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Pinto G, Mazzone G, Russo N, Toscano M. Trimethylphosphate and Dimethylphosphate Hydrolysis by Binuclear CdII
, MnII
, and ZnII
-FeII
Promiscuous Organophosphate-Degrading Enzyme: Reaction Mechanisms. Chemistry 2017; 23:13742-13753. [DOI: 10.1002/chem.201702379] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Gaspar Pinto
- Department Of Chemistry and Chemical Technologies; University of Calabria; Via P. Bucci 87036 Arcavacata di Rende Italy
| | - Gloria Mazzone
- Department Of Chemistry and Chemical Technologies; University of Calabria; Via P. Bucci 87036 Arcavacata di Rende Italy
| | - Nino Russo
- Department Of Chemistry and Chemical Technologies; University of Calabria; Via P. Bucci 87036 Arcavacata di Rende Italy
| | - Marirosa Toscano
- Department Of Chemistry and Chemical Technologies; University of Calabria; Via P. Bucci 87036 Arcavacata di Rende Italy
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2
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Jacquet P, Daudé D, Bzdrenga J, Masson P, Elias M, Chabrière E. Current and emerging strategies for organophosphate decontamination: special focus on hyperstable enzymes. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:8200-18. [PMID: 26832878 DOI: 10.1007/s11356-016-6143-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 01/20/2016] [Indexed: 06/05/2023]
Abstract
Organophosphorus chemicals are highly toxic molecules mainly used as pesticides. Some of them are banned warfare nerve agents. These compounds are covalent inhibitors of acetylcholinesterase, a key enzyme in central and peripheral nervous systems. Numerous approaches, including chemical, physical, and biological decontamination, have been considered for developing decontamination methods against organophosphates (OPs). This work is an overview of both validated and emerging strategies for the protection against OP pollution with special attention to the use of decontaminating enzymes. Considerable efforts have been dedicated during the past decades to the development of efficient OP degrading biocatalysts. Among these, the promising biocatalyst SsoPox isolated from the archaeon Sulfolobus solfataricus is emphasized in the light of recently published results. This hyperthermostable enzyme appears to be particularly attractive for external decontamination purposes with regard to both its catalytic and stability properties.
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Affiliation(s)
- Pauline Jacquet
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - David Daudé
- Gene&GreenTK, Faculté de Médecine, 27 boulevard Jean Moulin, Cedex 5, Marseille, 13385, France
| | - Janek Bzdrenga
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Patrick Masson
- Neuropharmacology Laboratory, Kazan Federal University, Kazan, 420008, Russia
| | - Mikael Elias
- Department of Biochemistry, Molecular Biology and Biophysics & Biotechnology Institute, University of Minnesota, St. Paul, MN, 55108, USA
| | - Eric Chabrière
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France.
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Iyer R, Iken B, Damania A. A comparison of organophosphate degradation genes and bioremediation applications. ENVIRONMENTAL MICROBIOLOGY REPORTS 2013; 5:787-798. [PMID: 24249287 DOI: 10.1111/1758-2229.12095] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 08/11/2013] [Accepted: 08/13/2013] [Indexed: 06/02/2023]
Abstract
Organophosphates (OPs) form the bulk of pesticides that are currently in use around the world accounting for more than 30% of the world market. They also form the core for many nerve-based warfare agents including sarin and soman. The widespread use and the resultant build-up of OP pesticides and chemical nerve agents has led to the development of major health problems due to their extremely toxic interaction with any biological system that encounters them. Growing concern over the accumulation of OP compounds in our food products, in the soils from which they are harvested and in wastewater run-off has fuelled a growing interest in microbial biotechnology that provides cheap, efficient OP detoxification to supplement expensive chemical methods. In this article, we review the current state of knowledge of OP pesticide and chemical agent degradation and attempt to clarify confusion over identification and nomenclature of two major families of OP-degrading enzymes through a comparison of their structure and function. The isolation, characterization, utilization and manipulation of the major detoxifying enzymes and the molecular basis of degradation of OP pesticides and chemical nerve agents are discussed as well as the achievements and technological advancements made towards the bioremediation of such compounds.
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Affiliation(s)
- Rupa Iyer
- College of Technology, University of Houston, 300 Technology Building Houston, TX 77204-4021, USA
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4
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Daumann LJ, Schenk G, Ollis DL, Gahan LR. Spectroscopic and mechanistic studies of dinuclear metallohydrolases and their biomimetic complexes. Dalton Trans 2013; 43:910-28. [PMID: 24135968 DOI: 10.1039/c3dt52287c] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An enhanced understanding of the metal ion binding and active site structural features of phosphoesterases such as the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ), and the organophosphate degrading agent from Agrobacterium radiobacter (OpdA) have important consequences for potential applications. Coupled with investigations of the metalloenzymes, programs of study to synthesise and characterise model complexes based on these metalloenzymes can add to our understanding of structure and function of the enzymes themselves. This review summarises some of our work and illustrates the significance and contributions of model studies to knowledge in the area.
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Affiliation(s)
- Lena J Daumann
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia.
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5
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Schenk G, Mitić N, Gahan LR, Ollis DL, McGeary RP, Guddat LW. Binuclear metallohydrolases: complex mechanistic strategies for a simple chemical reaction. Acc Chem Res 2012; 45:1593-603. [PMID: 22698580 DOI: 10.1021/ar300067g] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Binuclear metallohydrolases are a large family of enzymes that require two closely spaced transition metal ions to carry out a plethora of hydrolytic reactions. Representatives include purple acid phosphatases (PAPs), enzymes that play a role in bone metabolism and are the only member of this family with a heterovalent binuclear center in the active form (Fe(3+)-M(2+), M = Fe, Zn, Mn). Other members of this family are urease, which contains a di-Ni(2+) center and catalyzes the breakdown of urea, arginase, which contains a di-Mn(2+) center and catalyzes the final step in the urea cycle, and the metallo-β-lactamases, which contain a di-Zn(2+) center and are virulence factors contributing to the spread of antibiotic-resistant pathogens. Binuclear metallohydrolases catalyze numerous vital reactions and are potential targets of drugs against a wide variety of human disorders including osteoporosis, various cancers, antibiotic resistance, and erectile dysfunctions. These enzymes also tend to catalyze more than one reaction. An example is an organophosphate (OP)-degrading enzyme from Enterobacter aerogenes (GpdQ). Although GpdQ is part of a pathway that is used by bacteria to degrade glycerolphosphoesters, it hydrolyzes a variety of other phosphodiesters and displays low levels of activity against phosphomono- and triesters. Such a promiscuous nature may have assisted the apparent recent evolution of some binuclear metallohydrolases to deal with situations created by human intervention such as OP pesticides in the environment. OP pesticides were first used approximately 70 years ago, and therefore the enzymes that bacteria use to degrade them must have evolved very quickly on the evolutionary time scale. The promiscuous nature of enzymes such as GpdQ makes them ideal candidates for the application of directed evolution to produce new enzymes that can be used in bioremediation and against chemical warfare. In this Account, we review the mechanisms employed by binuclear metallohydrolases and use PAP, the OP-degrading enzyme from Agrobacterium radiobacter (OPDA), and GpdQ as representative systems because they illustrate both the diversity and similarity of the reactions catalyzed by this family of enzymes. The majority of binuclear metallohydrolases utilize metal ion-activated water molecules as nucleophiles to initiate hydrolysis, while some, such as alkaline phosphatase, employ an intrinsic polar amino acid. Here we only focus on catalytic strategies applied by the former group.
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Affiliation(s)
- Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Department of Chemistry, National University of Ireland—Maynooth, Maynooth, County Kildare, Ireland
| | - Nataša Mitić
- Department of Chemistry, National University of Ireland—Maynooth, Maynooth, County Kildare, Ireland
| | - Lawrence R. Gahan
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David L. Ollis
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Ross P. McGeary
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Luke W. Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
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Wu N, Courtois F, Surjadi R, Oakeshott J, Peat TS, Easton CJ, Abell C, Zhu Y. Enzyme synthesis and activity assay in microfluidic droplets on a chip. Eng Life Sci 2011. [DOI: 10.1002/elsc.201000043] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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7
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The organophosphate-degrading enzyme from Agrobacterium radiobacter displays mechanistic flexibility for catalysis. Biochem J 2011; 432:565-73. [PMID: 20868365 DOI: 10.1042/bj20101054] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The OP (organophosphate)-degrading enzyme from Agrobacterium radiobacter (OpdA) is a binuclear metallohydrolase able to degrade highly toxic OP pesticides and nerve agents into less or non-toxic compounds. In the present study, the effect of metal ion substitutions and site-directed mutations on the catalytic properties of OpdA are investigated. The study shows the importance of both the metal ion composition and a hydrogen-bond network that connects the metal ion centre with the substrate-binding pocket using residues Arg254 and Tyr257 in the mechanism and substrate specificity of this enzyme. For the Co(II) derivative of OpdA two protonation equilibria (pKa1 ~5; pKa2 ~10) have been identified as relevant for catalysis, and a terminal hydroxide acts as the likely hydrolysis-initiating nucleophile. In contrast, the Zn(II) and Cd(II) derivatives only have one relevant protonation equilibrium (pKa ~4-5), and the μOH is the proposed nucleophile. The observed mechanistic flexibility may reconcile contrasting reaction models that have been published previously and may be beneficial for the rapid adaptation of OP-degrading enzymes to changing environmental pressures.
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Wu N, Courtois F, Zhu Y, Oakeshott J, Easton C, Abell C. Management of the diffusion of 4-methylumbelliferone across phases in microdroplet-based systems for in vitro protein evolution. Electrophoresis 2010; 31:3121-8. [DOI: 10.1002/elps.201000140] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Hawwa R, Larsen SD, Ratia K, Mesecar AD. Structure-Based and Random Mutagenesis Approaches Increase the Organophosphate-Degrading Activity of a Phosphotriesterase Homologue from Deinococcus radiodurans. J Mol Biol 2009; 393:36-57. [DOI: 10.1016/j.jmb.2009.06.083] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2009] [Revised: 06/13/2009] [Accepted: 06/15/2009] [Indexed: 10/20/2022]
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Yang C, Liu N, Guo X, Qiao C. Cloning of mpd gene from a chlorpyrifos-degrading bacterium and use of this strain in bioremediation of contaminated soil. FEMS Microbiol Lett 2006; 265:118-25. [PMID: 17107423 DOI: 10.1111/j.1574-6968.2006.00478.x] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
An effective chlorpyrifos-degrading bacterium (named strain YC-1) was isolated from the sludge of the wastewater treating system of an organophosphorus pesticides manufacturer. Based on the results of phenotypic features, phylogenetic similarity of 16S rRNA gene sequences and BIOLOG test, strain YC-1 was identified as the genus Stenotrophomonas. The isolate utilized chlorpyrifos as the sole source of carbon and phosphorus for its growth and hydrolyzed chlorpyrifos to 3,5,6-trichloro-2-pyridinol. Parathion, methyl parathion, and fenitrothion also could be degraded by strain YC-1 when provided as the sole source of carbon and phosphorus. The gene encoding the organophosphorus hydrolase was cloned using a PCR cloning strategy based on the known methyl parathion degrading (mpd) gene of Plesiomonas sp. M6. Sequence blast result indicated this gene has 99% similar to mpd. The inoculation of strain YC-1 (10(6) cells g(-1)) to soil treated with 100 mg kg(-1) chlorpyrifos resulted in a higher degradation rate than in noninoculated soils. Theses results highlight the potential of this bacterium to be used in the cleanup of contaminated pesticide waste in the environment.
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Affiliation(s)
- Chao Yang
- State Key Laboratory of Integrated Management of Pest Insects & Rodents, Institute of Zoology, Chinese Academy of Sciences, No. 25 Bei Si Huan Xi Lu, Beijing, China
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