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Lahham M, Jha S, Goj D, Macheroux P, Wallner S. The family of sarcosine oxidases: Same reaction, different products. Arch Biochem Biophys 2021; 704:108868. [PMID: 33812916 DOI: 10.1016/j.abb.2021.108868] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/26/2021] [Accepted: 03/27/2021] [Indexed: 12/11/2022]
Abstract
The subfamily of sarcosine oxidase is a set of enzymes within the larger family of amine oxidases. It is ubiquitously distributed among different kingdoms of life. The member enzymes catalyze the oxidization of an N-methyl amine bond of amino acids to yield unstable imine species that undergo subsequent spontaneous non-enzymatic reactions, forming an array of different products. These products range from demethylated simple species to complex alkaloids. The enzymes belonging to the sarcosine oxidase family, namely, monomeric and heterotetrameric sarcosine oxidase, l-pipecolate oxidase, N-methyltryptophan oxidase, NikD, l-proline dehydrogenase, FsqB, fructosamine oxidase and saccharopine oxidase have unique features differentiating them from other amine oxidases. This review highlights the key attributes of the sarcosine oxidase family enzymes, in terms of their substrate binding motif, type of oxidation reaction mediated and FAD regeneration, to define the boundaries of this group and demarcate these enzymes from other amine oxidase families.
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Affiliation(s)
- Majd Lahham
- Institute of Biochemistry, Graz University of Technology, NAWI Graz, Graz, Austria; Department of Biochemistry and Microbiology, Aljazeera Private University, Ghabagheb, Syria
| | - Shalinee Jha
- Institute of Biochemistry, Graz University of Technology, NAWI Graz, Graz, Austria
| | - Dominic Goj
- Institute of Biochemistry, Graz University of Technology, NAWI Graz, Graz, Austria
| | - Peter Macheroux
- Institute of Biochemistry, Graz University of Technology, NAWI Graz, Graz, Austria
| | - Silvia Wallner
- Institute of Biochemistry, Graz University of Technology, NAWI Graz, Graz, Austria.
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2
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Tararina MA, Dam KK, Dhingra M, Janda KD, Palfey BA, Allen KN. Fast Kinetics Reveals Rate-Limiting Oxidation and the Role of the Aromatic Cage in the Mechanism of the Nicotine-Degrading Enzyme NicA2. Biochemistry 2021; 60:259-273. [PMID: 33464876 DOI: 10.1021/acs.biochem.0c00855] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In Pseudomonas putida, the flavoprotein nicotine oxidoreductase (NicA2) catalyzes the oxidation of (S)-nicotine to N-methyl-myosmine, which is nonenzymatically hydrolyzed to pseudooxynicotine. Structural analysis reveals a monoamine oxidase (MAO)-like fold with a conserved FAD-binding domain and variable substrate-binding domain. The flavoenzyme has a unique variation of the classic aromatic cage with flanking residue pair W427/N462. Previous mechanistic studies using O2 as the oxidizing substrate show that NicA2 has a low apparent Km of 114 nM for (S)-nicotine with a very low apparent turnover number (kcat of 0.006 s-1). Herein, the mechanism of NicA2 was analyzed by transient kinetics. Single-site variants of W427 and N462 were used to probe the roles of these residues. Although several variants had moderately higher oxidase activity (7-12-fold), their reductive half-reactions using (S)-nicotine were generally significantly slower than that of wild-type NicA2. Notably, the reductive half-reaction of wild-type NicA2 is 5 orders of magnitude faster than the oxidative half-reaction with an apparent pseudo-first-order rate constant for the reaction of oxygen similar to kcat. X-ray crystal structures of the N462V and N462Y/W427Y variants complexed with (S)-nicotine (at 2.7 and 2.3 Å resolution, respectively) revealed no significant active-site rearrangements. A second substrate-binding site was identified in N462Y/W427Y, consistent with observed substrate inhibition. Together, these findings elucidate the mechanism of a flavoenzyme that preferentially oxidizes tertiary amines with an efficient reductive half-reaction and a very slow oxidative half-reaction when O2 is the oxidizing substrate, suggesting that the true oxidizing agent is unknown.
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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
| | - Katie K Dam
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Manaswni Dhingra
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | | | - Bruce A Palfey
- Department of Biological Chemistry, University of Michigan, 5220E MSRB III 1150 West Medical Center Drive, Ann Arbor, Michigan 48109, 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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Luo Y, Liu YJ. Theoretical Insight into a Nonadiabatic Proton-Coupled Electron Transfer Mechanism of Reduced Flavin Oxygenation. J Phys Chem A 2019; 123:4354-4359. [PMID: 31058505 DOI: 10.1021/acs.jpca.9b02084] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The oxygenation of reduced flavin has been a fascinating research hotspot in flavin-dependent proteins because it plays an indispensable role in cellular metabolism and has potential applications in biocatalysis. This spin-forbidden reaction of high efficiency is far from being fully understood. Although investigation on the flavin chemistry has been going on for more than 60 years, there are few mechanistic explanations for the reaction of the singlet-reduced flavin with triplet oxygen. In this paper, the reaction between oxygen and the model of free reduced flavin (reduced lumiflavin anion) was studied by density functional and multireference calculations in detail. The results reveal that the reaction proceeds by an electronically nonadiabatic proton-coupled electron transfer mechanism. The intersystem crossing point has been captured.
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Affiliation(s)
- Yanling Luo
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry , Beijing Normal University , Beijing 100875 , China
| | - Ya-Jun Liu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry , Beijing Normal University , Beijing 100875 , China
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4
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Soluble expression of Thermomicrobium roseum sarcosine oxidase and characterization of N-demethylation activity. MOLECULAR CATALYSIS 2019. [DOI: 10.1016/j.mcat.2018.12.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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5
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Preparation, reconstruction, and characterization of a predicted Thermomicrobium roseum sarcosine oxidase. MOLECULAR CATALYSIS 2018. [DOI: 10.1016/j.mcat.2018.06.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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6
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Romero E, Gómez Castellanos JR, Gadda G, Fraaije MW, Mattevi A. Same Substrate, Many Reactions: Oxygen Activation in Flavoenzymes. Chem Rev 2018; 118:1742-1769. [DOI: 10.1021/acs.chemrev.7b00650] [Citation(s) in RCA: 216] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Elvira Romero
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - J. Rubén Gómez Castellanos
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
| | - Giovanni Gadda
- Departments of Chemistry and Biology, Center for Diagnostics and Therapeutics, and Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Marco W. Fraaije
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Andrea Mattevi
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
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Karasulu B, Thiel W. Amine Oxidation Mediated by N-Methyltryptophan Oxidase: Computational Insights into the Mechanism, Role of Active-Site Residues, and Covalent Flavin Binding. ACS Catal 2015. [DOI: 10.1021/cs501694q] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Bora Karasulu
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz
1, 45470 Mülheim, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz
1, 45470 Mülheim, Germany
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8
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Aldonolactone oxidoreductases. Methods Mol Biol 2014; 1146:95-111. [PMID: 24764090 DOI: 10.1007/978-1-4939-0452-5_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Vitamin C is a widely used vitamin. Here we review the occurrence and properties of aldonolactone oxidoreductases, an important group of flavoenzymes responsible for the ultimate production of vitamin C and its analogs in animals, plants, and single-cell organisms.
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Wongnate T, Surawatanawong P, Visitsatthawong S, Sucharitakul J, Scrutton NS, Chaiyen P. Proton-Coupled Electron Transfer and Adduct Configuration Are Important for C4a-Hydroperoxyflavin Formation and Stabilization in a Flavoenzyme. J Am Chem Soc 2013; 136:241-53. [DOI: 10.1021/ja4088055] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Thanyaporn Wongnate
- Department
of Biochemistry and Center of Excellence in Protein Structure and
Function, Faculty of Science, Mahidol University, Bangkok, 10400 Thailand
| | - Panida Surawatanawong
- Department
of Chemistry and Center of Excellence for Innovation in Chemistry, Mahidol University, Bangkok 10400 Thailand
| | - Surawit Visitsatthawong
- Department
of Chemistry and Center of Excellence for Innovation in Chemistry, Mahidol University, Bangkok 10400 Thailand
| | - Jeerus Sucharitakul
- Department
of Biochemistry, Faculty of Dentistry, Chulalongkorn University, Henri-Dunant
Road, Patumwan, Bangkok, 10300 Thailand
| | - Nigel S. Scrutton
- Manchester
Institute of Biotechnology and Faculty of Life Sciences, The University of Manchester, Manchester M1 7DN United Kingdom
| | - Pimchai Chaiyen
- Department
of Biochemistry and Center of Excellence in Protein Structure and
Function, Faculty of Science, Mahidol University, Bangkok, 10400 Thailand
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10
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Karasulu B, Patil M, Thiel W. Amine oxidation mediated by lysine-specific demethylase 1: quantum mechanics/molecular mechanics insights into mechanism and role of lysine 661. J Am Chem Soc 2013; 135:13400-13. [PMID: 23988016 DOI: 10.1021/ja403582u] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report classical molecular dynamics (MD) simulations and combined quantum mechanics/molecular mechanics (QM/MM) calculations to elucidate the catalytic mechanism of the rate-determining amine oxidation step in the lysine-specific demethylase 1 (LSD1)-catalyzed demethylation of the histone tail lysine (H3K4), with flavin adenine dinucleotide (FAD) acting as cofactor. The oxidation of substrate lysine (sLys) involves the cleavage of an α-CH bond accompanied by the transfer of a hydride ion equivalent to FAD, leading to an imine intermediate. This hydride transfer pathway is shown to be clearly favored for sLys oxidation over other proposed mechanisms, including the radical (or single-electron transfer) route as well as carbanion and polar-nucleophilic mechanisms. MD simulations on six NVT ensembles (covering different protonation states of sLys and K661 as well as the K661M mutant) identify two possible orientations of the reacting sLys and FAD subunits (called "downward" and "upward"). Calculations at the QM(B3LYP-D/6-31G*)/CHARMM22 level provide molecular-level insights into the mechanism, helping to understand how LSD1 achieves the activation of the rather inert methyl-CH bond in a metal-free environment. Factors such as proper alignment of sLys (downward orientation), transition-state stabilization (due to the protein environment and favorable orbital interactions), and product stabilization via adduct formation are found to be crucial for facilitating the oxidative α-CH bond cleavage. The current study also sheds light on the role of important active-site residues (Y761, K661, and W695) and of the conserved water-bridge motif. The steric influence of Y761 helps to position the reaction partners properly, K661 is predicted to get deprotonated prior to substrate binding and to act as an active-site base that accepts a proton from sLys to enable the subsequent amine oxidation, and the water bridge that is stabilized by K661 and W695 mediates this proton transfer.
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Affiliation(s)
- Bora Karasulu
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, 45470 Mülheim, Germany
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11
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Gannavaram S, Gadda G. Relative Timing of Hydrogen and Proton Transfers in the Reaction of Flavin Oxidation Catalyzed by Choline Oxidase. Biochemistry 2013; 52:1221-6. [DOI: 10.1021/bi3016235] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Swathi Gannavaram
- Department of Chemistry, ‡Department of Biology, and §The Center for
Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-4098, United States
| | - Giovanni Gadda
- Department of Chemistry, ‡Department of Biology, and §The Center for
Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-4098, United States
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12
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Chaiyen P, Fraaije MW, Mattevi A. The enigmatic reaction of flavins with oxygen. Trends Biochem Sci 2012; 37:373-80. [DOI: 10.1016/j.tibs.2012.06.005] [Citation(s) in RCA: 150] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Revised: 06/19/2012] [Accepted: 06/28/2012] [Indexed: 10/28/2022]
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13
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Gadda G. Oxygen Activation in Flavoprotein Oxidases: The Importance of Being Positive. Biochemistry 2012; 51:2662-9. [DOI: 10.1021/bi300227d] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Giovanni Gadda
- Department
of Chemistry, ‡Department of Biology, and §The Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia
30302-4098, United States
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Daithankar VN, Wang W, Trujillo JR, Thorpe C. Flavin-linked Erv-family sulfhydryl oxidases release superoxide anion during catalytic turnover. Biochemistry 2011; 51:265-72. [PMID: 22148553 DOI: 10.1021/bi201672h] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Typically, simple flavoprotein oxidases couple the oxidation of their substrates with the formation of hydrogen peroxide without release of significant levels of the superoxide ion. However, two evolutionarily related single-domain sulfhydryl oxidases (Erv2p; a yeast endoplasmic reticulum resident protein and augmenter of liver regeneration, ALR, an enzyme predominantly found in the mitochondrial intermembrane) release up to ~30% of the oxygen they reduce as the superoxide ion. Both enzymes oxidize dithiol substrates via a redox-active disulfide adjacent to the flavin cofactor within the helix-rich Erv domain. Subsequent reduction of the flavin is followed by transfer of reducing equivalents to molecular oxygen. Superoxide release was initially detected using tris(3-hydroxypropyl)phosphine (THP) as an alternative reducing substrate to dithiothreitol (DTT). THP, and other phosphines, showed anomalously high turnover numbers with Erv2p and ALR in the oxygen electrode, but oxygen consumption was drastically suppressed upon the addition of superoxide dismutase. The superoxide ion initiates a radical chain reaction promoting the aerobic oxidation of phosphines with the formation of hydrogen peroxide. Use of a known flux of superoxide generated by the xanthine/xanthine oxidase system showed that one superoxide ion stimulates the reduction of 27 and 4.5 molecules of oxygen using THP and tris(2-carboxyethyl)phosphine (TCEP), respectively. This superoxide-dependent amplification of oxygen consumption by phosphines provides a new kinetic method for the detection of superoxide. Superoxide release was also observed by a standard chemiluminescence method using a luciferin analogue (MCLA) when 2 mM DTT was employed as a substrate of Erv2p and ALR. The percentage of superoxide released from Erv2p increased to ~65% when monomeric mutants of the normally homodimeric enzyme were used. In contrast, monomeric multidomain quiescin sulfhydryl oxidase enzymes that also contain an Erv FAD-binding fold release only 1-5% of their total reduced oxygen species as the superoxide ion. Aspects of the mechanism and possible physiological significance of superoxide release from these Erv-domain flavoproteins are discussed.
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Affiliation(s)
- Vidyadhar N Daithankar
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716-2522, United States
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15
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McDonald CA, Fagan RL, Collard F, Monnier VM, Palfey BA. Oxygen reactivity in flavoenzymes: context matters. J Am Chem Soc 2011; 133:16809-11. [PMID: 21958058 DOI: 10.1021/ja2081873] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Many flavoenzymes--oxidases and monooxygenases--react faster with oxygen than free flavins do. There are many ideas on how enzymes cause this. Recent work has focused on the importance of a positive charge near N5 of the reduced flavin. Fructosamine oxidase has a lysine near N5 of its flavin. We measured a rate constant of 1.6 × 10(5) M(-1) s(-1) for its reaction with oxygen. The Lys276Met mutant reacted with a rate constant of 291 M(-1) s(-1), suggesting an important role for this lysine in oxygen activation. The dihydroorotate dehydrogenases from E. coli and L. lactis also have a lysine near N5 of the flavin. They react with O(2) with rate constants of 6.2 × 10(4) and 3.0 × 10(3) M(-1) s(-1), respectively. The Lys66Met and Lys43Met mutant enzymes react with rate constants that are nearly the same as those for the wild-type enzymes, demonstrating that simply placing a positive charge near N5 of the flavin does not guarantee increased oxygen reactivity. Our results show that the lysine near N5 does not exert an effect without an appropriate context; evolution did not find only one mechanism for activating the reaction of flavins with O(2).
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Affiliation(s)
- Claudia A McDonald
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-0606, USA
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