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Review
. 2017 Oct 15:632:41-46.
doi: 10.1016/j.abb.2017.05.012. Epub 2017 May 18.

Nitroalkane oxidase: Structure and mechanism

Paul F Fitzpatrick  1
Affiliations
Review

Nitroalkane oxidase: Structure and mechanism

Paul F Fitzpatrick. Arch Biochem Biophys. .

Abstract

The flavoprotein nitroalkane oxidase catalyzes the oxidation of neutral nitroalkanes to the corresponding aldehydes or ketones, releasing nitrite and transferring electrons to O2 to form H2O2. A combination of solution and structural analyses have provided a detailed understanding of the mechanism of this enzyme.

Keywords: Flavoprotein; Mechanism; Nitroalkane oxidase; Nitronate monooxygenase; Structure.

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Figures

Figure 1
Figure 1. Structures of (A) nitroalkane oxidase from F. oxysporum and (B) nitronate monooxygenase from Pseudomonas aeruginosa
Based on pdb files 2C12[12] and 4Q4K[13].
Figure 2
Figure 2. Comparison of the structures of MCAD and NAO
A) Structure of pig medium chain acylCoA dehydrogenase (PDB file 3MDE[38]). B) Overlays of the active sites of F. oxysporum nitroalkane oxidase D402N with spermine (tan carbons, PDB file 2C12[12]) and pig medium chain acylCoA dehydrogenase with 3-thiaoctanoyl-CoA (light blue carbons, PDB file 1UDY[39]).
Figure 3
Figure 3
Active site residues in nitroalkane oxidase (PDB file 2C12[12]).
Figure 4
Figure 4. Overlay of structures of D402N nitroalkane oxidase with nitroethane (NE), 1-nitrohexane (NH) or 1-nitrooctane (NO) bound
From PDB files 3FCJ, 3D9D, and 3D9E [22, 33].
Figure 5
Figure 5. Structure of nitroalkane oxidase trapped with cyanide during turnover with 1-nitrohexane
left, structure of active site containing cyanohexyl (green) flavin adduct; right, hydrogen bond network from active site to surface. Based on PDB file 3D9G [22].
Figure 6
Figure 6. Alignment of active-site residues in putative nitroalkane oxidases
Alignment of active site residues of F. oxysporum NAO with likely orthologs: NAO, F. oxysporum nitroalkane oxidase; PODANSg2158, Podospora anserina DSM 980 hypothetical protein; BC1G 11641, Botryotinia fuckeliana B05.10 hypothetical protein; SS1G 09730, Sclerotinia sclerotiorum 1980 hypothetical protein; NFIA 030710, Neosartorya fischeri putative acyl-CoA dehydrogenase; AN9162.2, Aspergillus nidulans hypothetical protein. Conserved residues are in bold and the active site catalytic triad Ser276, Asp402, and Arg409 in NAO are in bold and underlined. The numbering is for F. oxysporum NAO.
Scheme 1
Scheme 1
Oxidation of nitroalkane anions by D-amino acid oxidase.
Scheme 2
Scheme 2. Mechanism of nitronate monooxygenase
Adapted from reference [11].
Scheme 3
Scheme 3
Mechanism of formation of nitrobutyl flavin during turnover of nitroalkane oxidase with nitroethane.
Scheme 4
Scheme 4
Mechanism of nitroalkane oxidase.
See this image and copyright information in PMC

References

    1. Porter DJT, Voet JG, Bright HJ. Nitroalkanes as reductive substrates for flavoprotein oxidases. Z Naturforsch. 1972;27b:1052–1053. - PubMed
    1. Porter DJT, Voet JG, Bright HJ. Direct evidence for carbanions and covalent N5-flavin-carbanion adducts as catalytic intermediates in the oxidation of nitroethane by D-amino acid oxidase. J Biol Chem. 1973;248:4400–4416. - PubMed
    1. Porter DJT, Bright HJ. Mechanism of oxidation of nitroethane by glucose oxidase. J Biol Chem. 1977;252:4361–4370. - PubMed
    1. Kurtz KA, Fitzpatrick PF. pH and secondary kinetic isotope effects on the reaction of D-amino acid oxidase with nitroalkane anions: Evidence for direct attack on the flavin by carbanions. J Am Chem Soc. 1997;119:1155–1156.
    1. Kido T, Yamamoto T, Soda K. Microbial assimilation of alkyl nitro compounds and formation of nitrite. Arch Microbiol. 1975;106:165–169. - PubMed

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