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Trisrivirat D, Sutthaphirom C, Pimviriyakul P, Chaiyen P. Dual activities of oxidation and oxidative decarboxylation by flavoenzymes. Chembiochem 2022; 23:e202100666. [PMID: 35040514 DOI: 10.1002/cbic.202100666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/17/2022] [Indexed: 11/07/2022]
Abstract
Specific flavoenzyme oxidases catalyze oxidative decarboxylation in addition to their classical oxidation reactions in the same active sites. The mechanisms underlying oxidative decarboxylation by these enzymes and how they control their two activities are not clearly known. This article reviews the current state of knowledge of four enzymes from the l-amino acid oxidase and l-hydroxy acid oxidase families, including l-tryptophan 2-monooxygenase, l-phenylalanine 2-oxidase and l-lysine oxidase/monooxygenase and lactate monooxygenase which catalyze substrate oxidation and oxidative decarboxylation. Apart from specific interactions to allow substrate oxidation by the flavin cofactor, specific binding of oxidized product in the active sites appears to be important for enabling subsequent decarboxylation by these enzymes. Based on recent findings of l-lysine oxidase/monooxygenase, we propose that nucleophilic attack of H2O2 on the imino acid product is the mechanism enabling oxidative decarboxylation.
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Affiliation(s)
- Duangthip Trisrivirat
- VISTEC: Vidyasirimedhi Institute of Science and Technology, Biomolecular Science and Engineering, THAILAND
| | - Chalermroj Sutthaphirom
- VISTEC: Vidyasirimedhi Institute of Science and Technology, Biomolecular Science and Engineering, THAILAND
| | | | - Pimchai Chaiyen
- Vidyasirimedhi Institute of Science and Technology (VISTEC), School of Biomolecular Science and Engineering, 555 Moo 1 Payupnai, 21210, Wangchan District, THAILAND
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2
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Abstract
We have structure, a wealth of kinetic data, thousands of chemical ligands and clinical information for the effects of a range of drugs on monoamine oxidase activity in vivo. We have comparative information from various species and mutations on kinetics and effects of inhibition. Nevertheless, there are what seem like simple questions still to be answered. This article presents a brief summary of existing experimental evidence the background and poses questions that remain intriguing for chemists and biochemists researching the chemical enzymology of and drug design for monoamine oxidases (FAD-containing EC 4.1.3.4).
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3
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Reis RAG, Li H, Johnson M, Sobrado P. New frontiers in flavin-dependent monooxygenases. Arch Biochem Biophys 2021; 699:108765. [PMID: 33460580 DOI: 10.1016/j.abb.2021.108765] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 01/08/2021] [Accepted: 01/11/2021] [Indexed: 12/15/2022]
Abstract
Flavin-dependent monooxygenases catalyze a wide variety of redox reactions in important biological processes and are responsible for the synthesis of highly complex natural products. Although much has been learned about FMO chemistry in the last ~80 years of research, several aspects of the reactions catalyzed by these enzymes remain unknown. In this review, we summarize recent advancements in the flavin-dependent monooxygenase field including aspects of flavin dynamics, formation and stabilization of reactive species, and the hydroxylation mechanism. Novel catalysis of flavin-dependent N-oxidases involving consecutive oxidations of amines to generate oximes or nitrones is presented and the biological relevance of the products is discussed. In addition, the activity of some FMOs have been shown to be essential for the virulence of several human pathogens. We also discuss the biomedical relevance of FMOs in antibiotic resistance and the efforts to identify inhibitors against some members of this important and growing family enzymes.
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Affiliation(s)
| | - Hao Li
- Department of Biochemistry, Blacksburg, VA, 24061, USA
| | - Maxim Johnson
- Department of Biochemistry, Blacksburg, VA, 24061, USA
| | - Pablo Sobrado
- Department of Biochemistry, Blacksburg, VA, 24061, USA; Center for Drug Discovery, Virginia Tech, Blacksburg, VA, 24061, USA.
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4
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On the use of noncompetitive kinetic isotope effects to investigate flavoenzyme mechanism. Methods Enzymol 2019; 620:115-143. [PMID: 31072484 DOI: 10.1016/bs.mie.2019.03.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
This account describes the application of kinetic isotope effects (KIEs) to investigate the mechanistic properties of flavin dependent enzymes. Assays can be conducted during steady-state catalytic turnover of the flavoenzyme with its substrate or by using rapid-kinetic techniques to measure either the reductive or oxidative half-reactions of the enzyme. Great care should be taken to ensure that the observed effects are due to isotopic substitution and not other factors such as pH effects or changes in the solvent viscosity of the reaction mixture. Different types of KIEs are described along with a physical description of their origins and the unique information each can provide about the mechanism of an enzyme. Detailed experimental techniques are outlined with special emphasis on the proper controls and data analysis that must be carried out to avoid erroneous conclusions. Examples are provided for each type of KIE measurement from references in the literature. It is our hope that this article will clarify any confusion concerning the utility of KIEs in the study of flavoprotein mechanism and encourage their use by the community.
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Deng L, Hu C, Qin X, Li L, Zhang Y, Li P, Chen X. The remote arginine promoting the dehydrogenation of glucose in glucose oxidase via a proton-coupled double-electron transfer mechanism. J Catal 2018. [DOI: 10.1016/j.jcat.2018.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Tararina MA, Xue S, Smith LC, Muellers SN, Miranda PO, Janda KD, Allen KN. Crystallography Coupled with Kinetic Analysis Provides Mechanistic Underpinnings of a Nicotine-Degrading Enzyme. Biochemistry 2018; 57:3741-3751. [PMID: 29812904 PMCID: PMC6295333 DOI: 10.1021/acs.biochem.8b00384] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Nicotine oxidoreductase (NicA2) is a bacterial flavoenzyme, which catalyzes the first step of nicotine catabolism by oxidizing S-nicotine into N-methyl-myosmine. It has been proposed as a biotherapeutic for nicotine addiction because of its nanomolar substrate binding affinity. The first crystal structure of NicA2 has been reported, establishing NicA2 as a member of the monoamine oxidase (MAO) family. However, substrate specificity and structural determinants of substrate binding and/or catalysis have not been explored. Herein, analysis of the pH-rate profile, single-turnover kinetics, and binding data establish that pH does not significantly affect the catalytic rate and product release is not rate-limiting. The X-ray crystal structure of NicA2 with S-nicotine refined to 2.65 Å resolution reveals a hydrophobic binding site with a solvent exclusive cavity. Hydrophobic interactions predominantly orient the substrate, promoting the binding of a deprotonated species and supporting a hydride-transfer mechanism. Notably, NicA2 showed no activity against neurotransmitters oxidized by the two isoforms of human MAO. To further probe the substrate range of NicA2, enzyme activity was evaluated using a series of substrate analogues, indicating that S-nicotine is the optimal substrate and substitutions within the pyridyl ring abolish NicA2 activity. Moreover, mutagenesis and kinetic analysis of active-site residues reveal that removal of a hydrogen bond between the pyridyl ring of S-nicotine and the hydroxyl group of T381 has a 10-fold effect on KM, supporting the role of this bond in positioning the catalytically competent form of the substrate. Together, crystallography combined with kinetic analysis provides a deeper understanding of this enzyme's remarkable specificity.
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Affiliation(s)
- Margarita A. Tararina
- Program in Biomolecular Pharmacology, Boston University School of Medicine, 72 East Concord Street, Boston, Massachusetts 02118, United States
| | - Song Xue
- Departments of Chemistry and Immunology and The Skaggs Institute for Chemical Biology
| | - Lauren C. Smith
- Departments of Chemistry and Immunology and The Skaggs Institute for Chemical Biology
| | - Samantha N. Muellers
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Pedro O. Miranda
- Departments of Chemistry and Immunology and The Skaggs Institute for Chemical Biology
| | - Kim D. Janda
- Departments of Chemistry and Immunology and The Skaggs Institute for Chemical Biology
- Worm Institute for Medical Research (WIRM), The Scripps Research Institute, 10550 North Torrey Pines Road, BCC-582, La Jolla, California 92037, United States
| | - Karen N. Allen
- Program in Biomolecular Pharmacology, Boston University School of Medicine, 72 East Concord Street, Boston, Massachusetts 02118, United States
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
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Lorenzini L, Ghelardoni S, Saba A, Sacripanti G, Chiellini G, Zucchi R. Recovery of 3-Iodothyronamine and Derivatives in Biological Matrixes: Problems and Pitfalls. Thyroid 2017; 27:1323-1331. [PMID: 28859548 DOI: 10.1089/thy.2017.0111] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND Difficulties have been reported in quantitating 3-iodothyronamine (T1AM) in blood or serum, and tentatively attributed to problems in extraction or other pre-analytical steps. For this reason, even cell culture experiments have often be performed with unphysiological protein-free media. The aim of this study was to evaluate the recovery of exogenous T1AM added to a standard cell culture medium, namely Dulbecco's minimum essential medium (DMEM) supplemented with fetal bovine serum (FBS), and to other biological matrixes. METHODS Cell culture media (Krebs-Ringer buffer, DMEM, FBS, DMEM + FBS, used either in the absence or in the presence of NG108-15 cells) and other biological matrixes (rat brain and liver homogenates, human plasma, and blood) were spiked with T1AM and/or deuterated T1AM (d4-T1AM) and incubated for times ranging from 0 to 240 minutes. Samples were then extracted using a liquid/liquid method and analyzed using liquid chromatography coupled to mass spectrometry in order to assay T1AM and its metabolites, namely 3-iodothyroacetic acid (TA1), thyronamine, thyroacetic acid, N-acetyl-T1AM, and T1AM esters. RESULTS In FBS-containing buffers, T1AM decreased exponentially over time, with a half-life of 6-17 minutes, depending on FBS content, and after 60 minutes, it averaged 0-10% of the baseline. T1AM metabolites were not detected, except for minimum amounts of TA1. Notably, d4-T1AM decreased over time at a much lower rate, reaching 50-70% of the baseline at 60 minutes. These effects were completely abolished by protein denaturation and partly reduced by semicarbazide. In the presence of cells, T1AM concentration decreased virtually to 0 within 60 minutes, but TA1 accumulated in the incubation medium, with quantitative recovery. Spontaneous decrease in T1AM concentration with isotopic difference was confirmed in rat organ homogenates and human blood. CONCLUSIONS These results suggest binding and sequestration of T1AM and/or its aldehyde derivative by blood and tissue proteins, with significant isotope effects. These issues might account for the technical problems complicating the analytical assays of endogenous T1AM.
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Meyer AH, Dybala-Defratyka A, Alaimo PJ, Geronimo I, Sanchez AD, Cramer CJ, Elsner M. Cytochrome P450-catalyzed dealkylation of atrazine by Rhodococcus sp. strain NI86/21 involves hydrogen atom transfer rather than single electron transfer. Dalton Trans 2015; 43:12175-86. [PMID: 24851834 DOI: 10.1039/c4dt00891j] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cytochrome P450 enzymes are responsible for a multitude of natural transformation reactions. For oxidative N-dealkylation, single electron (SET) and hydrogen atom abstraction (HAT) have been debated as underlying mechanisms. Combined evidence from (i) product distribution and (ii) isotope effects indicate that HAT, rather than SET, initiates N-dealkylation of atrazine to desethyl- and desisopropylatrazine by the microorganism Rhodococcus sp. strain NI86/21. (i) Product analysis revealed a non-selective oxidation at both the αC and βC-atom of the alkyl chain, which is expected for a radical reaction, but not SET. (ii) Normal (13)C and (15)N as well as pronounced (2)H isotope effects (εcarbon: -4.0‰ ± 0.2‰; εnitrogen: -1.4‰ ± 0.3‰, KIEH: 3.6 ± 0.8) agree qualitatively with calculated values for HAT, whereas inverse (13)C and (15)N isotope effects are predicted for SET. Analogous results are observed with the Fe(iv)[double bond, length as m-dash]O model system [5,10,15,20-tetrakis(pentafluorophenyl)porphyrin-iron(iii)-chloride + NaIO4], but not with permanganate. These results emphasize the relevance of the HAT mechanism for N-dealkylation by P450.
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Affiliation(s)
- Armin H Meyer
- Institute of Groundwater Ecology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany.
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9
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Dellero Y, Mauve C, Boex-Fontvieille E, Flesch V, Jossier M, Tcherkez G, Hodges M. Experimental evidence for a hydride transfer mechanism in plant glycolate oxidase catalysis. J Biol Chem 2014; 290:1689-98. [PMID: 25416784 DOI: 10.1074/jbc.m114.618629] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In plants, glycolate oxidase is involved in the photorespiratory cycle, one of the major fluxes at the global scale. To clarify both the nature of the mechanism and possible differences in glycolate oxidase enzyme chemistry from C3 and C4 plant species, we analyzed kinetic parameters of purified recombinant C3 (Arabidopsis thaliana) and C4 (Zea mays) plant enzymes and compared isotope effects using natural and deuterated glycolate in either natural or deuterated solvent. The (12)C/(13)C isotope effect was also investigated for each plant glycolate oxidase protein by measuring the (13)C natural abundance in glycolate using natural or deuterated glycolate as a substrate. Our results suggest that several elemental steps were associated with an hydrogen/deuterium isotope effect and that glycolate α-deprotonation itself was only partially rate-limiting. Calculations of commitment factors from observed kinetic isotope effect values support a hydride transfer mechanism. No significant differences were seen between C3 and C4 enzymes.
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Affiliation(s)
- Younès Dellero
- From the Institut de Biologie des Plantes, CNRS UMR8618, Saclay Plant Sciences, Bâtiment 630, Université Paris Sud, 91405 Orsay Cedex, France
| | - Caroline Mauve
- From the Institut de Biologie des Plantes, CNRS UMR8618, Saclay Plant Sciences, Bâtiment 630, Université Paris Sud, 91405 Orsay Cedex, France, Plateforme Métabolisme-Métabolome, Saclay Plant Sciences, Institut de Biologie des Plantes, Bâtiment 630, 91405 Orsay Cedex, France, and
| | - Edouard Boex-Fontvieille
- From the Institut de Biologie des Plantes, CNRS UMR8618, Saclay Plant Sciences, Bâtiment 630, Université Paris Sud, 91405 Orsay Cedex, France
| | - Valérie Flesch
- From the Institut de Biologie des Plantes, CNRS UMR8618, Saclay Plant Sciences, Bâtiment 630, Université Paris Sud, 91405 Orsay Cedex, France
| | - Mathieu Jossier
- From the Institut de Biologie des Plantes, CNRS UMR8618, Saclay Plant Sciences, Bâtiment 630, Université Paris Sud, 91405 Orsay Cedex, France
| | - Guillaume Tcherkez
- From the Institut de Biologie des Plantes, CNRS UMR8618, Saclay Plant Sciences, Bâtiment 630, Université Paris Sud, 91405 Orsay Cedex, France, Plateforme Métabolisme-Métabolome, Saclay Plant Sciences, Institut de Biologie des Plantes, Bâtiment 630, 91405 Orsay Cedex, France, and Institut Universitaire de France, 103 Boulevard Saint-Michel, 75005 Paris, France
| | - Michael Hodges
- From the Institut de Biologie des Plantes, CNRS UMR8618, Saclay Plant Sciences, Bâtiment 630, Université Paris Sud, 91405 Orsay Cedex, France,
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The Oxidation of Thiols by Flavoprotein Oxidases: a Biocatalytic Route to Reactive Thiocarbonyls. Angew Chem Int Ed Engl 2014; 53:13206-9. [DOI: 10.1002/anie.201407520] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 09/09/2014] [Indexed: 11/07/2022]
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11
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Ewing TA, Dijkman WP, Vervoort JM, Fraaije MW, van Berkel WJH. The Oxidation of Thiols by Flavoprotein Oxidases: a Biocatalytic Route to Reactive Thiocarbonyls. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201407520] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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12
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Heterogeneous Multicatalytic System for Single-Pot Oxidation and C–C Coupling Reaction Sequences. Top Catal 2014. [DOI: 10.1007/s11244-014-0263-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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13
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Liu WR. Reports from the Chemical Biology of Texas Symposium at the 69th Southwest Regional Meeting of the American Chemical Society. ACS Chem Biol 2014; 9:319-22. [PMID: 24556200 DOI: 10.1021/cb500046f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Wenshe R Liu
- Department of Chemistry, Texas A&M University , College Station, Texas 77843, United States
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Serrano H, Blanchard JS. Kinetic and isotopic characterization of L-proline dehydrogenase from Mycobacterium tuberculosis. Biochemistry 2013; 52:5009-15. [PMID: 23834473 DOI: 10.1021/bi400338f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The monofunctional proline dehydrogenase (ProDH) from Mycobacterium tuberculosis performs the flavin-dependent oxidation of l-proline to Δ(1)-pyrroline-5-carboxylate in the proline catabolic pathway. The ProDH gene, prub, was cloned into the pYUB1062 vector, and the C-terminal His-tagged 37 kDa protein was expressed and purified by nickel affinity chromatography. A steady-state kinetic analysis revealed a ping-pong mechanism with an overall kcat of 33 ± 2 s(-1) and Km values of 5.7 ± 0.8 mM and 3.4 ± 0.3 μM for l-proline and 2,6-dichlorophenolindophenol (DCPIP), respectively. The pH dependence of kcat revealed that one enzyme group exhibiting a pK value of 6.8 must be deprotonated for optimal catalytic activity. Site-directed mutagenesis suggests that this group is Lys110. The primary kinetic isotope effects on V/KPro and V of 5.5 and 1.1, respectively, suggest that the transfer of hydride from l-proline to FAD is rate-limiting for the reductive half-reaction, but that FAD reoxidation is the rate-limiting step in the overall reaction. Solvent and multiple kinetic isotope effects suggest that l-proline oxidation occurs in a stepwise rather than concerted mechanism. Pre-steady-state kinetics reveal an overall kred of 88.5 ± 0.7 s(-1), and this rate is subject to a primary kinetic isotope effect of 5.2. These data confirm that the overall reaction is limited by reduced flavin reoxidation in the second half-reaction.
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Affiliation(s)
- Hector Serrano
- Department of Biochemistry, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States
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MacMillar S, Edmondson DE, Matsson O. Nitrogen kinetic isotope effects for the monoamine oxidase B-catalyzed oxidation of benzylamine and (1,1-(2)H2)benzylamine: nitrogen rehybridization and CH bond cleavage are not concerted. J Am Chem Soc 2011; 133:12319-21. [PMID: 21786798 DOI: 10.1021/ja205629b] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nitrogen kinetic isotope effects for the oxidation of benzylamine and (1,1-(2)H(2))benzylamine by recombinant human monoamine oxidase B show that cleavage of the CH bond is not concerted with rehybridization of the nitrogen atom.
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Affiliation(s)
- Susanna MacMillar
- Department of Biochemistry and Organic Chemistry, Uppsala University, P.O. Box 576, SE-75123 Uppsala, Sweden
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16
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Valley MP, Fenny NS, Ali SR, Fitzpatrick PF. Characterization of active site residues of nitroalkane oxidase. Bioorg Chem 2010; 38:115-9. [PMID: 20056514 PMCID: PMC2847678 DOI: 10.1016/j.bioorg.2009.12.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2009] [Revised: 12/03/2009] [Accepted: 12/04/2009] [Indexed: 11/30/2022]
Abstract
The flavoenzyme nitroalkane oxidase catalyzes the oxidation of primary and secondary nitroalkanes to the corresponding aldehydes and ketones plus nitrite. The structure of the enzyme shows that Ser171 forms a hydrogen bond to the flavin N5, suggesting that it plays a role in catalysis. Cys397 and Tyr398 were previously identified by chemical modification as potential active site residues. To more directly probe the roles of these residues, the S171A, S171V, S171T, C397S, and Y398F enzymes have been characterized with nitroethane as substrate. The C397S and Y398 enzymes were less stable than the wild-type enzyme, and the C397S enzyme routinely contained a substoichiometric amount of FAD. Analysis of the steady-state kinetic parameters for the mutant enzymes, including deuterium isotope effects, establishes that all of the mutations result in decreases in the rate constants for removal of the substrate proton by approximately 5-fold and decreases in the rate constant for product release of approximately 2-fold. Only the S171V and S171T mutations alter the rate constant for flavin oxidation. These results establish that these residues are not involved in catalysis, but rather are required for maintaining the protein structure.
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Affiliation(s)
- Michael P. Valley
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843
| | - Nana S. Fenny
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843
| | - Shah R. Ali
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843
| | - Paul F. Fitzpatrick
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229
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Kommoju PR, Bruckner RC, Ferreira P, Jorns MS. Probing the role of active site residues in NikD, an unusual amino acid oxidase that catalyzes an aromatization reaction important in nikkomycin biosynthesis. Biochemistry 2009; 48:6951-62. [PMID: 19530706 DOI: 10.1021/bi9006918] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
NikD catalyzes a remarkable aromatization reaction that converts piperideine 2-carboxylate (P2C) to picolinate, a key component of the nonribosomal peptide in nikkomycin antibiotics. The enzyme exhibits a FAD-Trp355 charge-transfer band at weakly alkaline pH that is abolished upon protonation of an unknown ionizable residue that exhibits a pK(a) of 7.3. Stopped-flow studies of the reductive half-reaction with wild-type nikD and P2C show that the enzyme oxidizes the enamine tautomer of P2C but do not distinguish among several possible paths for the initial two-electron oxidation step. Replacement of Glu101 or Asp276 with a neutral residue does not eliminate the ionizable group, although the observed pK(a) is 1 or 2 pH units higher, respectively, compared with that of wild-type nikD. Importantly, the mutations cause only a modest decrease (<5-fold) in the observed rate of oxidation of P2C to dihydropicolinate. The results rule out the only possible candidates for a catalytic base in the initial two-electron oxidation step. This outcome provides compelling evidence that nikD oxidizes the bond between N(1) and C(6) in the enamine tautomer of P2C, ruling out alternative paths that require an active site base to mediate the oxidation of a carbon-carbon bond. Because the same restraint applies to the second two-electron oxidation step, the dihydropicolinate intermediate must be converted to an isomer that contains an oxidizable carbon-nitrogen bond. A novel role is proposed for reduced FAD as an acid-base catalyst in the isomerization of dihydropicolinate.
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Affiliation(s)
- Phaneeswara-Rao Kommoju
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, USA
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Gaweska H, Henderson Pozzi M, Schmidt DMZ, McCafferty DG, Fitzpatrick PF. Use of pH and kinetic isotope effects to establish chemistry as rate-limiting in oxidation of a peptide substrate by LSD1. Biochemistry 2009; 48:5440-5. [PMID: 19408960 DOI: 10.1021/bi900499w] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The mechanism of oxidation of a peptide substrate by the flavoprotein lysine-specific demethylase (LSD1) has been examined using the effects of pH and isotopic substitution on steady-state and rapid-reaction kinetic parameters. The substrate contained the 21 N-terminal residues of histone H3, with a dimethylated lysyl residue at position 4. At pH 7.5, the rate constant for flavin reduction, k(red), equals k(cat), establishing the reductive half-reaction as rate-limiting at physiological pH. Deuteration of the lysyl methyls results in identical kinetic isotope effects of 3.1 +/- 0.2 on the k(red), k(cat), and k(cat)/K(m) values for the peptide, establishing C-H bond cleavage as rate-limiting with this substrate. No intermediates between oxidized and reduced flavin can be detected by stopped-flow spectroscopy, consistent with the expectation for a direct hydride transfer mechanism. The k(cat)/K(m) value for the peptide is bell-shaped, consistent with a requirement that the nitrogen at the site of oxidation be uncharged and that at least one of the other lysyl residues be charged for catalysis. The (D)(k(cat)/K(m)) value for the peptide is pH-independent, suggesting that the observed value is the intrinsic deuterium kinetic isotope effect for oxidation of this substrate.
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Affiliation(s)
- Helena Gaweska
- Department of Biochemistry and Biophysics and Johnson Research Foundation, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
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Pozzi MH, Gawandi V, Fitzpatrick PF. pH dependence of a mammalian polyamine oxidase: insights into substrate specificity and the role of lysine 315. Biochemistry 2009; 48:1508-16. [PMID: 19199575 PMCID: PMC2752350 DOI: 10.1021/bi802227m] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mammalian polyamine oxidases (PAOs) catalyze the oxidation of N1-acetylspermine and N1-acetylspermidine to produce N-acetyl-3-aminopropanaldehyde and spermidine or putrescine. Structurally, PAO is a member of the monoamine oxidase family of flavoproteins. The effects of pH on the kinetic parameters of mouse PAO have been determined to provide insight into the protonation state of the polyamine required for catalysis and the roles of ionizable residues in the active site in amine oxidation. For N1-acetylspermine, N1-acetylspermidine, and spermine, the k(cat)/K(amine)-pH profiles are bell-shaped. In each case, the profile agrees with that expected if the productive form of the substrate has a single positively charged nitrogen. The pK(i)-pH profiles for a series of polyamine analogues are most consistent with the nitrogen at the site of oxidation being neutral and one other nitrogen being positively charged in the reactive form of the substrate. With N1-acetylspermine as the substrate, the value of k(red), the limiting rate constant for flavin reduction, is pH-dependent, decreasing below a pK(a) value of 7.3, again consistent with the requirement for an uncharged nitrogen for substrate oxidation. Lys315 in PAO corresponds to a conserved active site residue found throughout the monoamine oxidase family. Mutation of Lys315 to methionine has no effect on the k(cat)/K(amine) profile for spermine; the k(red) value with N1-acetylspermine is only 1.8-fold lower in the mutant protein, and the pK(a) in the k(red)-pH profile with N1-acetylspermine shifts to 7.8. These results rule out Lys315 as a source of a pK(a) in the k(cat)/K(amine) or k(cat)/k(red) profiles. They also establish that this residue does not play a critical role in amine oxidation by PAO.
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Affiliation(s)
| | - Vijay Gawandi
- Department of Biochemistry and Biophysics, Texas A&M University, College Station TX 77843-2128
| | - Paul F. Fitzpatrick
- Department of Biochemistry and Biophysics, Texas A&M University, College Station TX 77843-2128
- Department of Chemistry, Texas A&M University, College Station TX 77843-2128
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