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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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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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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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Linder T. CMO1 encodes a putative choline monooxygenase and is required for the utilization of choline as the sole nitrogen source in the yeast Scheffersomyces stipitis (syn. Pichia stipitis). Microbiology (Reading) 2014; 160:929-940. [DOI: 10.1099/mic.0.073932-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sixteen yeasts with sequenced genomes belonging to the ascomycete subphyla Saccharomycotina and Taphrinomycotina were assayed for their ability to utilize a variety of primary, secondary, tertiary and quartenary aliphatic amines as nitrogen sources. The results support a previously proposed pathway of quaternary amine catabolism whereby glycine betaine is first converted into choline, which is then cleaved to release trimethylamine, followed by stepwise demethylation of trimethylamine to release free ammonia. There were only a few instances of utilization of N-methylated glycine species (sarcosine and N,N-dimethylglycine), which suggests that this pathway is not intact in any of the species tested. The ability to utilize choline as a sole nitrogen source correlated strongly with the presence of a putative Rieske non-haem iron protein homologous to bacterial ring-hydroxylating oxygenases and plant choline monooxygenases. Deletion of the gene encoding the Rieske non-haem iron protein in the yeast Scheffersomyces stipitis abolished its ability to utilize choline as the sole nitrogen source, but did not affect its ability to use methylamine, dimethylamine, trimethylamine, ethylamine, diethylamine, ethanolamine or glycine as nitrogen sources. The gene was named CMO1 for putative choline monooxygenase 1. A bioinformatic survey of eukaryotic genomes showed that CMO1 homologues are found throughout the eukaryotic domain.
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Affiliation(s)
- Tomas Linder
- Department of Microbiology, Swedish University of Agricultural Sciences, Box 7025, SE-750 07, Uppsala, Sweden
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Suenobu T, Shibata S, Fukuzumi S. Catalytic oxidation of formic acid by dioxygen with an organoiridium complex. Catal Sci Technol 2014. [DOI: 10.1039/c4cy00957f] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Catalytic oxidation of formic acid by dioxygen occurred efficiently using an organoiridium complex as a catalyst in a water-containing organic solvent as well as in water at ambient temperature.
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Affiliation(s)
- Tomoyoshi Suenobu
- Department of Material and Life Science
- Graduate School of Engineering
- Osaka University and ALCA
- Japan Science and Technology Agency (JST)
- Suita, Japan
| | - Satoshi Shibata
- Department of Material and Life Science
- Graduate School of Engineering
- Osaka University and ALCA
- Japan Science and Technology Agency (JST)
- Suita, Japan
| | - Shunichi Fukuzumi
- Department of Material and Life Science
- Graduate School of Engineering
- Osaka University and ALCA
- Japan Science and Technology Agency (JST)
- Suita, Japan
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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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Expression in Escherichia coli of an unnamed protein gene from Aspergillus oryzae RIB40 and cofactor analyses of the gene product as formate oxidase. Biosci Biotechnol Biochem 2009; 73:2645-9. [PMID: 19966484 DOI: 10.1271/bbb.90497] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
An unnamed protein of Aspergillus oryzae RIB40 (accession no. XP_001727378), the amino acid sequence of which shows high similarity to those of formate oxidase isoforms produced by Debaryomyces vanjiriae MH201, was produced in Escherichia coli in C-His(6)-tagged form. The gene product, purified by affinity column chromatography, catalyzed the oxidation of formate to yield hydrogen peroxide but showed no evidence of activity on the other substrates tested. The K(m) and V(max) values at 30 degrees C at pH 4.5 were 7.9 mM and 26.3 micromole/min mg respectively. The purified enzyme showed UV-visible spectra atypical of ordinary flavoproteins. The UV-visible spectra of the enzyme and the UV-visible spectra, fluorescence spectra, and mass spectrometry of the extract obtained by boiling the purified enzyme suggested that the enzyme has a non-covalently bound FAD analog, which is expected to be 8-formyl-FAD.
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