Has an absolute requirement for FAD . While nitroethane may be the physiological substrate , the enzyme also acts on several other nitroalkanes, including 1-nitropropane, 2-nitropropane, 1-nitrobutane, 1-nitropentane, 1-nitrohexane, nitrocyclohexane and some nitroalkanols . Differs from EC 1.13.11.16, nitronate monooxygenase, in that the preferred substrates are neutral nitroalkanes rather than anionic nitronates .
a nitroalkane + H2O + O2 = an aldehyde or ketone + nitrite + H2O2
Asp402 acts as the active site base of the enzyme, mechanism, substrate CH-bond cleavage is rate limiting for the reduction of the enzyme by nitroethane
a nitroalkane + H2O + O2 = an aldehyde or ketone + nitrite + H2O2
Asp402 acts as the active site base of the enzyme, mechanism: catalysis is initiated by the active site base Asp402 that deprotonates the neutral substrate to yield a carbanion that can attack the N-5 position of the oxidized flavin, CH-bond cleavage is rate limiting for the reduction of the enzyme by nitroethane
a nitroalkane + H2O + O2 = an aldehyde or ketone + nitrite + H2O2
detailed mechanism, with carbanion reaction intermediate formation, an aspartate residue is the active site base, substrate CH-bond cleavage is rate limiting for the reduction of the enzyme by nitroethane, the active site of the enzyme is a hydrophobic channel, tunneling, overview
a nitroalkane + H2O + O2 = an aldehyde or ketone + nitrite + H2O2
mechanism, involves removal of a proton from the nitroalkane, forming a carbanion which adds to the N5 of the flavin, elimination of nitrite from the resulting adduct forms an electrophilic imine intermediate which can be attacked by hydroxide
a nitroalkane + H2O + O2 = an aldehyde or ketone + nitrite + H2O2
mechanism, transition-state stabilization is essential, protein-substrate interactions in the transition state, reaction involves quantum mechaniscal tunneling, Asp402 is involved in initial abstraction of a proton from the neutral substrate, overview
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SYSTEMATIC NAME
IUBMB Comments
nitroalkane:oxygen oxidoreductase
Has an absolute requirement for FAD [4]. While nitroethane may be the physiological substrate [2], the enzyme also acts on several other nitroalkanes, including 1-nitropropane, 2-nitropropane, 1-nitrobutane, 1-nitropentane, 1-nitrohexane, nitrocyclohexane and some nitroalkanols [4]. Differs from EC 1.13.11.16, nitronate monooxygenase, in that the preferred substrates are neutral nitroalkanes rather than anionic nitronates [4].
solvent isotope and viscositiy effects: the kcat proton inventory is consistent with a single exchangeable proton in flight, while the kcat/KM is consistent with either a single proton in flight in the transition state or a medium effect. Increasing the solvent viscosity does not affect the kcat or kcat/KM value significantly, establishing that nitroethane binding is at equilibrium and that product release does not limit kcat
nitroethane is the only substrate, of diverse primary and secondary alkanes, for which deprotonation is fully rate limiting for the reductive half reaction
the neutral substrate form is preferred, 5fold lower activity with the substrate anion, the D402 mutant enzymes in contrast prefer the anionic substrate form
enzyme catalyzes the oxidation of nitroalkanes to the respective aldehydes or ketones with consumption of molecular oxygen and releasing nitrite and hydrogen peroxide
enzyme does not require anionic nitroalkanes for activity, enzyme catalyzes the oxidation of a number of primary and secondary nitroalkanes to the respective aldehydes or ketones with preference for primary nitroalkanes, monotonic increase with each additional methylene group from nitroethane to 1-nitrobutane increasing kcat/Km value by 20fold, no further increase with 1-nitropentane and 1-nitrohexane
absolutely required, binding structure, involving Ser171, and reactive structure analysis, the apoenzyme is inactive, removal of cofactor in its active form is reversible
noncompetitive inhibitor versus nitroethane due to formation of a dead-end complex between the oxidized enzyme and the product, competitive inhibitor versus oxygen
inactivation of the enzyme by trapping of the electrophilic imine reaction intermediate, formation of a cyanoalkyl intermediate, reaction with the substrate after proton abstraction but before flavin oxidation
thermodynamics, kinetic mechanism with nitroethane and 1-nitrobutane, isotopic effects, monotonic increase with each additional methylene group from nitroethane to 1-nitrobutane increasing kcat/Km value by 20fold, no further increase with 1-nitropentane and 1-nitrohexane
the pH-dependence of the reaction with the wild-type enzyme depends on the substrate form, at pH 7.4 activity with the neutral substrate increases while is decreases with the nitroethane anion
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystallization data of mutant D402N in complex with 1-nitrohexane or 1-nitrooctane show the presence of substrate in the binding site. The aliphatic chain of the substrate extends into a tunnel leading to the enzyme surface. The oxygens of the substrate nitro group interact both with amino acid residues and with the 2'-hydroxyl of the FAD. The structure of wild-type enzyme trapped with cyanide during oxidation of 1-nitrohexane shows the presence of the modified flavin. A continuous hydrogen bond network connects the nitrogen of the CN-hexyl-FAD through the FAD 2'-hydroxyl to a chain of water molecules extending to the protein surface. Data for mutant S276A in complex with nitrohexane
purified recombinant wild-type enzyme, crystallization of the native enzyme in 2 different crystal forms and of the selenomethionine-labeled enzyme in a third one, hanging drop vapour diffusion method, sodium cacodylate buffer, pH 7.5, containing spermidine hydrochloride, and PEG 4000 at varying concentrations for all 3 mixtures, crystal form 2 requires addition of 1,6-hexanediol at 8% w/v, crystal form 3 requires DTT at 10 mM, 4°C, 10-14 days, X-ray diffraction structure determinations and analysis at 3.2-2.0 A resolution or below, three-wavelength MAD data
the mutation results in decreases in the rate constants for removal of the substrate proton by about 5fold and decreases in the rate constant for product release of about 2fold, the mutant enzyme is less stable than the wild type enzyme
site-directed mutation of the active site base, 20fold reduced catalytic efficiency with neutral nitroethane as substrate compared to the wild-type enzyme, while the wild-type enzyme prefers the neutral substrate the mutant prefers the anion substrate form, altered pH-dependence with both substrate forms compared to the wild-type enzyme
site-directed mutation of the active site base, 140fold reduced catalytic efficiency with neutral nitroethane as substrate compared to the wild-type enzyme, while the wild-type enzyme prefers the neutral substrate the mutant prefers the anion substrate form, altered pH-dependence with both substrate forms compared to the wild-type enzyme
the mutation results in decreases in the rate constants for removal of the substrate proton by about 5fold and decreases in the rate constant for product release of about 2fold
the mutation results in decreases in the rate constants for removal of the substrate proton by about 5fold and decreases in the rate constant for product release of about 2fold, the mutation alters the rate constant for flavin oxidation
the mutation results in decreases in the rate constants for removal of the substrate proton by about 5fold and decreases in the rate constant for product release of about 2fold, the mutation alters the rate constant for flavin oxidation
the mutation results in decreases in the rate constants for removal of the substrate proton by about 5fold and decreases in the rate constant for product release of about 2fold, the mutant enzyme is less stable than the wild type enzyme
no detectable activity with neutral substrates. Crystallization data in complex with 1-nitrohexane or 1-nitrooctane show the presence of substrate in the binding site. The aliphatic chain of the substrate extends into a tunnel leading to the enzyme surface. The oxygens of the substrate nitro group interact both with amino acid residues and with the 2'-hydroxyl of the FAD
site-directed mutagenesis, altered kinetics compared to the wild-type enzyme, mutation has no effect on the rate of reaction of the reduced enzyme with oxygen, reaction mechanism analysis
mutation results in a decrease in the rate constant for proton abstraction of 18fold. The structure of the D402E enzyme, determined at 2.4 A resolution, shows that there is a smaller increase in the distance between Arg409 and the carboxylate at position 402. The interaction of this residue with Ser276 is perturbed
the mutation results in a decrease in the rate constant for proton abstraction of 18fold. The structure of the D402E enzyme shows that there is a smaller increase in the distance between Arg409 and the carboxylate at position 402 (compared to mutant enzyme R409K), and the interaction of this residue with Ser276 is perturbed
the mutation results in a decrease in the rate constant for proton abstraction of 100fold. Analysis of the three-dimensional structure of the R409K enzyme shows that the critical structural change is an increase in the distance between the carboxylate of Asp402 and the positively charged nitrogen in the side chain of the residue at position 409
the mutation results in a decrease in the rate constant for proton abstraction of 100fold. Analysis of the three-dimensional structure of the R409K enzyme, determined by X-ray crystallography to a resolution of 2.65 A, shows that the critical structural change is an increase in the distance between the carboxylate of Asp402 and the positively charged nitrogen in the side chain of the residue at position 409