1
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Tao Y, Zhao Q, Liu F, Liang X, Li Q. Enzymes encapsulated in organic-inorganic hybrid nanoflower with spatial localization for sensitive and colorimetric detection of formate. J Colloid Interface Sci 2024; 672:97-106. [PMID: 38833738 DOI: 10.1016/j.jcis.2024.05.231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/21/2024] [Accepted: 05/31/2024] [Indexed: 06/06/2024]
Abstract
Formate is an important environmental pollutant, and meanwhile its concentration change is associated with a variety of diseases. Thus, rapid and sensitive detection of formate is critical for the biochemical analysis of complex samples and clinical diagnosis of multiple diseases. Herein, a colorimetric biosensor was constructed based on the cascade catalysis of formate oxidase (FOx) and horseradish peroxidase (HRP). These two enzymes were co-immobilized in Cu3(PO4)2-based hybrid nanoflower with spatial localization, in which FOx and HRP were located in the shell and core of nanoflower, respectively (FOx@HRP). In this system, FOx could catalyze the oxidation of formate to generate H2O2, which was then utilized by HRP to oxidize 2,2'-azino-bis-3-ethylbenzothiazoline-6-sulphonic acid to yield blue product. Ideal linear correlation could be obtained between the absorbance at 420 nm and formate concentration. Meanwhile, FOx@HRP exhibited excellent detection performance with low limit of detection (6 μM), wide linear detection range (10-900 μM), and favorable specificity, stability and reusability. Moreover, it could be applied in the detection of formate in environmental, food and biological samples with high accuracy. Collectively, FOx@HRP provides a useful strategy for the simple and sensitive detection of formate and is potentially to be used in biochemical analysis and clinical diagnosis.
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Affiliation(s)
- Yu Tao
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Qixuan Zhao
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Fengmei Liu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Xiao Liang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China.
| | - Quanshun Li
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China; Center for Supramolecular Chemical Biology, Jilin University, Changchun 130012, China.
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2
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Wen K, Wang S, Sun Y, Wang M, Zhang Y, Zhu J, Li Q. Mechanistic insights into the conversion of flavin adenine dinucleotide (FAD) to 8-formyl FAD in formate oxidase: a combined experimental and in-silico study. BIORESOUR BIOPROCESS 2024; 11:67. [PMID: 38985371 PMCID: PMC11236828 DOI: 10.1186/s40643-024-00782-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 07/02/2024] [Indexed: 07/11/2024] Open
Abstract
Formate oxidase (FOx), which contains 8-formyl flavin adenine dinucleotide (FAD), exhibits a distinct advantage in utilizing ambient oxygen molecules for the oxidation of formic acid compared to other glucose-methanol-choline (GMC) oxidoreductase enzymes that contain only the standard FAD cofactor. The FOx-mediated conversion of FAD to 8-formyl FAD results in an approximate 10-fold increase in formate oxidase activity. However, the mechanistic details underlying the autocatalytic formation of 8-formyl FAD are still not well understood, which impedes further utilization of FOx. In this study, we employ molecular dynamics simulation, QM/MM umbrella sampling simulation, enzyme activity assay, site-directed mutagenesis, and spectroscopic analysis to elucidate the oxidation mechanism of FAD to 8-formyl FAD. Our results reveal that a catalytic water molecule, rather than any catalytic amino acids, serves as a general base to deprotonate the C8 methyl group on FAD, thus facilitating the formation of a quinone-methide tautomer intermediate. An oxygen molecule subsequently oxidizes this intermediate, resulting in a C8 methyl hydroperoxide anion that is protonated and dissociated to form OHC-RP and OH-. During the oxidation of FAD to 8-formyl FAD, the energy barrier for the rate-limiting step is calculated to be 22.8 kcal/mol, which corresponds to the required 14-hour transformation time observed experimentally. Further, the elucidated oxidation mechanism reveals that the autocatalytic formation of 8-formyl FAD depends on the proximal arginine and serine residues, R87 and S94, respectively. Enzymatic activity assay validates that the mutation of R87 to lysine reduces the kcat value to 75% of the wild-type, while the mutation to histidine results in a complete loss of activity. Similarly, the mutant S94I also leads to the deactivation of enzyme. This dependency arises because the nucleophilic OH- group and the quinone-methide tautomer intermediate are stabilized through the noncovalent interaction provided by R87 and S94. These findings not only explain the mechanistic details of each reaction step but also clarify the functional role of R87 and S94 during the oxidative maturation of 8-formyl FAD, thereby providing crucial theoretical support for the development of novel flavoenzymes with enhanced redox properties.
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Affiliation(s)
- Kai Wen
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Sirui Wang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Yixin Sun
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Mengsong Wang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Yingjiu Zhang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun, 130012, China.
| | - Jingxuan Zhu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun, 130012, China.
| | - Quanshun Li
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun, 130012, China.
- Center for Supramolecular Chemical Biology, Jilin University, Changchun, 130012, China.
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3
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Li R, Kong W, An Z. Controlling Radical Polymerization with Biocatalysts. Macromolecules 2023. [DOI: 10.1021/acs.macromol.2c02307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Ruoyu Li
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Weina Kong
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Zesheng An
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
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4
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Wang L, Carta M, Malpass-Evans R, McKeown NB, Fletcher PJ, Estrela P, Roldan A, Marken F. Artificial Formate Oxidase Reactivity with Nano-Palladium Embedded in Intrinsically Microporous Polyamine (Pd@PIM-EA-TB) Driving the H2O2 – 3,5,3’,5’-Tetramethylbenzidine (TMB) Colour Reaction. J Catal 2022. [DOI: 10.1016/j.jcat.2022.11.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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5
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Chen J, Ma Q, Yu Z, Li M, Dong S. Platinum‐Gold Alloy Catalyzes the Aerobic Oxidation of Formic Acid for Hydrogen Peroxide Synthesis. Angew Chem Int Ed Engl 2022; 61:e202213930. [DOI: 10.1002/anie.202213930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Jinxing Chen
- State Key Laboratory of Electroanalytical Chemistry Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun 130022 China
- University of Science and Technology of China Hefei 230026 China
| | - Qian Ma
- State Key Laboratory of Electroanalytical Chemistry Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun 130022 China
- University of Science and Technology of China Hefei 230026 China
| | - Zhixuan Yu
- State Key Laboratory of Electroanalytical Chemistry Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun 130022 China
- University of Science and Technology of China Hefei 230026 China
| | - Minghua Li
- State Key Laboratory of Electroanalytical Chemistry Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun 130022 China
| | - Shaojun Dong
- State Key Laboratory of Electroanalytical Chemistry Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun 130022 China
- University of Science and Technology of China Hefei 230026 China
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6
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Phylogeny and Structure of Fatty Acid Photodecarboxylases and Glucose-Methanol-Choline Oxidoreductases. Catalysts 2020. [DOI: 10.3390/catal10091072] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Glucose-methanol-choline (GMC) oxidoreductases are a large and diverse family of flavin-binding enzymes found in all kingdoms of life. Recently, a new related family of proteins has been discovered in algae named fatty acid photodecarboxylases (FAPs). These enzymes use the energy of light to convert fatty acids to the corresponding Cn-1 alkanes or alkenes, and hold great potential for biotechnological application. In this work, we aimed at uncovering the natural diversity of FAPs and their relations with other GMC oxidoreductases. We reviewed the available GMC structures, assembled a large dataset of GMC sequences, and found that one active site amino acid, a histidine, is extremely well conserved among the GMC proteins but not among FAPs, where it is replaced with alanine. Using this criterion, we found several new potential FAP genes, both in genomic and metagenomic databases, and showed that related bacterial, archaeal and fungal genes are unlikely to be FAPs. We also identified several uncharacterized clusters of GMC-like proteins as well as subfamilies of proteins that lack the conserved histidine but are not FAPs. Finally, the analysis of the collected dataset of potential photodecarboxylase sequences revealed the key active site residues that are strictly conserved, whereas other residues in the vicinity of the flavin adenine dinucleotide (FAD) cofactor and in the fatty acid-binding pocket are more variable. The identified variants may have different FAP activity and selectivity and consequently may prove useful for new biotechnological applications, thereby fostering the transition from a fossil carbon-based economy to a bio-economy by enabling the sustainable production of hydrocarbon fuels.
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7
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Doubayashi D, Oki M, Mikami B, Uchida H. The microenvironment surrounding FAD mediates its conversion to 8-formyl-FAD in Aspergillus oryzae RIB40 formate oxidase. J Biochem 2019; 166:67-75. [PMID: 30715389 DOI: 10.1093/jb/mvz009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 01/29/2019] [Indexed: 11/15/2022] Open
Abstract
Aspergillus oryzae RIB40 formate oxidase has Arg87 and Arg554 near the formyl group and O(4) atom of 8-formyl-flavin adenine dinucleotide (FAD), respectively, with Asp396 neighbouring Arg554. Herein, we probed the roles of these three residues in modification of FAD to 8-formyl-FAD. Replacement of Arg87 or Arg554 with Lys or Ala decreased and abolished the modification, respectively. Replacement of Asp396 with Ala or Asn lowered the modification rate. The observation of unusual effects of maintaining pH 7.0 on the modification in R87K, R554K and D396 variants indicates initial and subsequent processes with different pH dependencies. Comparison of the initial process at pH 4.5 and 7.0 suggests that the microenvironment around Arg87 and the protonation state of Asp396 affect the initial process in the native enzyme. Comparison of the crystal structures of native and R554 variants showed that the replacements had minimal effect on catalytic site structure. The positively charged Arg87 might contribute to the formation of an anionic quinone-methide tautomer intermediate, while the positively charged Arg554, in collaboration with the negatively charged Asp396, might stabilize this intermediate and form a hydrogen bonding network with the N(5)/O(4) region, thereby facilitating efficient FAD modification.
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Affiliation(s)
- Daiju Doubayashi
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, University of Fukui, Fukuishi, Japan
| | - Masaya Oki
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, University of Fukui, Fukuishi, Japan
| | - Bunzo Mikami
- Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Ujishi, Japan
| | - Hiroyuki Uchida
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, University of Fukui, Fukuishi, Japan
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8
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Tieves F, Willot SJ, van Schie MMCH, Rauch MCR, Younes SHH, Zhang W, Dong J, Gomez de Santos P, Robbins JM, Bommarius B, Alcalde M, Bommarius AS, Hollmann F. Formate Oxidase (FOx) from Aspergillus oryzae: One Catalyst Enables Diverse H 2 O 2 -Dependent Biocatalytic Oxidation Reactions. Angew Chem Int Ed Engl 2019; 58:7873-7877. [PMID: 30945422 PMCID: PMC6563469 DOI: 10.1002/anie.201902380] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Indexed: 12/29/2022]
Abstract
An increasing number of biocatalytic oxidation reactions rely on H2 O2 as a clean oxidant. The poor robustness of most enzymes towards H2 O2 , however, necessitates more efficient systems for in situ H2 O2 generation. In analogy to the well-known formate dehydrogenase to promote NADH-dependent reactions, we here propose employing formate oxidase (FOx) to promote H2 O2 -dependent enzymatic oxidation reactions. Even under non-optimised conditions, high turnover numbers for coupled FOx/peroxygenase catalysis were achieved.
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Affiliation(s)
- Florian Tieves
- Department of BiotechnologyUniversity of Technology Delftvan der Massweg 92629HZDelftThe Netherlands
| | | | | | | | - Sabry Hamdy Hamed Younes
- Department of BiotechnologyUniversity of Technology Delftvan der Massweg 92629HZDelftThe Netherlands
- Chemistry DepartmentFaculty of ScienceSohag UniversitySohag82524Egypt
| | - Wuyuan Zhang
- Department of BiotechnologyUniversity of Technology Delftvan der Massweg 92629HZDelftThe Netherlands
| | - JiaJia Dong
- Department of BiotechnologyUniversity of Technology Delftvan der Massweg 92629HZDelftThe Netherlands
| | | | - John Mick Robbins
- School of Chemical and Biomolecular EngineeringGeorgia Institute of Technology311 Ferst Drive, N.W.AtlantaGA30332USA
| | - Bettina Bommarius
- School of Chemical and Biomolecular EngineeringGeorgia Institute of Technology311 Ferst Drive, N.W.AtlantaGA30332USA
| | - Miguel Alcalde
- Department of BiocatalysisInstitute of CatalysisCSIC28049MadridSpain
| | - Andreas Sebastian Bommarius
- School of Chemical and Biomolecular EngineeringGeorgia Institute of Technology311 Ferst Drive, N.W.AtlantaGA30332USA
- School of Chemistry and BiochemistryGeorgia Institute of Technology901 Atlantic Drive, N.W.AtlantaGA30332USA
| | - Frank Hollmann
- Department of BiotechnologyUniversity of Technology Delftvan der Massweg 92629HZDelftThe Netherlands
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9
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Tieves F, Willot SJ, van Schie MMCH, Rauch MCR, Younes SHH, Zhang W, Dong J, Gomez de Santos P, Robbins JM, Bommarius B, Alcalde M, Bommarius AS, Hollmann F. Formiat‐Oxidase (FOx) aus
Aspergillus oryzae
: ein Katalysator für verschiedene H
2
O
2
‐abhängige biokatalytische Oxidationen. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201902380] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Florian Tieves
- Department of BiotechnologyUniversity of Technology Delft van der Massweg 9 2629HZ Delft Niederlande
| | | | | | | | - Sabry Hamdy Hamed Younes
- Department of BiotechnologyUniversity of Technology Delft van der Massweg 9 2629HZ Delft Niederlande
- Chemistry DepartmentFaculty of ScienceSohag University Sohag 82524 Ägypten
| | - Wuyuan Zhang
- Department of BiotechnologyUniversity of Technology Delft van der Massweg 9 2629HZ Delft Niederlande
| | - JiaJia Dong
- Department of BiotechnologyUniversity of Technology Delft van der Massweg 9 2629HZ Delft Niederlande
| | | | - John Mick Robbins
- School of Chemical and Biomolecular EngineeringGeorgia Institute of Technology 311 Ferst Drive, N.W. Atlanta GA 30332 USA
| | - Bettina Bommarius
- School of Chemical and Biomolecular EngineeringGeorgia Institute of Technology 311 Ferst Drive, N.W. Atlanta GA 30332 USA
| | - Miguel Alcalde
- Department of BiocatalysisInstitute of CatalysisCSIC 28049 Madrid Spanien
| | - Andreas Sebastian Bommarius
- School of Chemical and Biomolecular EngineeringGeorgia Institute of Technology 311 Ferst Drive, N.W. Atlanta GA 30332 USA
- School of Chemistry and BiochemistryGeorgia Institute of Technology 901 Atlantic Drive, N.W. Atlanta GA 30332 USA
| | - Frank Hollmann
- Department of BiotechnologyUniversity of Technology Delft van der Massweg 9 2629HZ Delft Niederlande
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10
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Robbins JM, Geng J, Barry BA, Gadda G, Bommarius AS. Photoirradiation Generates an Ultrastable 8-Formyl FAD Semiquinone Radical with Unusual Properties in Formate Oxidase. Biochemistry 2018; 57:5818-5826. [PMID: 30226367 DOI: 10.1021/acs.biochem.8b00571] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Formate oxidase (FOX) was previously shown to contain a noncovalently bound 8-formyl FAD (8-fFAD) cofactor. However, both the absorption spectra and the kinetic parameters previously reported for FOX are inconsistent with more recent reports. The ultraviolet-visible (UV-vis) absorption spectrum reported in early studies closely resembles the spectra observed for protein-bound 8-formyl flavin semiquinone species, thus suggesting FOX may be photosensitive. Therefore, the properties of dark and light-exposed FOX were investigated using steady-state kinetics and site-directed mutagenesis analysis along with inductively coupled plasma optical emission spectroscopy, UV-vis absorption spectroscopy, circular dichroism spectroscopy, liquid chromatography and mass spectrometry, and electron paramagnetic resonance (EPR) spectroscopy. Surprisingly, these experimental results demonstrate that FOX is deactivated in the presence of light through generation of an oxygen stable, anionic (red) 8-fFAD semiquinone radical capable of persisting either in an aerobic environment for multiple weeks or in the presence of a strong reducing agent like sodium dithionite. Herein, we study the photoinduced formation of the 8-fFAD semiquinone radical in FOX and report the first EPR spectrum of this radical species. The stability of the 8-fFAD semiquinone radical suggests FOX to be a model enzyme for probing the structural and mechanistic features involved in stabilizing flavin semiquinone radicals. It is likely that the photoinduced formation of a stable 8-fFAD semiquinone radical is a defining characteristic of 8-formyl flavin-dependent enzymes. Additionally, a better understanding of the radical stabilization process may yield a FOX enzyme with more robust activity and broader industrial usefulness.
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Affiliation(s)
- John M Robbins
- School of Chemical and Biomolecular Engineering , Georgia Institute of Technology , Atlanta , Georgia 30332-0100 , United States.,Engineered Biosystems Building (EBB) , Georgia Institute of Technology , Atlanta , Georgia 30332-2000 , United States
| | - Jiafeng Geng
- School of Chemistry and Biochemistry, Parker H. Petit Institute of Bioengineering and Bioscience , Georgia Institute of Technology , Atlanta , Georgia 30332-0363 , United States
| | - Bridgette A Barry
- School of Chemistry and Biochemistry, Parker H. Petit Institute of Bioengineering and Bioscience , Georgia Institute of Technology , Atlanta , Georgia 30332-0363 , United States
| | - Giovanni Gadda
- Department of Chemistry , Georgia State University , Atlanta , Georgia 30302-3965 , United States.,Center for Diagnostics and Therapeutics , Georgia State University , Atlanta , Georgia 30302-3965 , United States.,Center for Biotechnology and Drug Design , Georgia State University , Atlanta , Georgia 30302-3965 , United States.,Department of Biology , Georgia State University , Atlanta , Georgia 30302-3965 , United States
| | - Andreas S Bommarius
- School of Chemical and Biomolecular Engineering , Georgia Institute of Technology , Atlanta , Georgia 30332-0100 , United States.,Engineered Biosystems Building (EBB) , Georgia Institute of Technology , Atlanta , Georgia 30332-2000 , United States.,School of Chemistry and Biochemistry, Parker H. Petit Institute of Bioengineering and Bioscience , Georgia Institute of Technology , Atlanta , Georgia 30332-0363 , United States
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11
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Robbins JM, Bommarius AS, Gadda G. Mechanistic studies of formate oxidase from Aspergillus oryzae : A novel member of the glucose-Methanol-choline oxidoreductase enzyme superfamily that oxidizes carbon acids. Arch Biochem Biophys 2018; 643:24-31. [DOI: 10.1016/j.abb.2018.02.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Revised: 01/18/2018] [Accepted: 02/13/2018] [Indexed: 10/18/2022]
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12
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Augustin P, Toplak M, Fuchs K, Gerstmann EC, Prassl R, Winkler A, Macheroux P. Oxidation of the FAD cofactor to the 8-formyl-derivative in human electron-transferring flavoprotein. J Biol Chem 2018; 293:2829-2840. [PMID: 29301933 PMCID: PMC5827430 DOI: 10.1074/jbc.ra117.000846] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 12/14/2017] [Indexed: 11/06/2022] Open
Abstract
The heterodimeric human (h) electron-transferring flavoprotein (ETF) transfers electrons from at least 13 different flavin dehydrogenases to the mitochondrial respiratory chain through a non-covalently bound FAD cofactor. Here, we describe the discovery of an irreversible and pH-dependent oxidation of the 8α-methyl group to 8-formyl-FAD (8f-FAD), which represents a unique chemical modification of a flavin cofactor in the human flavoproteome. Furthermore, a set of hETF variants revealed that several conserved amino acid residues in the FAD-binding pocket of electron-transferring flavoproteins are required for the conversion to the formyl group. Two of the variants generated in our study, namely αR249C and αT266M, cause glutaric aciduria type II, a severe inherited disease. Both of the variants showed impaired formation of 8f-FAD shedding new light on the potential molecular cause of disease development. Interestingly, the conversion of FAD to 8f-FAD yields a very stable flavin semiquinone that exhibited slightly lower rates of electron transfer in an artificial assay system than hETF containing FAD. In contrast, the formation of 8f-FAD enhanced the affinity to human dimethylglycine dehydrogenase 5-fold, indicating that formation of 8f-FAD modulates the interaction of hETF with client enzymes in the mitochondrial matrix. Thus, we hypothesize that the FAD cofactor bound to hETF is subject to oxidation in the alkaline (pH 8) environment of the mitochondrial matrix, which may modulate electron transport between client dehydrogenases and the respiratory chain. This discovery challenges the current concepts of electron transfer processes in mitochondria.
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Affiliation(s)
- Peter Augustin
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II
| | - Marina Toplak
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II
| | - Katharina Fuchs
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II
| | | | - Ruth Prassl
- Institute of Biophysics, Medical University of Graz, Neue Stiftingtalstrasse 6/IV, 8010 Graz, Austria
| | - Andreas Winkler
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II
| | - Peter Macheroux
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II.
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13
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Robbins JM, Souffrant MG, Hamelberg D, Gadda G, Bommarius AS. Enzyme-Mediated Conversion of Flavin Adenine Dinucleotide (FAD) to 8-Formyl FAD in Formate Oxidase Results in a Modified Cofactor with Enhanced Catalytic Properties. Biochemistry 2017. [PMID: 28640638 DOI: 10.1021/acs.biochem.7b00335] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Flavins, including flavin adenine dinucleotide (FAD), are fundamental catalytic cofactors that are responsible for the redox functionality of a diverse set of proteins. Alternatively, modified flavin analogues are rarely found in nature as their incorporation typically results in inactivation of flavoproteins, thus leading to the disruption of important cellular pathways. Here, we report that the fungal flavoenzyme formate oxidase (FOX) catalyzes the slow conversion of noncovalently bound FAD to 8-formyl FAD and that this conversion results in a nearly 10-fold increase in formate oxidase activity. Although the presence of an enzyme-bound 8-formyl FMN has been reported previously as a result of site-directed mutagenesis studies of lactate oxidase, FOX is the first reported case of 8-formyl FAD in a wild-type enzyme. Therefore, the formation of the 8-formyl FAD cofactor in formate oxidase was investigated using steady-state kinetics, site-directed mutagenesis, ultraviolet-visible, circular dichroism, and fluorescence spectroscopy, liquid chromatography with mass spectrometry, and computational analysis. Surprisingly, the results from these studies indicate not only that 8-formyl FAD forms spontaneously and results in the active form of FOX but also that its autocatalytic formation is dependent on a nearby arginine residue, R87. Thus, this work describes a new enzyme cofactor and provides insight into the little-understood mechanism of enzyme-mediated 8α-flavin modifications.
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Affiliation(s)
- John M Robbins
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0100, United States.,Engineered Biosystems Building (EBB), Georgia Institute of Technology , Atlanta, Georgia 30332-2000, United States
| | - Michael G Souffrant
- Department of Chemistry, Georgia State University , Atlanta, Georgia 30302-3965, United States.,Center for Diagnostics and Therapeutics, Georgia State University , Atlanta, Georgia 30302-3965, United States.,Molecular Basis of Disease Program, Georgia State University , Atlanta, Georgia 30303, United States
| | - Donald Hamelberg
- Department of Chemistry, Georgia State University , Atlanta, Georgia 30302-3965, United States.,Center for Diagnostics and Therapeutics, Georgia State University , Atlanta, Georgia 30302-3965, United States.,Molecular Basis of Disease Program, Georgia State University , Atlanta, Georgia 30303, United States
| | - Giovanni Gadda
- Department of Chemistry, Georgia State University , Atlanta, Georgia 30302-3965, United States.,Center for Diagnostics and Therapeutics, Georgia State University , Atlanta, Georgia 30302-3965, United States.,Center for Biotechnology and Drug Design, Georgia State University , Atlanta, Georgia 30302-3965, United States.,Department of Biology, Georgia State University , Atlanta, Georgia 30302-3965, United States
| | - Andreas S Bommarius
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0100, United States.,Engineered Biosystems Building (EBB), Georgia Institute of Technology , Atlanta, Georgia 30332-2000, United States.,School of Chemistry and Biochemistry, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
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14
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Biochemical analysis of recombinant AlkJ from Pseudomonas putida reveals a membrane-associated, flavin adenine dinucleotide-dependent dehydrogenase suitable for the biosynthetic production of aliphatic aldehydes. Appl Environ Microbiol 2014; 80:2468-77. [PMID: 24509930 DOI: 10.1128/aem.04297-13] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The noncanonical alcohol dehydrogenase AlkJ is encoded on the alkane-metabolizing alk operon of the mesophilic bacterium Pseudomonas putida GPo1. To gain insight into the enzymology of AlkJ, we have produced the recombinant protein in Escherichia coli and purified it to homogeneity using His6 tag affinity and size exclusion chromatography (SEC). Despite synthesis in the cytoplasm, AlkJ was associated with the bacterial cell membrane, and solubilization with n-dodecyl-β-D-maltoside was necessary to liberate the enzyme. SEC and spectrophotometric analysis revealed a dimeric quaternary structure with stoichiometrically bound reduced flavin adenine dinucleotide (FADH2). The holoenzyme showed thermal denaturation at moderate temperatures around 35°C, according to both activity assay and temperature-dependent circular dichroism spectroscopy. The tightly bound coenzyme was released only upon denaturation with SDS or treatment with urea-KBr and, after air oxidation, exhibited the characteristic absorption spectrum of FAD. The enzymatic activity of purified AlkJ for 1-butanol, 1-hexanol, and 1-octanol as well as the n-alkanol derivative ω-hydroxy lauric acid methyl ester (HLAMe) was quantified in the presence of the artificial electron acceptors phenazine methosulfate (PMS) and 2,6-dichlorophenolindophenol (DCPIP), indicating broad substrate specificity with the lowest activity on the shortest alcohol, 1-butanol. Furthermore, AlkJ was able to accept as cosubstrates/oxidants the ubiquinone derivatives Q0 and Q1, also in conjunction with cytochrome c, which suggests coupling to the bacterial respiratory chain of this membrane-associated enzyme in its physiological environment. Using gas chromatographic analysis, we demonstrated specific biocatalytic conversion by AlkJ of the substrate HLAMe to the industrially relevant aldehyde, thus enabling the biotechnological production of 12-amino lauric acid methyl ester via subsequent enzymatic transamination.
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Maeda Y, Doubayashi D, Ootake T, Oki M, Mikami B, Uchida H. Crystallization and preliminary X-ray analysis of formate oxidase, an enzyme of the glucose-methanol-choline oxidoreductase family. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:1064-6. [PMID: 20823527 DOI: 10.1107/s1744309110028605] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Accepted: 07/17/2010] [Indexed: 05/26/2023]
Abstract
Formate oxidase (FOD), which catalyzes the oxidation of formate to yield carbon dioxide and hydrogen peroxide, belongs to the glucose-methanol-choline oxidoreductase (GMCO) family. FOD from Aspergillus oryzae RIB40, which has a modified FAD as a cofactor, was crystallized at 293 K by the hanging-drop vapour-diffusion method. The crystal was orthorhombic and belonged to space group C222(1). Diffraction data were collected from a single crystal to 2.4 A resolution.
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Affiliation(s)
- Yoshifumi Maeda
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, University of Fukui, 9-1 Bunkyo 3-chome, Fukui-shi 910-8507, Japan
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