zn(II) B3 GOB-18. These MβLs hydrolyse carbapenems via a similar mechanism, with accumulation of the same anionic intermediates. We characterize the Michaelis complex formed by mono-Zn(II) enzymes, and we identify all intermediate species, enabling us to propose a chemical mechanism for mono and binuclear MβLs. This common mechanism open avenues for rationally designed inhibitors of all MβLs, notwithstanding the profound differences between these enzymes’ active site structure, β-lactam specificity and metal content. Carbapenem-resistant bacteria pose a major health threat by expressing metallo-β-lactamases (MβLs), enzymes able to hydrolyse these life-saving drugs. Here the authors use biophysical and computational methods and show that different MβLs share the same reaction mechanism, suggesting new strategies for drug design.
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14
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Sadaf A, Sinha R, Khare SK. Structure and Functional Characterisation of a Distinctive β-Lactamase from an Environmental Strain EMB20 of Bacillus cereus. Appl Biochem Biotechnol 2017; 184:197-211. [PMID: 28664525 DOI: 10.1007/s12010-017-2539-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 06/14/2017] [Indexed: 11/30/2022]
Abstract
The rampant use and misuse of antibiotics in human medicine, agriculture and veterinary have become the key contributors to global antimicrobial resistance. One of the significant resistance mechanisms that inactivates antibiotics and impedes treatment of bacterial infections is the expression of β-lactamases. Rising evidence of newer variants of β-lactamases in the environment is therefore a serious threat to the presently available antibiotic armoury. The present work describes the purification of a variant β-lactamase isolated from a soil strain EMB20 of Bacillus cereus. The lactamase was purified using three-phase partitioning and gel filtration chromatography to a 30-fold purification and 15% recovery yield. Contrary to the general trend, the lactamase was not a metalloenzyme, but its activity was enhanced in the presence of Mg2+ and Mn2+. The EMB20 lactamase exhibited improved stability against inhibitors and denaturing agents such as urea and GdmCl as compared to its commercial analogue. The improved stability of EMB20 lactamase was further validated by circular dichroism and fluorescence spectroscopy. This study reemphasizes the rising prevalence of environmental lactamase variants. Decoding the structure-function correlation of such lactamases in the presence of inhibitors will provide insights into the response of this enzyme towards inhibitors as well as its substrates.
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Affiliation(s)
- Ayesha Sadaf
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology, Hauz Khas, New Delhi, 110016, India
| | - Rajeshwari Sinha
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology, Hauz Khas, New Delhi, 110016, India
| | - S K Khare
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology, Hauz Khas, New Delhi, 110016, India.
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15
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Brem J, Struwe WB, Rydzik AM, Tarhonskaya H, Pfeffer I, Flashman E, van Berkel SS, Spencer J, Claridge TDW, McDonough MA, Benesch JLP, Schofield CJ. Studying the active-site loop movement of the São Paolo metallo-β-lactamase-1†Electronic supplementary information (ESI) available: Procedures for protein expression and purification, 19F-labelling, crystallisation, data collection, and structure determination, table of crystallographic data, table of crystallographic parameters and refinement statistics, figures showing binding mode and distances, procedures for mass spectrometry measurements, differential scanning fluorimetry measurements, stopped-flow measurements and other kinetics measurements. See DOI: 10.1039/c4sc01752hClick here for additional data file. Chem Sci 2015; 6:956-963. [PMID: 25717359 PMCID: PMC4333608 DOI: 10.1039/c4sc01752h] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 10/24/2014] [Indexed: 11/21/2022] Open
Abstract
Metallo-β-lactamases (MBLs) catalyse the hydrolysis of almost all β-lactam antibiotics. We report biophysical and kinetic studies on the São Paulo MBL (SPM-1), which reveal its Zn(ii) ion usage and mechanism as characteristic of the clinically important di-Zn(ii) dependent B1 MBL subfamily. Biophysical analyses employing crystallography, dynamic 19F NMR and ion mobility mass spectrometry, however, reveal that SPM-1 possesses loop and mobile element regions characteristic of the B2 MBLs. These include a mobile α3 region which is important in catalysis and determining inhibitor selectivity. SPM-1 thus appears to be a hybrid B1/B2 MBL. The results have implications for MBL evolution and inhibitor design.
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Affiliation(s)
- Jürgen Brem
- Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK .
| | - Weston B Struwe
- Department of Chemistry , Physical and Theoretical Chemistry Laboratory , University of Oxford , South Parks Road , Oxford , OX1 3QZ , UK .
| | - Anna M Rydzik
- Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK .
| | - Hanna Tarhonskaya
- Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK .
| | - Inga Pfeffer
- Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK .
| | - Emily Flashman
- Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK .
| | - Sander S van Berkel
- Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK .
| | - James Spencer
- School of Cellular and Molecular Medicine , University of Bristol , Medical Sciences Building , Bristol , BS8 1TD , UK
| | - Timothy D W Claridge
- Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK .
| | - Michael A McDonough
- Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK .
| | - Justin L P Benesch
- Department of Chemistry , Physical and Theoretical Chemistry Laboratory , University of Oxford , South Parks Road , Oxford , OX1 3QZ , UK .
| | - Christopher J Schofield
- Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK .
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16
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Aitha M, Marts AR, Bergstrom A, Møller A, Moritz L, Turner L, Nix JC, Bonomo RA, Page RC, Tierney DL, Crowder MW. Biochemical, mechanistic, and spectroscopic characterization of metallo-β-lactamase VIM-2. Biochemistry 2014; 53:7321-31. [PMID: 25356958 PMCID: PMC4245990 DOI: 10.1021/bi500916y] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 09/10/2014] [Indexed: 11/29/2022]
Abstract
This study examines metal binding to metallo-β-lactamase VIM-2, demonstrating the first successful preparation of a Co(II)-substituted VIM-2 analogue. Spectroscopic studies of the half- and fully metal loaded enzymes show that both Zn(II) and Co(II) bind cooperatively, where the major species present, regardless of stoichiometry, are apo- and di-Zn (or di-Co) enzymes. We determined the di-Zn VIM-2 structure to a resolution of 1.55 Å, and this structure supports results from spectroscopic studies. Kinetics, both steady-state and pre-steady-state, show that VIM-2 utilizes a mechanism that proceeds through a very short-lived anionic intermediate when chromacef is used as the substrate. Comparison with other B1 enzymes shows that those that bind Zn(II) cooperatively are better poised to protonate the intermediate on its formation, compared to those that bind Zn(II) non-cooperatively, which uniformly build up substantial amounts of the intermediate.
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Affiliation(s)
- Mahesh Aitha
- Department
of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, United States
| | - Amy R. Marts
- Department
of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, United States
| | - Alex Bergstrom
- Department
of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, United States
| | - Abraham
Jon Møller
- Department
of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, United States
| | - Lindsay Moritz
- Department
of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, United States
| | - Lucien Turner
- Department
of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, United States
| | - Jay C. Nix
- Molecular
Biology Consortium, Beamline 4.2.2, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Robert A. Bonomo
- Research
Service, Louis Stokes Cleveland Department
of Veterans Affairs Medical Center, 10701 East Boulevard, Cleveland, Ohio 44106, United
States
- Department
of Medicine, Pharmacology, and Molecular Biology and Microbiology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Richard C. Page
- Department
of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, United States
| | - David L. Tierney
- Department
of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, United States
| | - Michael W. Crowder
- Department
of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, United States
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17
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Yang H, Aitha M, Marts AR, Hetrick A, Bennett B, Crowder MW, Tierney DL. Spectroscopic and mechanistic studies of heterodimetallic forms of metallo-β-lactamase NDM-1. J Am Chem Soc 2014; 136:7273-85. [PMID: 24754678 PMCID: PMC4046764 DOI: 10.1021/ja410376s] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Indexed: 11/29/2022]
Abstract
In an effort to characterize the roles of each metal ion in metallo-β-lactamase NDM-1, heterodimetallic analogues (CoCo-, ZnCo-, and CoCd-) of the enzyme were generated and characterized. UV-vis, (1)H NMR, EPR, and EXAFS spectroscopies were used to confirm the fidelity of the metal substitutions, including the presence of a homogeneous, heterodimetallic cluster, with a single-atom bridge. This marks the first preparation of a metallo-β-lactamase selectively substituted with a paramagnetic metal ion, Co(II), either in the Zn1 (CoCd-NDM-1) or in the Zn2 site (ZnCo-NDM-1), as well as both (CoCo-NDM-1). We then used these metal-substituted forms of the enzyme to probe the reaction mechanism, using steady-state and stopped-flow kinetics, stopped-flow fluorescence, and rapid-freeze-quench EPR. Both metal sites show significant effects on the kinetic constants, and both paramagnetic variants (CoCd- and ZnCo-NDM-1) showed significant structural changes on reaction with substrate. These changes are discussed in terms of a minimal kinetic mechanism that incorporates all of the data.
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Affiliation(s)
- Hao Yang
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Mahesh Aitha
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Amy R. Marts
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Alyssa Hetrick
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Brian Bennett
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Michael W. Crowder
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - David L. Tierney
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
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18
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Motara H, Mistry D, Brown DR, Cryan RA, Nigen M, Page MI. pH and basicity of ligands control the binding of metal-ions to B. cereus B1 β-lactamase. Chem Sci 2014. [DOI: 10.1039/c4sc00601a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Metallo-β-lactamases (MBLs) are a group of enzymes responsible for a significant proportion of bacterial resistance to β-lactam antibiotics by catalysing the hydrolysis of the β-lactam.
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Affiliation(s)
- Hasina Motara
- IPOS
- The Page Laboratories
- Department of Chemical and Biological Sciences
- The University of Huddersfield
- Huddersfield, UK
| | - Dharmit Mistry
- IPOS
- The Page Laboratories
- Department of Chemical and Biological Sciences
- The University of Huddersfield
- Huddersfield, UK
| | - David R. Brown
- IPOS
- The Page Laboratories
- Department of Chemical and Biological Sciences
- The University of Huddersfield
- Huddersfield, UK
| | - Robert A. Cryan
- IPOS
- The Page Laboratories
- Department of Chemical and Biological Sciences
- The University of Huddersfield
- Huddersfield, UK
| | - Michaël Nigen
- Centre d'Ingénierie des Protéines
- Institut de Chimie B6
- Université de Liège
- B-4000 Liège, Belgium
| | - Michael I. Page
- IPOS
- The Page Laboratories
- Department of Chemical and Biological Sciences
- The University of Huddersfield
- Huddersfield, UK
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19
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Phelan EK, Miraula M, Selleck C, Ollis DL, Schenk G, Mitić N. Metallo-β-Lactamases: A Major Threat to Human Health. ACTA ACUST UNITED AC 2014. [DOI: 10.4236/ajmb.2014.43011] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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20
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Lisa MN, Morán-Barrio J, Guindón MF, Vila AJ. Probing the role of Met221 in the unusual metallo-β-lactamase GOB-18. Inorg Chem 2012; 51:12419-25. [PMID: 23113650 DOI: 10.1021/ic301801h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metallo-β-lactamases (MβLs) are the main mechanism of bacterial resistance against last generation β-lactam antibiotics such as carbapenems. Most MβLs display unusual structural features in their active sites, such as binuclear zinc centers without carboxylate bridging ligands and/or a Cys ligand in a catalytic zinc site. Cys221 is an essential residue for catalysis conserved in B1 and B2 lactamases, while most B3 enzymes present a Ser in this position. GOB lactamases stand as an exception within this picture, with a Met residue in position 221. Then, we obtained a series of GOB-18 point mutants in order to analyze the role of this unusual Met221 residue. We found that Met221 is essential for the protein stability, most likely due to its involvement in a hydrophobic core. In contrast to other known MβLs, residue 221 is not involved in metal binding or in catalysis in GOB enzymes, according to spectroscopic and kinetic studies. Our findings show that the essential catalytic features are maintained despite the structural heterogeneity among MβLs and suggest that a strategy to design general inhibitors should be undertaken on the basis of mechanistic rather than structural information.
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Affiliation(s)
- María-Natalia Lisa
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR) and Departamento de Química Biológica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Ocampo y Esmeralda, Predio CONICET Rosario, 2000 Rosario, Argentina
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21
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Metallo-β-lactamases withstand low Zn(II) conditions by tuning metal-ligand interactions. Nat Chem Biol 2012; 8:698-700. [PMID: 22729148 PMCID: PMC3470787 DOI: 10.1038/nchembio.1005] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Accepted: 05/14/2012] [Indexed: 11/25/2022]
Abstract
A number of multiresistant bacterial pathogens inactivate antibiotics by producing ZnII-dependent β-lactamases. We show that metal uptake leading to an active dinuclear enzyme in the periplasmic space of Gram-negative bacteria is ensured by a cysteine residue, an unusual metal ligand in oxidizing environments. Kinetic, structural and affinity data show that such ZnII-Cys interaction is an adaptive trait tuning the metal binding affinity, thus enabling antibiotic resistance at restrictive ZnII concentrations.
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22
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Sgrignani J, Magistrato A, Dal Peraro M, Vila AJ, Carloni P, Pierattelli R. On the active site of mononuclear B1 metallo β-lactamases: a computational study. J Comput Aided Mol Des 2012; 26:425-35. [PMID: 22532071 DOI: 10.1007/s10822-012-9571-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 04/09/2012] [Indexed: 11/28/2022]
Abstract
Metallo-β-lactamases (MβLs) are Zn(II)-based bacterial enzymes that hydrolyze β-lactam antibiotics, hampering their beneficial effects. In the most relevant subclass (B1), X-ray crystallography studies on the enzyme from Bacillus Cereus point to either two zinc ions in two metal sites (the so-called '3H' and 'DCH' sites) or a single Zn(II) ion in the 3H site, where the ion is coordinated by Asp120, Cys221 and His263 residues. However, spectroscopic studies on the B1 enzyme from B. Cereus in the mono-zinc form suggested the presence of the Zn(II) ion also in the DCH site, where it is bound to an aspartate, a cysteine, a histidine and a water molecule. A structural model of this enzyme in its DCH mononuclear form, so far lacking, is therefore required for inhibitor design and mechanistic studies. By using force field based and mixed quantum-classical (QM/MM) molecular dynamics (MD) simulations of the protein in aqueous solution we constructed such structural model. The geometry and the H-bond network at the catalytic site of this model, in the free form and in complex with two common β-lactam drugs, is compared with experimental and theoretical findings of CphA and the recently solved crystal structure of new B2 MβL from Serratia fonticola (Sfh-I). These are MβLs from the B2 subclass, which features an experimentally well established mono-zinc form, in which the Zn(II) is located in the DCH site. From our simulations the εεδ and δεδ protomers emerge as possible DCH mono-zinc reactive species, giving a novel contribution to the discussion on the MβL reactivity and to the drug design process.
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Affiliation(s)
- Jacopo Sgrignani
- CERM and Department of Chemistry Ugo Schiff, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
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23
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Breece RM, Llarrull LI, Tioni MF, Vila AJ, Tierney DL. X-ray absorption spectroscopy of metal site speciation in the metallo-β-lactamase BcII from Bacillus cereus. J Inorg Biochem 2012; 111:182-6. [PMID: 22381913 DOI: 10.1016/j.jinorgbio.2011.12.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Revised: 12/12/2011] [Accepted: 12/13/2011] [Indexed: 01/25/2023]
Abstract
Cobalt and zinc binding by the subclass B1 metallo-β-lactamase BcII from Bacillus cereus is examined by X-ray absorption spectroscopy, at various levels of metal loading. The data show that a significant amount of the dinuclear enzyme is formed, even at substoichiometric levels of metal loading, whether the added metal is Zn(II) or Co(II). Increasing metal addition, from 0.5 to 1.0 to 2.0eq/mol of enzyme, are shown to result in a more ordered active site. While Zn(II) appears to show no preference for the Zn(1) (3H) or Zn(2) (DCH) sites, the extended X-ray absorption fine structure (EXAFS) suggests that Co(II) shows a slight preference for the DCH site at low levels of added Co(II). The results are discussed in the context of similar metal-binding studies of other B1 metallo-β-lactamases.
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Affiliation(s)
- Robert M Breece
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, United States
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24
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GU WEI, ZHU JIANG, LIU HAIYAN. DIFFERENT PROTONATION STATES OF THE BACILLUS CEREUS BINUCLEAR ZINC METALLO-β-LACTAMASE ACTIVE SITE STUDIED BY COMBINED QUANTUM MECHANICAL AND MOLECULAR MECHANICAL SIMULATIONS. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2012. [DOI: 10.1142/s0219633602000038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Three different protonation states of the active site of the Bacillus cereus zinc-β-lactamase in its binuclear form are studied using combined quantum mechanics/molecular mechanics molecular dynamics simulations. The reliability of the quantum mechanical model, the self-consistent-charge density-functional-based tight binding method, in describing the zinc centers are tested through comparisons with ab initio quantum mechanical results. We found that this model gave relatively accurate results for structures and performed much better than the MNDO type semi-empirical method for the particular systems. The enzyme simulations suggested that when the overall charge of the active site is +1, i.e., both Asp90 and Wat1 (a water molecule coordinated with the first zinc ion) deprotonated, the second zinc ion is coordinated with Asp90 and Wat1, and a second water molecule cannot coordinate with the second zinc ion. When the overall charge is +2, i.e., either Asp90 or Wat1 protonated, Asp90 and Wat1 form a stable hydrogen bond. Depending on the proton being on Asp90 or on Wat1, the active site structure produced by the simulations is either similar to molecule A or to molecule B, both contained in the same crystal structure that has two enzyme molecules in a single asymmetric unit. The simulations of the +2 charge states also reproduced the experimentally observed "loose" coordination around the second zinc for the Bacillus Cereus enzyme. Based on the simulations and a gas phase potential energy surface scanning using ab initio model, we argue that the penta-coordination around the second zinc ion is not a stable arrangement. Mechanistic implications of these results are discussed.
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Affiliation(s)
- WEI GU
- School of Life Science, University of Science and Technology of China (USTC), Laboratory of Structural Biology, Chinese Academy of Science (CAS), USTC, Hefei, Anhui, 230026, China
| | - JIANG ZHU
- School of Life Science, University of Science and Technology of China (USTC), Laboratory of Structural Biology, Chinese Academy of Science (CAS), USTC, Hefei, Anhui, 230026, China
| | - HAIYAN LIU
- School of Life Science, University of Science and Technology of China (USTC), Laboratory of Structural Biology, Chinese Academy of Science (CAS), USTC, Hefei, Anhui, 230026, China
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Saini A, Bansal R. Insights on the structural characteristics of NDM-1: The journey so far. ACTA ACUST UNITED AC 2012. [DOI: 10.4236/abc.2012.24040] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Thomas PW, Zheng M, Wu S, Guo H, Liu D, Xu D, Fast W. Characterization of Purified New Delhi Metallo-β-lactamase-1. Biochemistry 2011; 50:10102-13. [DOI: 10.1021/bi201449r] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Pei W. Thomas
- Division of
Medicinal Chemistry,
College of Pharmacy, The University of Texas, Austin, Texas 78712, United States
| | - Min Zheng
- Key Laboratory of Green Chemistry
and Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Schuan 610064, China
| | - Shanshan Wu
- Key Laboratory of Green Chemistry
and Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Schuan 610064, China
| | - Hua Guo
- Department of Chemistry and Chemical
Biology, University of New Mexico, Albuquerque,
New Mexico 87131, United States
| | - Dali Liu
- Department of Chemistry, Bioinformatics
Program, Loyola University Chicago, Chicago,
Illinois 60660, United States
| | - Dingguo Xu
- Key Laboratory of Green Chemistry
and Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Schuan 610064, China
| | - Walter Fast
- Division of
Medicinal Chemistry,
College of Pharmacy, The University of Texas, Austin, Texas 78712, United States
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The CphAII protein from Aquifex aeolicus exhibits a metal-dependent phosphodiesterase activity. Extremophiles 2011; 16:45-55. [PMID: 22009263 DOI: 10.1007/s00792-011-0404-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Accepted: 10/05/2011] [Indexed: 10/16/2022]
Abstract
The CphAII protein from the hyperthermophile Aquifex aeolicus shows the five conserved motifs of the metallo-β-lactamase (MBL) superfamily and presents 28% identity with the Aeromonas hydrophila subclass B2 CphA MBL. The gene encoding CphAII was amplified by PCR from the A. aeolicus genomic DNA and overexpressed in Escherichia coli using a pLex-based expression system. The recombinant CphAII protein was purified by a combination of heating (to denature E. coli proteins) and two steps of immobilized metal affinity chromatography. The purified enzyme preparation did not exhibit a β-lactamase activity but showed a metal-dependent phosphodiesterase activity versus bis-p-nitrophenyl phosphate and thymidine 5'-monophosphate p-nitrophenyl ester, with an optimum at 85°C. The circular dichroism spectrum was in agreement with the percentage of secondary structures characteristic of the MBL αββα fold.
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Sun L, Zhang L, Zhang H, He ZG. Characterization of a bifunctional β-lactamase/ribonuclease and its interaction with a chaperone-like protein in the pathogen Mycobacterium tuberculosis H37Rv. BIOCHEMISTRY (MOSCOW) 2011; 76:350-8. [PMID: 21568871 DOI: 10.1134/s0006297911030096] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Most mycobacteria appear to be naturally resistant to β-lactam antibiotics such as penicillin. However, very few β-lactamases and their regulation have been clearly characterized in Mycobacterium tuberculosis H37Rv. In this study, a unique bifunctional protein, Rv2752c, from M. tuberculosis showed both β-lactamase and RNase activities. Two residues, D184 and H397, appear to be involved in Zn(2+)-binding and are essential for the dual functions. Both activities are lost upon deletion of the C-terminal 100 a.a. long Rv2752c tail, which contains an additional loop when compared with the RNase J of Bacillus subtilis. A chaperone-like protein, Rv2373c, physically interacted with Rv2752c and inhibited both activities. This is the first report of characterization of a bifunctional β-lactamase and its regulation in mycobacteria. These data offered important clues for further investigation of the structure and function of microbial β-lactamases. Increased understanding of this protein will provide further insights into the mechanism of microbial drug resistance.
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Affiliation(s)
- Lei Sun
- National Key Laboratory of Agricultural Microbiology, Center for Proteomics Research, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
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29
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Griffin DH, Richmond TK, Sanchez C, Moller AJ, Breece RM, Tierney DL, Bennett B, Crowder MW. Structural and kinetic studies on metallo-β-lactamase IMP-1. Biochemistry 2011; 50:9125-34. [PMID: 21928807 DOI: 10.1021/bi200839h] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In an effort to probe for metal binding to metallo-β-lactamase (MβL) IMP-1, the enzyme was overexpressed, purified, and characterized. The resulting enzyme was shown to bind 2 equiv of Zn(II), exhibit significant catalytic activity, and yield EXAFS results similar to crystallographic data previously reported. Rapid kinetic studies showed that IMP-1 does not stabilize a nitrocefin-derived reaction intermediate; rather, the enzyme follows a simple Michaelis mechanism to hydrolyze nitrocefin. Metal-substituted and metal-reconstituted analogues of IMP-1 were prepared by directly adding metal ion stocks to metal-free enzyme, which was generated by dialysis versus EDTA. UV-vis studies on IMP-1 containing 1 equiv of Co(II) showed a strong ligand-to-metal charge transition at 340 nm, and the intensity of this feature increased when the second equivalent of Co(II) was added to the enzyme. EXAFS fits on IMP-1 containing 1 equiv of Co(II) strongly suggest the presence of a metal-metal interaction, and EPR spectra of the IMP-1 containing 1 and 2 equiv of Co(II) are very similar. Taken together, steady-state kinetic and spectroscopic studies suggest that metal binding to metal-free IMP-1 follows a positive-cooperative mode.
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Affiliation(s)
- Dionne H Griffin
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
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Yamaguchi Y, Ding S, Murakami E, Imamura K, Fuchigami S, Hashiguchi R, Yutani K, Mori H, Suzuki S, Arakawa Y, Kurosaki H. A demetallation method for IMP-1 metallo-β-lactamase with restored enzymatic activity upon addition of metal ion(s). Chembiochem 2011; 12:1979-83. [PMID: 21739563 DOI: 10.1002/cbic.201100342] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Indexed: 11/11/2022]
Affiliation(s)
- Yoshihiro Yamaguchi
- Environmental Safety Center, Kumamoto University, 39-1 Kurokami 2-Chome, Kumamoto 860-8555, Japan.
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Yamaguchi Y, Imamura K, Sasao A, Murakami E, Arakawa Y, Kurosaki H. Metal preference of Zn(ii) and Co(ii) for the dinuclear metal binding site of IMP-1 metallo-β-lactamase and spectroscopic properties of Co(ii)-substituted IMP-1 with mercaptoacetic acid. MEDCHEMCOMM 2011. [DOI: 10.1039/c1md00062d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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González JM, Buschiazzo A, Vila AJ. Evidence of Adaptability in Metal Coordination Geometry and Active-Site Loop Conformation among B1 Metallo-β-lactamases,. Biochemistry 2010; 49:7930-8. [DOI: 10.1021/bi100894r] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Javier M. González
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Suipacha 531, S2002LRK Rosario, Argentina
| | - Alejandro Buschiazzo
- Institut Pasteur de Montevideo, Unidad de Cristalografía de Proteínas, Mataojo 2020, 11400 Montevideo, Uruguay, and Institut Pasteur, Department of Structural Biology and Chemistry, 25 rue du Dr Roux, 75015 Paris, France
| | - Alejandro J. Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Suipacha 531, S2002LRK Rosario, Argentina
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33
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The mechanisms of catalysis by metallo beta-lactamases. Bioinorg Chem Appl 2010:576297. [PMID: 18551183 PMCID: PMC2422870 DOI: 10.1155/2008/576297] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2007] [Revised: 01/29/2008] [Accepted: 02/26/2008] [Indexed: 01/03/2023] Open
Abstract
Class B β-lactamases or metallo-β-lactamases (MBLs) require zinc ions to catalyse the hydrolysis of β-lactam antibiotics such as penicillins, cephalosporins, carbapenems, and cephamycins. There are no clinically useful inhibitors against MBLs which are responsible for the resistance of some bacteria to antibiotics. There are two metal-ion binding sites that have different zinc ligands but the exact roles of the metal-ion remain controversial, and distinguishing between their relative importance is complex. The metal-ion can act as a Lewis acid by co-ordination to the β-lactam carbonyl oxygen to facilitate nucleophilic attack and stabilise the negative charge developed on this oxygen in the tetrahedral intermediate anion. The metal-ion also lowers the pKa of the directly co-ordinated water molecule so that the metal-bound hydroxide ion is a better nucleophile than water and is used to attack the β-lactam carbonyl carbon. An intrinsic property of binuclear metallo hydrolytic enzymes that depend on a metal-bound water both as the attacking nucleophile and as a ligand for the second metal-ion is that this water molecule, which is consumed during hydrolysis of the substrate, has to be replaced to maintain the catalytic cycle. With MBL this is reflected in some unusual kinetic profiles.
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Campos-Bermudez VA, González JM, Tierney DL, Vila AJ. Spectroscopic signature of a ubiquitous metal binding site in the metallo-β-lactamase superfamily. J Biol Inorg Chem 2010; 15:1209-18. [PMID: 20535505 DOI: 10.1007/s00775-010-0678-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2010] [Accepted: 05/24/2010] [Indexed: 11/24/2022]
Abstract
The metallo-β-lactamase (MβL) superfamily is a functionally diverse group of metalloproteins sharing a distinctive αβ/αβ fold and a characteristic metal binding motif. A large number of open reading frames identified in genomic sequencing efforts have been annotated as members of this superfamily through sequence comparisons. However, structural and functional studies performed on purified proteins are normally needed to unequivocally include a newly discovered protein in the MβL superfamily. Here we report the spectroscopic characterization of recombinant YcbL, a gene product annotated as a member of the MβL superfamily whose function in vivo remains unknown. By taking advantage of the structural features characterizing the MβL superfamily metal binding motif, we performed spectroscopic studies on Zn(II)- and Co(II)-substituted YcbL to structurally interrogate the metal binding site. The dinuclear center in Co(II)-YcbL was shown to display characteristic electronic absorption features in the visible region, which were also observed in an engineered MβL aimed at mimicking this metal site. Thus, the spectroscopic features reported herein can be employed as a signature to readily identify and characterize the presence of these ubiquitous metal binding sites.
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Affiliation(s)
- Valeria A Campos-Bermudez
- Instituto de Biología Molecular y Celular de Rosario, IBR-CONICET, Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario Suipacha 531, S2002LRK, Rosario, Argentina
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Yamaguchi Y, Takashio N, Wachino JI, Yamagata Y, Arakawa Y, Matsuda K, Kurosaki H. Structure of metallo- -lactamase IND-7 from a Chryseobacterium indologenes clinical isolate at 1.65-A resolution. J Biochem 2010; 147:905-15. [DOI: 10.1093/jb/mvq029] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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Lisa MN, Hemmingsen L, Vila AJ. Catalytic role of the metal ion in the metallo-beta-lactamase GOB. J Biol Chem 2009; 285:4570-7. [PMID: 20007696 DOI: 10.1074/jbc.m109.063743] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Metallo-beta-lactamases (MbetaLs) stand as one of the main mechanisms of bacterial resistance toward carbapenems. The rational design of an inhibitor for MbetaLs has been limited by an incomplete knowledge of their catalytic mechanism and by the structural diversity of their active sites. Here we show that the MbetaL GOB from Elizabethkingia meningoseptica is active as a monometallic enzyme by using different divalent transition metal ions as surrogates of the native Zn(II) ion. Of the metal derivatives in which Zn(II) is replaced, Co(II) and Cd(II) give rise to the most active enzymes and are shown to occupy the same binding site as the native ion. However, Zn(II) is the only metal ion capable of stabilizing an anionic intermediate that accumulates during nitrocefin hydrolysis, in which the C-N bond has already been cleaved. This finding demonstrates that the catalytic role of the metal ion in GOB is to stabilize the formation of this intermediate prior to nitrogen protonation. This role may be general to all MbetaLs, whereas nucleophile activation by a Zn(II) ion is not a conserved mechanistic feature.
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Affiliation(s)
- María-Natalia Lisa
- Departamento de Química Biológica and Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, Argentina
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37
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Positively cooperative binding of zinc ions to Bacillus cereus 569/H/9 beta-lactamase II suggests that the binuclear enzyme is the only relevant form for catalysis. J Mol Biol 2009; 392:1278-91. [PMID: 19665032 DOI: 10.1016/j.jmb.2009.07.092] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2009] [Revised: 07/27/2009] [Accepted: 07/31/2009] [Indexed: 11/21/2022]
Abstract
Metallo-beta-lactamases catalyze the hydrolysis of most beta-lactam antibiotics and hence represent a major clinical concern. While enzymes belonging to subclass B1 have been shown to display maximum activity as dizinc species, the actual metal-to-protein stoichiometry and the affinity for zinc are not clear. We have further investigated the process of metal binding to the beta-lactamase II from Bacillus cereus 569/H/9 (known as BcII). Zinc binding was monitored using complementary biophysical techniques, including circular dichroism in the far-UV, enzymatic activity measurements, competition with a chromophoric chelator, mass spectrometry, and nuclear magnetic resonance. Most noticeably, mass spectrometry and nuclear magnetic resonance experiments, together with catalytic activity measurements, demonstrate that two zinc ions bind cooperatively to the enzyme active site (with K(1)/K(2)> or =5) and, hence, that catalysis is associated with the dizinc enzyme species only. Furthermore, competitive experiments with the chromophoric chelator Mag-Fura-2 indicates K(2)<80 nM. This contrasts with cadmium binding, which is clearly a noncooperative process with the mono form being the only species significantly populated in the presence of 1 molar equivalent of Cd(II). Interestingly, optical measurements reveal that although the apo and dizinc species exhibit undistinguishable tertiary structural organizations, the metal-depleted enzyme shows a significant decrease in its alpha-helical content, presumably associated with enhanced flexibility.
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Limphong P, McKinney RM, Adams NE, Bennett B, Makaroff CA, Gunasekera T, Crowder MW. Human glyoxalase II contains an Fe(II)Zn(II) center but is active as a mononuclear Zn(II) enzyme. Biochemistry 2009; 48:5426-34. [PMID: 19413286 DOI: 10.1021/bi9001375] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human glyoxalase II (Glx2) was overexpressed in rich medium and in minimal medium containing zinc, iron, or cobalt, and the resulting Glx2 analogues were characterized using metal analyses, steady-state and pre-steady-state kinetics, and NMR and EPR spectroscopies to determine the nature of the metal center in the enzyme. Recombinant human Glx2 tightly binds nearly 1 equiv each of Zn(II) and Fe. In contrast to previous reports, this study demonstrates that an analogue containing 2 equiv of Zn(II) cannot be prepared. EPR studies suggest that most of the iron in recombinant Glx2 is Fe(II). NMR studies show that Fe(II) binds to the consensus Zn(2) site in Glx2 and that this site can also bind Co(II) and Ni(II), suggesting that Zn(II) binds to the consensus Zn(1) site. The NMR studies also reveal the presence of a dinuclear Co(II) center in Co(II)-substituted Glx2. Steady-state and pre-steady-state kinetic studies show that Glx2 containing only 1 equiv of Zn(II) is catalytically active and that the metal ion in the consensus Zn(2) site has little effect on catalytic activity. Taken together, these studies suggest that Glx2 contains a Fe(II)Zn(II) center in vivo but that the catalytic activity is due to Zn(II) in the Zn(1) site.
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Affiliation(s)
- Pattraranee Limphong
- Department of Chemistry and Biochemistry, 160 Hughes Hall, Miami University, Oxford, Ohio 45056, USA
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39
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X-ray structure and spectroscopic characterization of divalent dinuclear cobalt complexes containing carboxylate- and phosphodiester- auxiliary bridges. Inorganica Chim Acta 2009. [DOI: 10.1016/j.ica.2009.02.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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40
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Tioni MF, Llarrull LI, Poeylaut-Palena AA, Martí MA, Saggu M, Periyannan GR, Mata EG, Bennett B, Murgida DH, Vila AJ. Trapping and characterization of a reaction intermediate in carbapenem hydrolysis by B. cereus metallo-beta-lactamase. J Am Chem Soc 2009; 130:15852-63. [PMID: 18980308 DOI: 10.1021/ja801169j] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metallo-beta-lactamases hydrolyze most beta-lactam antibiotics. The lack of a successful inhibitor for them is related to the previous failure to characterize a reaction intermediate with a clinically useful substrate. Stopped-flow experiments together with rapid freeze-quench EPR and Raman spectroscopies were used to characterize the reaction of Co(II)-BcII with imipenem. These studies show that Co(II)-BcII is able to hydrolyze imipenem in both the mono- and dinuclear forms. In contrast to the situation met for penicillin, the species that accumulates during turnover is an enzyme-intermediate adduct in which the beta-lactam bond has already been cleaved. This intermediate is a metal-bound anionic species with a novel resonant structure that is stabilized by the metal ion at the DCH or Zn2 site. This species has been characterized based on its spectroscopic features. This represents a novel, previously unforeseen intermediate that is related to the chemical nature of carbapenems, as confirmed by the finding of a similar intermediate for meropenem. Since carbapenems are the only substrates cleaved by B1, B2, and B3 lactamases, identification of this intermediate could be exploited as a first step toward the design of transition-state-based inhibitors for all three classes of metallo-beta-lactamases.
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Affiliation(s)
- Mariana F Tioni
- Instituto de Biologia Molecular y Celular de Rosario and Biophysics Section, Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina, Universidad Nacional de Rosario, Rosario, Argentina
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Adaptive protein evolution grants organismal fitness by improving catalysis and flexibility. Proc Natl Acad Sci U S A 2008; 105:20605-10. [PMID: 19098096 DOI: 10.1073/pnas.0807989106] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Protein evolution is crucial for organismal adaptation and fitness. This process takes place by shaping a given 3-dimensional fold for its particular biochemical function within the metabolic requirements and constraints of the environment. The complex interplay between sequence, structure, functionality, and stability that gives rise to a particular phenotype has limited the identification of traits acquired through evolution. This is further complicated by the fact that mutations are pleiotropic, and interactions between mutations are not always understood. Antibiotic resistance mediated by beta-lactamases represents an evolutionary paradigm in which organismal fitness depends on the catalytic efficiency of a single enzyme. Based on this, we have dissected the structural and mechanistic features acquired by an optimized metallo-beta-lactamase (MbetaL) obtained by directed evolution. We show that antibiotic resistance mediated by this enzyme is driven by 2 mutations with sign epistasis. One mutation stabilizes a catalytically relevant intermediate by fine tuning the position of 1 metal ion; whereas the other acts by augmenting the protein flexibility. We found that enzyme evolution (and the associated antibiotic resistance) occurred at the expense of the protein stability, revealing that MbetaLs have not exhausted their stability threshold. Our results demonstrate that flexibility is an essential trait that can be acquired during evolution on stable protein scaffolds. Directed evolution aided by a thorough characterization of the selected proteins can be successfully used to predict future evolutionary events and design inhibitors with an evolutionary perspective.
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Llarrull LI, Tioni MF, Vila AJ. Metal Content and Localization during Turnover in B. cereus Metallo-β-lactamase. J Am Chem Soc 2008; 130:15842-51. [DOI: 10.1021/ja801168r] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Leticia I. Llarrull
- IBR (Instituto de Biología Molecular y Celular de Rosario), Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina (CONICET), and Biophysics Section, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, Argentina
| | - Mariana F. Tioni
- IBR (Instituto de Biología Molecular y Celular de Rosario), Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina (CONICET), and Biophysics Section, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, Argentina
| | - Alejandro J. Vila
- IBR (Instituto de Biología Molecular y Celular de Rosario), Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina (CONICET), and Biophysics Section, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, Argentina
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Abriata LA, González LJ, Llarrull LI, Tomatis PE, Myers WK, Costello AL, Tierney DL, Vila AJ. Engineered mononuclear variants in Bacillus cereus metallo-beta-lactamase BcII are inactive. Biochemistry 2008; 47:8590-9. [PMID: 18652482 PMCID: PMC2565585 DOI: 10.1021/bi8006912] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metallo-beta-lactamases (MbetaLs) are zinc enzymes able to hydrolyze almost all beta-lactam antibiotics, rendering them inactive, at the same time endowing bacteria high levels of resistance. The design of inhibitors active against all classes of MbetaLs has been hampered by their structural diversity and by the heterogeneity in metal content in enzymes from different sources. BcII is the metallo-beta-lactamase from Bacillus cereus, which is found in both the mononuclear and dinuclear forms. Despite extensive studies, there is still controversy about the nature of the active BcII species. Here we have designed two mutant enzymes in which each one of the metal binding sites was selectively removed. Both mutants were almost inactive, despite preserving most of the structural features of each metal site. These results reveal that neither site isolated in the MbetaL scaffold is sufficient to render a fully active enzyme. This suggests that only the dinuclear species is active or that the mononuclear variants can be active only if aided by other residues that would be metal ligands in the dinuclear species.
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Affiliation(s)
| | | | | | | | | | | | | | - Alejandro J. Vila
- To whom correspondence should be addressed. Phone: +54−341−4350661, ext. 108. Fax: +54−341−4390465. E-mail:
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Zinc and antibiotic resistance: metallo-β-lactamases and their synthetic analogues. J Biol Inorg Chem 2008; 13:1039-53. [DOI: 10.1007/s00775-008-0407-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2008] [Accepted: 07/02/2008] [Indexed: 10/21/2022]
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Hu Z, Periyannan GR, Crowder MW. Folding strategy to prepare Co(II)-substituted metallo-beta-lactamase L1. Anal Biochem 2008; 378:177-83. [PMID: 18445468 PMCID: PMC2587373 DOI: 10.1016/j.ab.2008.04.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2008] [Revised: 04/01/2008] [Accepted: 04/03/2008] [Indexed: 11/24/2022]
Abstract
In an effort to overcome previous problems with the preparation of Co(II)-substituted metallo-beta-lactamase L1, two strategies were undertaken. Attempts to prepare Co(II)-substituted L1 using biological incorporation resulted in an enzyme that contained only 1 Eq of cobalt and exhibited no catalytic activity. Co(II)-substituted L1 could be prepared by refolding metal-free L1 in the presence of Co(II), and the resulting enzyme contained 1.8 Eq of cobalt, yielded a UV-Vis spectrum consistent with 5-coordinate Co(II), and exhibited a k(cat) of 63 s(-1) and K(m) of 20 microM when using nitrocefin as the substrate. Pre-steady-state fluorescence and UV-Vis studies demonstrated that refolded, Co(II)-substituted L1 uses the same kinetic mechanism as Zn(II)-containing L1, in which a reaction intermediate is formed when using nitrocefin as substrate. The described refolding strategy can be used to prepare other Co(II)-substituted Zn(II)-metalloenzymes, particularly those that contain a solvent-exposable disulfide, which often causes oxidation of Co(II) to Co(III).
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Affiliation(s)
- Zhenxin Hu
- Department of Chemistry and Biochemistry, 160 Hughes Hall, Miami University, Oxford, OH 45056
| | - Gopal R. Periyannan
- Department of Chemistry and Biochemistry, 160 Hughes Hall, Miami University, Oxford, OH 45056
| | - Michael W. Crowder
- Department of Chemistry and Biochemistry, 160 Hughes Hall, Miami University, Oxford, OH 45056
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Loss of enzyme activity during turnover of the Bacillus cereus beta-lactamase catalysed hydrolysis of beta-lactams due to loss of zinc ion. J Biol Inorg Chem 2008; 13:919-28. [PMID: 18449576 DOI: 10.1007/s00775-008-0379-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2008] [Accepted: 04/15/2008] [Indexed: 10/22/2022]
Abstract
Metallo-beta-lactamases are zinc-ion-dependent and are known to exist either as mononuclear or as dinuclear enzymes. The kinetics and mechanism of hydrolysis of the native zinc Bacillus cereus metallo-beta-lactamase (BcII) have been investigated under pre-steady-state conditions at different pHs and zinc-ion concentrations. Biphasic kinetics are observed for the hydrolysis of cefuroxime and benzylpenicillin with submicromolar concentrations of enzyme and zinc. The initial burst of product formation far exceeds the concentration of enzyme and the subsequent slower rate of hydrolysis is attributed to a branched kinetic pathway. The pH and metal-ion dependence of the microscopic rate constants of this branching were determined, from which it is concluded that two enzyme species with different metal-to-enzyme stoichiometries are formed during catalytic turnover. The dizinc enzyme is responsible for the fast route but during the catalytic cycle it slowly loses the less tightly bound zinc ion via the branching route to give an inactive monozinc enzyme; the latter is only catalytic following the uptake of a second zinc ion. The rate constant for product formation from the dinuclear enzyme and the branching rate constant show a sigmoidal dependence on pH indicative of important ionizing groups with pK(a)s of 9.0+/-0.1 and 8.2+/-0.1, respectively. The rate constant for the regeneration of enzyme activity depends on zinc-ion concentration. This unusual behaviour is attributed to an intrinsic property of metallo hydrolytic enzymes that depend on a metal bound water both as a ligand for the second metal ion and as the nucleophile which is consumed during hydrolysis of the substrate and so has to be replaced to maintain the catalytic cycle.
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Biochemical characterization of metallo-beta-lactamase VIM-11 from a Pseudomonas aeruginosa clinical strain. Antimicrob Agents Chemother 2008; 52:2250-2. [PMID: 18362187 DOI: 10.1128/aac.01025-07] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A detailed biochemical characterization of the Pseudomonas aeruginosa VIM-11 metallo-beta-lactamase (MbetaL) is reported. The only substitution differentiating VIM-11 from VIM-2 (N165S) promoted a slightly improved catalytic efficiency of the former on 3 out of 12 substrates, notably the bulky cephalosporins. Thus, MbetaL-mediated resistance also may be modulated by remote mutations.
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González JM, Medrano Martín FJ, Costello AL, Tierney DL, Vila AJ. The Zn2 Position in Metallo-β-Lactamases is Critical for Activity: A Study on Chimeric Metal Sites on a Conserved Protein Scaffold. J Mol Biol 2007; 373:1141-56. [PMID: 17915249 DOI: 10.1016/j.jmb.2007.08.031] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2007] [Revised: 07/31/2007] [Accepted: 08/01/2007] [Indexed: 10/22/2022]
Abstract
Metallo-beta-lactamases (MbetaLs) are bacterial Zn(II)-dependent hydrolases that confer broad-spectrum resistance to beta-lactam antibiotics. These enzymes can be subdivided into three subclasses (B1, B2 and B3) that differ in their metal binding sites and their characteristic tertiary structure. To date there are no clinically useful pan-MbetaL inhibitors available, mainly due to the unawareness of key catalytic features common to all MbetaL brands. Here we have designed, expressed and characterized two double mutants of BcII, a di-Zn(II) B1-MbetaL from Bacillus cereus, namely BcII-R121H/C221D (BcII-HD) and BcII-R121H/C221S (BcII-HS). These mutants display modified environments at the so-called Zn2 site or DCH site, reproducing the metal coordination environments of structurally related metallohydrolases. Through a combination of structural and functional studies, we found that BcII-HD is an impaired beta-lactamase even as a di-Zn(II) enzyme, whereas BcII-HS exhibits the ability to exist as mono or di-Zn(II) species in solution, with different catalytic performances. We show that these effects result from an altered position of Zn2, which is incapable of providing a productive interaction with the substrate beta-lactam ring. These results indicate that the position of Zn2 is essential for a productive substrate binding and hydrolysis.
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Affiliation(s)
- Javier M González
- Departamento de Química Biológica, Instituto de Biología Molecular y Celular de Rosario, IBR-CONICET. Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, S2002LRK, Argentina
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Llarrull LI, Tioni MF, Kowalski J, Bennett B, Vila AJ. Evidence for a dinuclear active site in the metallo-beta-lactamase BcII with substoichiometric Co(II). A new model for metal uptake. J Biol Chem 2007; 282:30586-95. [PMID: 17715135 DOI: 10.1074/jbc.m704613200] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Metallo-beta-lactamases are zinc-dependent enzymes that constitute one of the main resistance mechanisms to beta-lactam antibiotics. Metallo-beta-lactamases have been characterized both in mono- and dimetallic forms. Despite many studies, the role of each metal binding site in substrate binding and catalysis is still unclear. This is mostly due to the difficulties in assessing the metal content and site occupancy in solution. For this reason, Co(II) has been utilized as a useful probe of the active site structure. We have employed UV-visible, EPR, and NMR spectroscopy to study Co(II) binding to the metallo-beta-lactamase BcII from Bacillus cereus. The spectroscopic features were attributed to the two canonical metal binding sites, the 3H (His(116), His(118), and His(196)) and DCH (Asp(120), Cys(221), and His(263)) sites. These data clearly reveal the coexistence of mononuclear and dinuclear Co(II)-loaded forms at Co(II)/enzyme ratios as low as 0.6. This picture is consistent with the macroscopic dissociation constants here determined from competition binding experiments. A spectral feature previously assigned to the DCH site in the dinuclear species corresponds to a third, weakly bound Co(II) site. The present work emphasizes the importance of using different spectroscopic techniques to follow the metal content and localization during metallo-beta-lactamase turnover.
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Affiliation(s)
- Leticia I Llarrull
- Molecular Biology Division, Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina
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Tamilselvi A, Nethaji M, Mugesh G. Antibiotic resistance: mono- and dinuclear zinc complexes as metallo-beta-lactamase mimics. Chemistry 2007; 12:7797-806. [PMID: 16906495 DOI: 10.1002/chem.200600629] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Biomimetic systems containing one or two zinc(II) ions supported by phenolate ligands were developed as functional mimics of metallo-beta-lactamase. These complexes were shown to catalytically hydrolyze beta-lactam substrates, such as oxacillin and penicillin G. The dinuclear zinc complex 1, which has a coordinated water molecule, exhibits high beta-lactamase activity, whereas the dinuclear zinc complex 2, which has no water molecules, but labile chloride ligands, shows a much lower activity. The high beta-lactamase activity of complex 1 can be ascribed to the presence of a zinc-bound water molecule that is activated by being hydrogen bonded to acetate substituents. The kinetics of the hydrolysis of oxacillin by complex 1 and the effect of pH on the reaction rates are reported in detail. In addition, the kinetic parameters obtained for the synthetic analogues are compared with those of the natural metallo-beta-lactamase from Bacillus cereus (BcII). To understand the role of the second metal ion in hydrolysis, the syntheses and catalytic activities of two mononuclear complexes (3 and 4) that include coordinated water molecules are described. Interestingly, the mononuclear zinc complexes 3 and 4 also exhibit high activity, supporting the assumption that the second zinc ion is not crucial for the beta-lactamase activity.
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Affiliation(s)
- A Tamilselvi
- Department of Inorganic and Physical Chemistry Indian Institute of Science, Bangalore 560 012, India
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