1
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Yildiz I, Yildiz BS. Mechanistic study of L-6-hydroxynicotine oxidase by DFT and ONIOM methods. J Mol Model 2021; 27:53. [PMID: 33507404 DOI: 10.1007/s00894-020-04646-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 12/10/2020] [Indexed: 10/22/2022]
Abstract
L-6-Hydroxynicotine oxidase (LHNO) is a member of monoamine oxidase (MAO) family and catalyzes conversion of (S)-6-hydroxynicotine to 6-hydroxypseudooxynicotine during bacterial degradation of nicotine. Recent studies indicated that the enzyme catalyzes oxidation of carbon-nitrogen bond instead of previously proposed carbon-carbon bond. Based on kinetics and mutagenesis studies, Asn166, Tyr311, and Lys287 as well as an active site water molecule have roles in the catalysis of the enzyme. A number of studies including experimental and computational methods support hydride transfer mechanism in MAO family as a common mechanism in which a hydride ion transfer from amine substrate to flavin cofactor is the rate-limiting step. In this study, we formulated computational models to study the hydride transfer mechanism using crystal structure of enzyme-substrate complex. The calculations involved ONIOM and DFT methods, and we evaluated the geometry and energetics of the hydride transfer process while probing the roles of active site residues. Based on the calculations involving hydride, radical, and polar mechanisms, it was concluded that hydride transfer mechanism is the only viable mechanism for LHNO.
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Affiliation(s)
- Ibrahim Yildiz
- Chemistry Department, Khalifa University, PO Box 127788, Abu Dhabi, United Arab Emirates.
| | - Banu Sizirici Yildiz
- CIVE Department, Khalifa University, PO Box 127788, Abu Dhabi, United Arab Emirates
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2
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An active site mutation in 6-hydroxy-l-Nicotine oxidase from Arthrobacter nicotinovorans changes the substrate specificity in favor of (S)-nicotine. Arch Biochem Biophys 2020; 692:108520. [DOI: 10.1016/j.abb.2020.108520] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 07/17/2020] [Accepted: 07/27/2020] [Indexed: 11/20/2022]
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3
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Fitzpatrick PF, Dougherty V, Subedi B, Quilantan J, Hinck CS, Lujan AI, Tormos JR. Mechanism of the Flavoprotein d-6-Hydroxynicotine Oxidase: Substrate Specificity, pH and Solvent Isotope Effects, and Roles of Key Active-Site Residues. Biochemistry 2019; 58:2534-2541. [PMID: 31046245 PMCID: PMC6786761 DOI: 10.1021/acs.biochem.9b00297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The flavoprotein d-6-hydroxynicotine oxidase catalyzes an early step in the oxidation of ( R)-nicotine, the oxidation of a carbon-nitrogen bond in the pyrrolidine ring of ( R)-6-hydroxynicotine. The enzyme is a member of the vanillyl alcohol oxidase/ p-cresol methylhydroxylase family of flavoproteins. The effects of substrate modifications on the steady-state and rapid-reaction kinetic parameters are not consistent with the quinone-methide mechanism of p-cresol methylhydroxylase. There is no solvent isotope effect on the kcat/ Kamine value with either ( R)-6-hydroxynicotine or the slower substrate ( R)-6-hydroxynornicotine. The effect of pH on the rapid-reaction kinetic parameters establishes that only the neutral form of the substrate and the correctly protonated form of the enzyme bind. The active-site residues Lys348, Glu350, and Glu352 are all properly positioned for substrate binding. The K348M substitution has only a small effect on the kinetic parameters; the E350A and E350Q substitutions decrease the kcat/ Kamine value by ∼20- and ∼220-fold, respectively, and the E352Q substitution decreases this parameter ∼3800-fold. The kcat/ Kamine-pH profile is bell-shaped. The p Ka values in that profile are altered by replacement of ( R)-6-hydroxynicotine with ( R)-6-hydroxynornicotine as the substrate and by the substitutions for Glu350 and Glu352, although the profiles remain bell-shaped. The results are consistent with a network of hydrogen-bonded residues in the active site being involved in binding the neutral form of the amine substrate, followed by the transfer of a hydride from the amine to the flavin.
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Affiliation(s)
- Paul F. Fitzpatrick
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, Texas 78229, United States
| | - Vi Dougherty
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, Texas 78229, United States
| | - Bishnu Subedi
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, Texas 78229, United States
| | - Jesus Quilantan
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, Texas 78229, United States
| | - Cynthia S. Hinck
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, Texas 78229, United States
| | - Andreina I. Lujan
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, Texas 78229, United States
| | - Jose R. Tormos
- Department of Chemistry, St. Mary’s University, San Antonio, Texas 78228, United States
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4
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Fitzpatrick PF. The enzymes of microbial nicotine metabolism. Beilstein J Org Chem 2018; 14:2295-2307. [PMID: 30202483 PMCID: PMC6122326 DOI: 10.3762/bjoc.14.204] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 08/20/2018] [Indexed: 12/27/2022] Open
Abstract
Because of nicotine's toxicity and the high levels found in tobacco and in the waste from tobacco processing, there is a great deal of interest in identifying bacteria capable of degrading it. A number of microbial pathways have been identified for nicotine degradation. The first and best-understood is the pyridine pathway, best characterized for Arthrobacter nicotinovorans, in which the first reaction is hydroxylation of the pyridine ring. The pyrrolidine pathway, which begins with oxidation of a carbon-nitrogen bond in the pyrrolidine ring, was subsequently characterized in a number of pseudomonads. Most recently, a hybrid pathway has been described, which incorporates the early steps in the pyridine pathway and ends with steps in the pyrrolidine pathway. This review summarizes the present status of our understanding of these pathways, focusing on what is known about the individual enzymes involved.
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Affiliation(s)
- Paul F Fitzpatrick
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX, 78229, USA
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5
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Cosgrove SC, Hussain S, Turner NJ, Marsden SP. Synergistic Chemo/Biocatalytic Synthesis of Alkaloidal Tetrahydroquinolines. ACS Catal 2018. [DOI: 10.1021/acscatal.8b01220] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sebastian C. Cosgrove
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Institute of Process Research and Development and School of Chemistry, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Shahed Hussain
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Nicholas J. Turner
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Stephen P. Marsden
- Institute of Process Research and Development and School of Chemistry, University of Leeds, Leeds, LS2 9JT, United Kingdom
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6
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Deng G, Wan N, Qin L, Cui B, An M, Han W, Chen Y. Deracemization of Phenyl-Substituted 2-Methyl-1,2,3,4-Tetrahydroquinolines by a Recombinant Monoamine Oxidase from Pseudomonas monteilii
ZMU-T01. ChemCatChem 2018. [DOI: 10.1002/cctc.201701995] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Guozhong Deng
- Generic Drug Research Center of Guizhou Province; School of Pharmacy; Zunyi Medical University; Zunyi 563000 P.R. China
- Green Pharmaceuticals Engineering Research Center of Guizhou Province; School of Pharmacy; Zunyi Medical University; Zunyi 563000 P.R. China
| | - Nanwei Wan
- Generic Drug Research Center of Guizhou Province; School of Pharmacy; Zunyi Medical University; Zunyi 563000 P.R. China
- Green Pharmaceuticals Engineering Research Center of Guizhou Province; School of Pharmacy; Zunyi Medical University; Zunyi 563000 P.R. China
| | - Lei Qin
- Generic Drug Research Center of Guizhou Province; School of Pharmacy; Zunyi Medical University; Zunyi 563000 P.R. China
- Green Pharmaceuticals Engineering Research Center of Guizhou Province; School of Pharmacy; Zunyi Medical University; Zunyi 563000 P.R. China
| | - Baodong Cui
- Generic Drug Research Center of Guizhou Province; School of Pharmacy; Zunyi Medical University; Zunyi 563000 P.R. China
- Green Pharmaceuticals Engineering Research Center of Guizhou Province; School of Pharmacy; Zunyi Medical University; Zunyi 563000 P.R. China
| | - Miao An
- Generic Drug Research Center of Guizhou Province; School of Pharmacy; Zunyi Medical University; Zunyi 563000 P.R. China
- Green Pharmaceuticals Engineering Research Center of Guizhou Province; School of Pharmacy; Zunyi Medical University; Zunyi 563000 P.R. China
| | - Wenyong Han
- Generic Drug Research Center of Guizhou Province; School of Pharmacy; Zunyi Medical University; Zunyi 563000 P.R. China
- Green Pharmaceuticals Engineering Research Center of Guizhou Province; School of Pharmacy; Zunyi Medical University; Zunyi 563000 P.R. China
| | - Yongzheng Chen
- Generic Drug Research Center of Guizhou Province; School of Pharmacy; Zunyi Medical University; Zunyi 563000 P.R. China
- Green Pharmaceuticals Engineering Research Center of Guizhou Province; School of Pharmacy; Zunyi Medical University; Zunyi 563000 P.R. China
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Yu W, Wang R, Li H, Liang J, Wang Y, Huang H, Xie H, Wang S. Green route to synthesis of valuable chemical 6-hydroxynicotine from nicotine in tobacco wastes using genetically engineered Agrobacterium tumefaciens S33. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:288. [PMID: 29213327 PMCID: PMC5713474 DOI: 10.1186/s13068-017-0976-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 11/26/2017] [Indexed: 05/17/2023]
Abstract
BACKGROUND Tobacco is widely planted as an important nonfood economic crop throughout the world, and large amounts of tobacco wastes are generated during the tobacco manufacturing process. Tobacco and its wastes contain high nicotine content. This issue has become a major concern for health and environments due to its toxicity and complex physiological effects. The microbial transformation of nicotine into valuable functionalized pyridine compounds is a promising way to utilize tobacco and its wastes as a potential biomass resource. Agrobacterium tumefaciens S33 is able to degrade nicotine via a novel hybrid of the pyridine and pyrrolidine pathways, in which several intermediates, such as 6-hydroxynicotine, can be used as renewable precursors to synthesize drugs and insecticides. This provides an opportunity to produce valuable chemical 6-hydroxynicotine from nicotine via biocatalysis using strain S33. RESULTS To accumulate the intermediate 6-hydroxynicotine, we firstly identified the key enzyme decomposing 6-hydroxynicotine, named 6-hydroxynicotine oxidase, and then disrupted its encoding gene in A. tumefaciens S33. With the whole cells of the mutant as a biocatalyst, we tested the possibility to produce 6-hydroxynicotine from the nicotine of tobacco and its wastes and optimized the reaction conditions. At 30 °C and pH 7.0, nicotine could be efficiently transformed into 6-hydroxynicotine by the whole cells cultivated with glucose/ammonium/6-hydroxy-3-succinoylpyridine medium. The molar conversion and the specific catalytic rate reached approximately 98% and 1.01 g 6-hydroxynicotine h-1 g-1 dry cells, respectively. The product could be purified easily by dichloromethane extraction with a recovery of 76.8%, and was further confirmed by UV spectroscopy, mass spectroscopy, and NMR analysis. CONCLUSIONS We successfully developed a novel biocatalytic route to 6-hydroxynicotine from nicotine by blocking the nicotine catabolic pathway via gene disruption, which provides an alternative green strategy to utilize tobacco and its wastes as a biomass resource by converting nicotine into valuable hydroxylated-pyridine compounds.
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Affiliation(s)
- Wenjun Yu
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100 People’s Republic of China
| | - Rongshui Wang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100 People’s Republic of China
| | - Huili Li
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100 People’s Republic of China
| | - Jiyu Liang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100 People’s Republic of China
| | - Yuanyuan Wang
- Institute of Basic Medicine, Shandong Academy of Medical Science, Jinan, 250062 People’s Republic of China
| | - Haiyan Huang
- Institute of Basic Medicine, Shandong Academy of Medical Science, Jinan, 250062 People’s Republic of China
| | - Huijun Xie
- Environment Research Institute, Shandong University, Jinan, 250100 People’s Republic of China
| | - Shuning Wang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100 People’s Republic of China
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8
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Tararina MA, Janda KD, Allen KN. Structural Analysis Provides Mechanistic Insight into Nicotine Oxidoreductase from Pseudomonas putida. Biochemistry 2016; 55:6595-6598. [PMID: 27933790 PMCID: PMC6250430 DOI: 10.1021/acs.biochem.6b00963] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The first structure of nicotine oxidoreductase (NicA2) was determined by X-ray crystallography. Pseudomonas putida has evolved nicotine-degrading activity to provide a source of carbon and nitrogen. The structure establishes NicA2 as a member of the monoamine oxidase family. Residues 1-50 are disordered and may play a role in localization. The nicotine-binding site proximal to the isoalloxazine ring of flavin shows an unusual composition of the classical aromatic cage (W427 and N462). The active site architecture is consistent with the proposed binding of the deprotonated form of the substrate and the flavin-dependent oxidation of the pyrrolidone C-N bond followed by nonenzymatic hydrolysis.
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Affiliation(s)
- Margarita A. Tararina
- Program in Biomolecular Pharmacology, Boston University School of Medicine, 72 East Concord St, Boston, MA, 02118, United States
| | - Kim D. Janda
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute of Medical Research (WIRM), The Scripps Research Institute, 10550 North Torrey Pines Road BCC-582, La Jolla, CA 92037, United States
| | - Karen N. Allen
- Program in Biomolecular Pharmacology, Boston University School of Medicine, 72 East Concord St, Boston, MA, 02118, United States
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA 02215, United States
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9
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Fitzpatrick PF, Chadegani F, Zhang S, Roberts KM, Hinck CS. Mechanism of the Flavoprotein L-Hydroxynicotine Oxidase: Kinetic Mechanism, Substrate Specificity, Reaction Product, and Roles of Active-Site Residues. Biochemistry 2016; 55:697-703. [PMID: 26744768 PMCID: PMC4738163 DOI: 10.1021/acs.biochem.5b01325] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The flavoprotein L-hydroxynicotine oxidase (LHNO) catalyzes an early step in the bacterial catabolism of nicotine. Although the structure of the enzyme establishes that it is a member of the monoamine oxidase family, LHNO is generally accepted to oxidize a carbon-carbon bond in the pyrrolidine ring of the substrate and has been proposed to catalyze the subsequent tautomerization and hydrolysis of the initial oxidation product to yield 6-hydroxypseudooxynicotine [Kachalova, G., et al. (2011) Proc. Natl. Acad. Sci. U.S.A. 108, 4800-4805]. Analysis of the product of the enzyme from Arthrobacter nicotinovorans by nuclear magnetic resonance and continuous-flow mass spectrometry establishes that the enzyme catalyzes the oxidation of the pyrrolidine carbon-nitrogen bond, the expected reaction for a monoamine oxidase, and that hydrolysis of the amine to form 6-hydroxypseudooxynicotine is nonenzymatic. On the basis of the kcat/Km and kred values for (S)-hydroxynicotine and several analogues, the methyl group contributes only marginally (∼ 0.5 kcal/mol) to transition-state stabilization, while the hydroxyl oxygen and pyridyl nitrogen each contribute ∼ 4 kcal/mol. The small effects on activity of mutagenesis of His187, Glu300, or Tyr407 rule out catalytic roles for all three of these active-site residues.
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Affiliation(s)
- Paul F. Fitzpatrick
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229
| | - Fatemeh Chadegani
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229
| | - Shengnan Zhang
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229
| | - Kenneth M. Roberts
- Department of Chemistry & Physics, University of South Carolina Aiken, Aiken, SC 29801
| | - Cynthia S. Hinck
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229
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10
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Nicotine Dehydrogenase Complexed with 6-Hydroxypseudooxynicotine Oxidase Involved in the Hybrid Nicotine-Degrading Pathway in Agrobacterium tumefaciens S33. Appl Environ Microbiol 2016; 82:1745-1755. [PMID: 26729714 DOI: 10.1128/aem.03909-15] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Accepted: 12/29/2015] [Indexed: 01/04/2023] Open
Abstract
Nicotine, a major toxic alkaloid in tobacco wastes, is degraded by bacteria, mainly via pyridine and pyrrolidine pathways. Previously, we discovered a new hybrid of the pyridine and pyrrolidine pathways in Agrobacterium tumefaciens S33 and characterized its key enzyme 6-hydroxy-3-succinoylpyridine (HSP) hydroxylase. Here, we purified the nicotine dehydrogenase initializing the nicotine degradation from the strain and found that it forms a complex with a novel 6-hydroxypseudooxynicotine oxidase. The purified complex is composed of three different subunits encoded by ndhAB and pno, where ndhA and ndhB overlap by 4 bp and are ∼26 kb away from pno. As predicted from the gene sequences and from chemical analyses, NdhA (82.4 kDa) and NdhB (17.1 kDa) harbor a molybdopterin cofactor and two [2Fe-2S] clusters, respectively, whereas Pno (73.3 kDa) harbors an flavin mononucleotide and a [4Fe-4S] cluster. Mutants with disrupted ndhA or ndhB genes did not grow on nicotine but grew well on 6-hydroxynicotine and HSP, whereas the pno mutant did not grow on nicotine or 6-hydroxynicotine but grew well on HSP, indicating that NdhA and NdhB are responsible for initialization of nicotine oxidation. We successfully expressed pno in Escherichia coli and found that the recombinant Pno presented 2,6-dichlorophenolindophenol reduction activity when it was coupled with 6-hydroxynicotine oxidation. The determination of reaction products catalyzed by the purified enzymes or mutants indicated that NdhAB catalyzed nicotine oxidation to 6-hydroxynicotine, whereas Pno oxidized 6-hydroxypseudooxynicotine to 6-hydroxy-3-succinoylsemialdehyde pyridine. These results provide new insights into this novel hybrid pathway of nicotine degradation in A. tumefaciens S33.
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11
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Heath RS, Pontini M, Bechi B, Turner NJ. Development of anR-Selective Amine Oxidase with Broad Substrate Specificity and High Enantioselectivity. ChemCatChem 2014. [DOI: 10.1002/cctc.201301008] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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12
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Flavoprotein oxidases: classification and applications. Appl Microbiol Biotechnol 2013; 97:5177-88. [PMID: 23640366 DOI: 10.1007/s00253-013-4925-7] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 04/10/2013] [Accepted: 04/11/2013] [Indexed: 10/26/2022]
Abstract
This review provides an overview of oxidases that utilise a flavin cofactor for catalysis. This class of oxidative flavoenzymes has shown to harbour a large number of biotechnologically interesting enzymes. Applications range from their use as biocatalysts for the synthesis of pharmaceutical compounds to the integration in biosensors. Through the recent developments in genome sequencing, the number of newly discovered oxidases is steadily growing. Recent progress in the field of flavoprotein oxidase discovery and the obtained biochemical knowledge on these enzymes are reviewed. Except for a structure-based classification of known flavoprotein oxidases, also their potential in recent biotechnological applications is discussed.
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13
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Crystallographic snapshots of the complete reaction cycle of nicotine degradation by an amine oxidase of the monoamine oxidase (MAO) family. Proc Natl Acad Sci U S A 2011; 108:4800-5. [PMID: 21383134 DOI: 10.1073/pnas.1016684108] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
FAD-linked oxidases constitute a class of enzymes which catalyze dehydrogenation as a fundamental biochemical reaction, followed by reoxidation of reduced flavin. Here, we present high-resolution crystal structures showing the flavoenzyme 6-hydroxy-l-nicotine oxidase in action. This enzyme was trapped during catalytic degradation of the native substrate in a sequence of discrete reaction states corresponding to the substrate-reduced enzyme, a complex of the enzyme with the intermediate enamine product and formation of the final aminoketone product. The inactive d-stereoisomer binds in mirror symmetry with respect to the catalytic axis, revealing absolute stereospecificity of hydrogen transfer to the flavin. The structural data suggest deprotonation of the substrate when bound at the active site, an overall binary complex mechanism and oxidation by direct hydride transfer. The amine nitrogen has a critical role in the dehydrogenation step and may activate carbocation formation at the α-carbon via delocalization from the lone pair to σ* C(α)-H. Enzymatically assisted hydrolysis of the intermediate product occurs at a remote (P site) cavity. Substrate entry and product exit follow different paths. Structural and kinetic data suggest that substrate can also bind to the reduced enzyme, associated with slower reoxidation as compared to the rate of reoxidation of free enzyme. The results are of general relevance for the mechanisms of flavin amine oxidases.
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14
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Kachalova GS, Bourenkov GP, Mengesdorf T, Schenk S, Maun HR, Burghammer M, Riekel C, Decker K, Bartunik HD. Crystal Structure Analysis of Free and Substrate-Bound 6-Hydroxy-l-Nicotine Oxidase from Arthrobacter nicotinovorans. J Mol Biol 2010; 396:785-99. [DOI: 10.1016/j.jmb.2009.12.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2009] [Revised: 12/04/2009] [Accepted: 12/07/2009] [Indexed: 10/20/2022]
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15
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Novel nicotine oxidoreductase-encoding gene involved in nicotine degradation by Pseudomonas putida strain S16. Appl Environ Microbiol 2008; 75:772-8. [PMID: 19060159 DOI: 10.1128/aem.02300-08] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
There are quite a few ongoing biochemical investigations of nicotine degradation in different organisms. In this work, we identified and sequenced a gene (designated nicA) involved in nicotine degradation by Pseudomonas putida strain S16. The gene product, NicA, was heterologously expressed and characterized as a nicotine oxidoreductase catalyzing the initial steps of nicotine metabolism. Biochemical analyses using resting cells and the purified enzyme suggested that nicA encodes an oxidoreductase, which converts nicotine to 3-succinoylpyridine through pseudooxynicotine. Based on enzymatic reactions and direct evidence obtained using H(2)(18)O labeling, the process may consist of enzyme-catalyzed dehydrogenation, followed by spontaneous hydrolysis and then repetition of the dehydrogenation and hydrolysis steps. Sequence comparisons revealed that the gene showed 40% similarity to genes encoding NADH dehydrogenase subunit I and cytochrome c oxidase subunit I in eukaryotes. Our findings demonstrate that the molecular mechanism for nicotine degradation in strain S16 involves the pyrrolidine pathway and is similar to the mechanism in mammals, in which pseudooxynicotine, the direct precursor of a potent tobacco-specific lung carcinogen, is produced.
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16
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17
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Two closely related pathways of nicotine catabolism in Arthrobacter nicotinovorans and Nocardioides sp. strain JS614. Arch Microbiol 2007; 189:511-7. [PMID: 18071673 DOI: 10.1007/s00203-007-0340-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2007] [Revised: 11/16/2007] [Accepted: 11/26/2007] [Indexed: 10/22/2022]
Abstract
A virtually identical nicotine catabolic pathway including the heterotrimeric molybdenum enzyme nicotine and 6-hydroxy-pseudo-oxynicotine dehydrogenase, 6-hydroxy-L: -nicotine oxidase, 2,6-dihydroxy-pseudo-oxynicotine hydrolase, and 2,6-dihydroxypyridine hydroxylase have been identified in A. nicotinovorans and Nocardioides sp. JS614. Enzymes catalyzing the same reactions and similar protein antigens were detected in the extracts of the two microorganisms. Nicotine blue and methylamine, two end products of nicotine catabolism were detected in the growth medium of both bacterial species. Nicotine catabolic genes are clustered on pAO1 in A. nicotinovorans, but located chromosomally in Nocardioides sp. JS614.
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18
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Wang SN, Liu Z, Tang HZ, Meng J, Xu P. Characterization of environmentally friendly nicotine degradation by Pseudomonas putida biotype A strain S16. Microbiology (Reading) 2007; 153:1556-1565. [PMID: 17464070 DOI: 10.1099/mic.0.2006/005223-0] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nicotine and some related alkaloids in tobacco and tobacco wastes are harmful to health and the environment, and a major environmental requirement is to remove them from tobacco and tobacco wastes. In this study, an isolated strain, S16, identified as Pseudomonas putida biotype A, was used to investigate nicotine degradation. Possible intermediates were identified based on the results of NMR, Fourier-transform (FT)-IR and UV spectroscopy, GC-MS and high-resolution MS (HR-MS) analysis. The pathway of nicotine degradation in P. putida was proposed to be from nicotine to 2,5-dihydroxypyridine through the intermediates N-methylmyosmine, 2'-hydroxynicotine, pseudooxynicotine, 3-pyridinebutanal,C-oxo, 3-succinoylpyridine and 6-hydroxy-3-succinoylpyridine. N-Methylmyosmine, 2,5-dihydroxypyridine and succinic acid were detected and satisfactorily verified for the first time as intermediates of nicotine degradation. In addition, an alcohol compound, 1-butanone,4-hydroxy-1-(3-pyridinyl), was found to be a novel product of nicotine degradation. These findings provide new insights into the microbial metabolism of nicotine and the environmentally friendly route of nicotine degradation.
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MESH Headings
- Biodegradation, Environmental
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Industrial Waste
- Magnetic Resonance Spectroscopy
- Metabolic Networks and Pathways
- Models, Biological
- Molecular Sequence Data
- Molecular Structure
- Nicotine/chemistry
- Nicotine/metabolism
- Pseudomonas putida/chemistry
- Pseudomonas putida/genetics
- Pseudomonas putida/isolation & purification
- Pseudomonas putida/metabolism
- Pyridines/chemistry
- Pyridines/metabolism
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Soil Microbiology
- Spectrophotometry, Ultraviolet
- Spectroscopy, Fourier Transform Infrared
- Succinic Acid/analysis
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Affiliation(s)
- Shu Ning Wang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, People's Republic of China 250100
| | - Zhen Liu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, People's Republic of China 250100
| | - Hong Zhi Tang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, People's Republic of China 250100
| | - Jing Meng
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, People's Republic of China 250100
| | - Ping Xu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, People's Republic of China 250100
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Koetter JWA, Schulz GE. Crystal Structure of 6-Hydroxy-d-nicotine Oxidase from Arthrobacter nicotinovorans. J Mol Biol 2005; 352:418-28. [PMID: 16095622 DOI: 10.1016/j.jmb.2005.07.041] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2005] [Revised: 07/12/2005] [Accepted: 07/13/2005] [Indexed: 11/21/2022]
Abstract
The crystal structure of 6-hydroxy-d-nicotine oxidase (EC 1.5.3.6) was solved by X-ray diffraction analysis in three crystal forms at resolutions up to 1.9 A. The enzyme is monomeric in solution and also in the mother liquor but formed disulfide-dimers in all crystals. It belongs to the p-cresol methylhydroxylase-vanillyl-alcohol oxidase family and contains an FAD covalently bound to the polypeptide. The covalent bond of this enzyme was the first for which a purely autocatalytic formation had been shown. In contrast to previous reports, the bond does not involve N(epsilon2) (N3) of His72 but the N(delta1) (N1) atom. The geometry of this reaction is proposed and the autoflavinylation is discussed in the light of homologous structures. The enzyme is specific for 6-hydroxy-D-nicotine and is inhibited by the L-enantiomer. This observation was verified by modeling enzyme-substrate and enzyme-inhibitor complexes, which also showed the geometry of the catalyzed reaction. The binding models indicated that the deprotonation of the substrate rather than the hydride transfer is the specificity-determining step. The functionally closely related 6-hydroxy-L-nicotine oxidase processing the L-enantiomer is sequence-related to the greater glutathione reductase family with quite a different chainfold. A model of this "sister enzyme" derived from known homologous structures suggests that the reported L-substrate specificity and D-enantiomer inhibition are also determined by the location of the deprotonating base.
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Affiliation(s)
- Jochen W A Koetter
- Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität, Albertstr. 21, 79104 Freiburg im Breisgau, Germany
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20
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Sandu C, Chiribau CB, Brandsch R. Characterization of HdnoR, the transcriptional repressor of the 6-hydroxy-D-nicotine oxidase gene of Arthrobacter nicotinovorans pAO1, and its DNA-binding activity in response to L- and D-nicotine Derivatives. J Biol Chem 2003; 278:51307-15. [PMID: 14534317 DOI: 10.1074/jbc.m307797200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Utilization of L-nicotine as growth substrate by Arthrobacter nicotinovorans pAO1 starts with hydroxylation of the pyridine ring at C6. Next, the pyrrolidine ring is oxidized by 6-hydroxy-L-nicotine oxidase, which acts strictly stereo-specific on the L-enantiomer. Surprisingly, L-nicotine also induces the synthesis of a 6-hydroxy-d-nicotine-specific oxidase in the bacteria. Genes of nicotine-degrading enzymes are located on the catabolic plasmid pAO1. The pAO1 sequence revealed that the 6-hydroxy-D-nicotine oxidase gene is flanked by two open reading frames with a similarity to amino acid permeases and a divergently transcribed open reading frame with a similarity to proteins of the tetracycline repressor TetR family. Reverse transcription PCR and primer extension analysis of RNA transcripts isolated from A. nicotinovorans pAO1 indicated that the 6-hydroxy-D-nicotine oxidase gene represents a transcriptional unit. DNA electromobility shift assays established that the purified TetR-similar protein represents the 6-hydroxy-D-nicotine oxidase gene repressor HdnoR and binds to the 6-hydroxy-D-nicotine oxidase gene operator with a Kd of 21 nM. The enantiomers 6-hydroxy-D- and 6-hydroxy-L-nicotine acted in vitro as inducers. In vivo analysis of 6-hydroxy-D-nicotine oxidase gene transcripts from bacteria grown with L- and D-nicotine confirmed this conclusion. The poor discrimination by HdnoR between the 6-hydroxy-L- and 6-hydroxy-D-nicotine enantiomers explains the presence of the 6-hydroxy-D-nicotine-specific enzyme in bacteria grown on L-nicotine.
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Affiliation(s)
- Cristinel Sandu
- Institute of Biochemistry and Molecular Biology, University of Freiburg, 79104 Freiburg, Germany
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22
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Brandsch R, Bichler V. In vivo and in vitro expression of the 6-hydroxy-D-nicotine oxidase gene of Arthrobacter oxidans, cloned into Escherichia coli, as an enzymatically active, covalently flavinylated polypeptide. FEBS Lett 1985; 192:204-8. [PMID: 3905431 DOI: 10.1016/0014-5793(85)80108-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The 6-hydroxy-D-nicotine oxidase gene of Arthrobacter oxidans was cloned into E.coli with the aid of the expression vector pKK223-3. This enzyme, as well as the E.coli enzymes succinate dehydrogenase and fumarate reductase, bears the cofactor FAD covalently attached to the polypeptide through a His-N3-8 alpha-linkage. The amino acid sequence surrounding the histidine residue involved in FAD binding in 6-hydroxy-D-nicotine oxidase and the two E.coli enzymes, however, show no homology. Nevertheless, 6-hydroxy-D-nicotine oxidase is expressed in E.coli in vivo and in an E.coli-derived coupled transcription-translation system as a covalently flavinylated, enzymatically active polypeptide.
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Swafford JR, Reeves HC, Brandsch R. Localization of the enantiozymes of 6-hydroxy-nicotine oxidase in Arthrobacter oxidans by electron immunochemistry. J Bacteriol 1985; 163:792-5. [PMID: 4019415 PMCID: PMC219194 DOI: 10.1128/jb.163.2.792-795.1985] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
During the course of growth of Arthrobacter oxidans, induction of the enantiozymes 6-hydroxy-D-nicotine oxidase and 6-hydroxy-L-nicotine oxidase occurred in the presence of DL-nicotine. Cryoultramicrotomed sections obtained from cells grown to stationary phase were gold immunolabeled. The results obtained demonstrate that both enzymes are localized in the cytoplasm.
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Hamm HH, Decker K. Regulation of flavoprotein synthesis studied in vivo in a riboflavin-requiring mutant of Arthrobacter oxidans. Arch Microbiol 1978; 119:65-70. [PMID: 718370 DOI: 10.1007/bf00407929] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The biosynthesis of two flavoproteins, 6-hydroxy-D-nicotine oxidase with covalently bound FAD and 6-hydroxy-L-nicotine oxidase containing non-covalently bound FAD, was studied in wild-type cells and in a riboflavin-requiring mutant of Arthrobacter oxidans. In the mutant cells, the rate of synthesis and the maximal activity level of both enzymes after induction by nicotine depended on the amount of added riboflavin. The low rate of synthesis in the presence of 2 micron riboflavin could be enhanced during the induction phase by further addition of riboflavin (33 micron). Inhibitors of translation (chloramphenicol or streptomycin) completely blocked the synthesis of both flavoproteins. Inhibitors of transcription (rifamycin S or actinomycin D) stopped the synthesis of both enantiozymes in wild-type cells and in the mutant grown in the presence of a saturating supply of riboflavin (15 micron). Under conditions of restricted flavoprotein synthesis (2 micron riboflavin in the medium), however, the mutant cells continued to synthesize the enzyme for 2--3 h after the addition of the transcription inhibitors. It appears, that in these cells a rather stable m-RNA accumulated during riboflavin-limited flavoprotein synthesis. The dependence of the effect of transcription inhibitors on the extracellular supply of riboflavin suggests that the regulation of the synthesis of both flavoproteins occurs not only by control of gene expression (induction by nicotine), but also at the level of translation through the availability of FAD.
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Schimz A, Decker K. Covalently bound FAD in D-6-hydroxynicotine oxidase from Arthrobacter oxidans. Arch Microbiol 1978. [DOI: 10.1007/bf00406033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Brühmüller M, Schimz A, Messmer L, Decker K. Covalently bound FAD in d-6-hydroxynicotine oxidase. Immunological studies of D- and L-6-hydroxynicotine oxidase: evidence for a D-enzyme precursor. J Biol Chem 1975. [DOI: 10.1016/s0021-9258(19)40878-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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29
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Brühmüller M, Decker K. Covalently bound flavin in D-6-hydroxynicotine oxidase from Arthrobacter oxidans. Amino-acid sequence of the FAD-peptide. EUROPEAN JOURNAL OF BIOCHEMISTRY 1973; 37:256-8. [PMID: 4745730 DOI: 10.1111/j.1432-1033.1973.tb02983.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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30
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Brühmüller M, Möhler H, Decker K. Covalently bound flavin in D-6-hydroxynicotine oxidase from Arthrobacter oxidans. Purification and properties of D-6-hydroxynicotine oxidase. EUROPEAN JOURNAL OF BIOCHEMISTRY 1972; 29:143-51. [PMID: 4628374 DOI: 10.1111/j.1432-1033.1972.tb01968.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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31
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32
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Dai VD, Decker K, Sund H. Purification and properties of L-6-hydroxynicotine oxidase. EUROPEAN JOURNAL OF BIOCHEMISTRY 1968; 4:95-102. [PMID: 5646150 DOI: 10.1111/j.1432-1033.1968.tb00177.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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