Involvement of a flavosemiquinone in the enzymatic oxidation of nitroalkanes catalyzed by 2-nitropropane dioxygenase

A Novel Cold-Adapted Nitronate Monooxygenase from Psychrobacter sp. ANT206: Identification, Characterization and Degradation of 2-Nitropropane at Low Temperature

Aliphatic nitro compounds cause environmental pollution by being discharged into water with industrial waste. Biodegradation needs to be further explored as a green and pollution-free method of environmental remediation. In this study, we successfully cloned a novel nitronate monooxygenase gene (psnmo) from the genomic DNA library of Psychrobacter sp. ANT206 and investigated its ability to degrade 2-nitropropane (2-NP). Homology modeling demonstrated that PsNMO had a typical I nitronate monooxygenase catalytic site and cold-adapted structural features, such as few hydrogen bonds. The specific activity of purified recombinant PsNMO (rPsNMO) was 97.34 U/mg, rPsNMO exhibited thermal instability and reached maximum catalytic activity at 30 °C. Moreover, rPsNMO was most active in 1.5 M NaCl and remained at 104% of its full activity in 4.0 M NaCl, demonstrating its significant salt tolerance. Based on this finding, a novel bacterial cold-adapted enzyme was obtained in this work. Furthermore, rPsNMO protected E. coli BL21 (DE3)/pET28a(+) from the toxic effects of 2-NP at 30 °C because the 2-NP degradation rate reached 96.1% at 3 h and the final product was acetone. These results provide a reliable theoretical basis for the low-temperature degradation of 2-NP by NMO.

The C2H2 Zinc Finger Protein MaNCP1 Contributes to Conidiation through Governing the Nitrate Assimilation Pathway in the Entomopathogenic Fungus Metarhizium acridum

Zinc finger proteins are an important class of multifunctional regulators. Here, the roles of a C2H2 zinc finger protein MaNCP1 (Metarhizium acridum nitrate-related conidiation pattern shift regulatory factor 1) in nitrogen utilization and conidiation were explored in the entomopathogenic fungus M. acridum. The results showed that MaNCP1-disruption mutant (ΔMaNCP1) impaired the ability to utilize nitrate, ammonium and glutamine and reduced the expression of nitrate assimilation-related genes, suggesting that MaNCP1 was involved in governing nitrogen utilization. In addition, the conidial yield of the ΔMaNCP1 strain, cultured on the microcycle conidiation medium (SYA), was significantly decreased, which could be restored or even enhanced than that of the WT strain through increasing the nitrate content in SYA medium. Further study showed that MaAreA, a core regulator in the nitrogen catabolism repression (NCR) pathway, was a downstream target gene of MaNCP1. Screening the differential expression genes between WT and ΔMaNCP1 strains revealed that the conidial yield of M. acridum regulated by nitrate might be related to NCR pathway on SYA medium. It could be concluded that MaNCP1 contributes to the nitrate assimilation and conidiation, which will provide further insights into the relationship between the nitrogen utilization and conidiation in fungi.

Diversity and Potential Function of Prokaryotic and Eukaryotic Communities from Different Mangrove Sediments

Mangrove trees generally play important roles in protecting intertidal ecosystems. The mangrove root-associated sediments provide a repertoire of microbial communities that contribute to pivotal ecological functions in the system. In the present study, we used the high-throughput sequencing and PICRUSt-predicted functional information (based on 16S/18S rDNA profiles) to investigate the bacterial, archaeal, and fungal communities in two mangrove systems, located in the estuary of the Jiulong River (China), with different contaminated conditions and frequencies of human activity. Diverse distribution patterns for microbial communities were observed in six sediment samples collected from the two survey areas, which were found to be related mainly to the substrates in mangrove sediments. The sediments were predominated by relatively higher ratios of heterotrophic bacteria that participated in the degradation of organic matters, including phylum of Chloroflexi, Acidobacteriota, Desulfobacterota, and Proteobacteria. In addition, Crenarchaeota and Ascomycota presented the highest abundances of archaea and fungi, respectively. The relatively high concentrations of calcium, nitrogen, magnesium, and phosphorus in mangrove sediments correlated significantly with the microbial communities. In addition, although the potential functions were similar in the two sites based on COG and KEGG pathways, the abundances of enzymes involved in the degradation processes of cellulose and hemicellulose and the metabolism of nitrogen and sulfur presented distinctions. These results provide insights into the environmental conditions shaping microbial assemblies of the mangrove sediments under the impacts of human activities; for instance, a more abundant amount of calcium was found in urban areas in this study.

Peculiarities of nitronate monooxygenases and perspectives for in vivo and in vitro applications

Nitroalkanes such as nitromethane, nitroethane, 1-nitropropane (1NP), and 2-nitropropane (2NP), derived from anthropogenic activities, are hazardous environmental pollutants due to their toxicity and carcinogenic activity. In nature, 3-nitropropionate (3NPA) and its derivatives are produced as a defense mechanism by many groups of organisms, including bacteria, fungi, insects, and plants. 3NPA is highly toxic as its conjugate base, propionate-3-nitronate (P3N), is a potent inhibitor of mitochondrial succinate dehydrogenase, essential to the tricarboxylic acid cycle, and can inhibit isocitrate lyase, a critical enzyme of the glyoxylate cycle. In response to these toxic compounds, several organisms on the phylogenetic scale express genes that code for enzymes involved in the catabolism of nitroalkanes: nitroalkane oxidases (NAOs) and nitronate monooxygenases (NMOs) (previously classified as nitropropane dioxygenases, NPDs). Two types of NMOs have been identified: class I and class II, which differ in structure, catalytic efficiency, and preferred substrates. This review focuses on the biochemical properties, structure, classification, and physiological functions of NMOs, and offers perspectives for their in vivo and in vitro applications. KEY POINTS: • Nitronate monooxygenases (NMOs) are key enzymes in nitroalkane catabolism. • NMO enzymes are involved in defense mechanisms in different organisms. • NMO applications include organic synthesis, biocatalysts, and bioremediation.

Genetically engineered thermotolerant facultative anaerobes for high-efficient degradation of multiple hazardous nitroalkanes

Nitroalkanes are important industrial raw materials but also toxic pollutants, which are difficult to degrade once released into the environment. In this study, to significantly improve the degradation-efficiency of multiple nitroalkanes, a facultative anaerobe was genetically engineered, possible influencing factors and simulated application experiments of bioreactor were tested and evaluated. Among all engineered recombinants, the most effective strains NG-S1 (anaerobic) and NG-S2 (aerobic) displayed 2-fold and 2.8-fold final degradation rates higher than the wild type, respectively. Exogenous components, particularly those that enhance coenzyme synthesis, helped to increase the degradation rate, as the level of coenzymes affected full function of overexpressed nitroalkane oxidase. Importantly, simulated mixed-nitroalkane-wastewater bioreactor experiments proved excellent and sustainable degradation performance of the engineered strains for potential industrial applications. Collectively, these findings provide a promising thermophilic biological engineering platform and a new perspective for high-efficient and continuous environmental bioremediation of hazardous pollutants under aerobic and anaerobic conditions.

The devil is in the details: The chemical basis and mechanistic versatility of flavoprotein monooxygenases

The ubiquitous flavoenzymes commonly catalyze redox chemistry such as the monooxygenation of organic substrates and are both widely utilized in nature (e.g., in primary and secondary metabolism) and of significant industrial interest. In this work, we highlight the structural and mechanistic characteristics of the distinct types of flavoprotein monooxygenases (FPMOs). We thereby illustrate the chemical basis of FPMO catalysis, which enables reactions such as (aromatic) hydroxylation, epoxidation, (de)halogenation, heteroatom oxygenation, Baeyer-Villiger oxidation, α-hydroxylation of ketones, or non-oxidative carbon-hetero bond cleavage. This seemingly unmatched versatility in oxygenation chemistry results from extensive fine-tuning and regiospecific functionalization of the flavin cofactor that is tightly controlled by the surrounding protein matrix. Accordingly, FPMOs steer the formation of covalent flavin-oxygen adducts for oxygen transfer in the form of the classical flavin-C4a-(hydro)peroxide or the recently discovered N5-functionalized flavins (i.e. the flavin-N5-oxide and the flavin-N5-peroxide), while in rare cases covalent oxygen adduct formation may be foregone entirely. Finally, we speculate about hitherto undiscovered flavin-mediated oxygenation reactions and compare FPMOs to cytochrome P450 monooxygenases, before addressing open questions and challenges for the future investigation of FPMOs.

Microbial communities and gene contributions in smokeless tobacco products

Smokeless tobacco products (STP) contain bacteria, mold, and fungi due to exposure from surrounding environments and tobacco processing. This has been a cause for concern since the presence of microorganisms has been linked to the formation of highly carcinogenic tobacco-specific nitrosamines. These communities have also been reported to produce toxins and other pro-inflammatory molecules that can cause mouth lesions and elicit inflammatory responses in STP users. Moreover, microbial species in these products could transfer to the mouth and gastrointestinal tract, potentially altering the established respective microbiotas of the consumer. Here, we present the first metagenomic analysis of select smokeless tobacco products, specifically US domestic moist and dry snuff. Bacterial, eukaryotic, and viral species were found in all tobacco products where 68% of the total species was comprised of Bacteria with 3 dominant phyla but also included 32% Eukarya and 1% share abundance for Archaea and Viruses. Furthermore, 693,318 genes were found to be present and included nitrate and nitrite reduction and transport enzymes, antibiotic resistance genes associated with resistance to vancomycin, β-lactamases, their derivatives, and other antibiotics, as well as genes encoding multi-drug transporters and efflux pumps. Additional analyses showed the presence of endo- and exotoxin genes in addition to other molecules associated with inflammatory responses. Our results present a novel aspect of the smokeless tobacco microbiome and provide a better understanding of these products' microbiology. KEY POINTS: • The findings presented will help understand microbial contributions to overall STP chemistries. • Gene function categorization reveals harmful constituents outside canonical forms. • Pathway genes for TSNA precursor activity may occur at early stages of production. • Bacteria in STPs carry antibiotic resistance genes and gene transfer mechanisms.

Members of the nitronate monooxygenase gene family from Metarhizium brunneum are induced during the process of infection to Plutella xylostella

Metarhizium species are the most abundant fungi that can be isolated from soil, with a well-known biopesticide capacity. Metarhizium recognizes their hosts when the conidium interacts with insects, where the fungi are in contact with the hydrocarbons of the outermost lipid layer cuticle. These cuticular hydrocarbons comprise a mixture of n-alkanes, n-alkenes, and methyl-branched chains. Metarhizium can degrade insect hydrocarbons and use these hydrocarbons for energy production and the biosynthesis of cellular components. The metabolism of nitroalkanes involves nitronate monooxygenase activity. In this work, we isolated a family of six genes with potential nitronate monooxygenase activity from Metarhizium brunneum. The six genes were expressed in Escherichia coli, and the nitronate monooxygenase activity was verified in the recombinant proteins. Additionally, when the conidia of M. brunneum were grown in medium with nitroalkanes, virulence against Plutella xylostella increased. Furthermore, we analyzed the expression of the six Npd genes during the infection to this insect, which showed differential expression of the six Npd genes during infection.

Characterization of conserved active site residues in class I nitronate monooxygenase

Propionate 3-nitronate (P3N) is a natural toxin that irreversibly inhibits mitochondrial succinate dehydrogenase. P3N poisoning leads to a variety of neurological disorders and even death. Nitronate monooxygenase (NMO) from Pseudomonas aeruginosa PAO1 was the first NMO characterized in bacteria and serves as a paradigm for Class I NMO. Here, we hypothesized that the carboxylate group of P3N might form a hydrogen bond with one or more of the four tyrosine or a lysine residues that are conserved in the active site of the enzyme. In the wild-type enzyme, the kcat value was pH independent between pH 6.0 and 11.0, while the kcat/KP3N value decreased at high pH, suggesting that a protonated group with a pKa value of 9.5 is required for binding the anionic substrate. A pH titration of the UV-visible absorption spectrum of the enzyme showed an increased absorbance at 297 nm with increasing pH, defining a pKa value of 9.5 and a Δε297 nm of 2.4 M-1cm-1, consistent with a tyrosine being important for substrate binding. The N3 atom of the oxidized flavin, instead, did not ionize likely because its pKa was perturbed by the ionization of a tyrosine in the active site of the enzyme. The Y109F, Y254F, Y299F, Y303F, and K307 M, substitutions had small effects (i.e., <3.5-fold) on the steady-state kinetic parameters of the enzyme. With all mutated enzymes, the kcat/KP3N value was less than 2.5-fold different from the wild-type enzyme, suggesting that none of the residues is solely essential for substrate binding.

On the use of noncompetitive kinetic isotope effects to investigate flavoenzyme mechanism

This account describes the application of kinetic isotope effects (KIEs) to investigate the mechanistic properties of flavin dependent enzymes. Assays can be conducted during steady-state catalytic turnover of the flavoenzyme with its substrate or by using rapid-kinetic techniques to measure either the reductive or oxidative half-reactions of the enzyme. Great care should be taken to ensure that the observed effects are due to isotopic substitution and not other factors such as pH effects or changes in the solvent viscosity of the reaction mixture. Different types of KIEs are described along with a physical description of their origins and the unique information each can provide about the mechanism of an enzyme. Detailed experimental techniques are outlined with special emphasis on the proper controls and data analysis that must be carried out to avoid erroneous conclusions. Examples are provided for each type of KIE measurement from references in the literature. It is our hope that this article will clarify any confusion concerning the utility of KIEs in the study of flavoprotein mechanism and encourage their use by the community.

Novel thermostable enzymes from Geobacillus thermoglucosidasius W-2 for high-efficient nitroalkane removal under aerobic and anaerobic conditions

In this study, a thermophilic facultative anaerobic strain Geobacillus thermoglucosidasius W-2 was found to degrade nitroalkane under both aerobic and anaerobic conditions. Bioinformatical analysis revealed three putative nitroalkane-oxidizing enzymes (Gt-NOEs) genes from the W-2 genome. The three identified proteins Gt2929, Gt1378, and Gt1208 displayed optimal activities at high temperatures (70, 70, and 80 °C, respectively). Among these, Gt2929 exhibited excellent degradation capability, pH stability, and metal ion tolerance for nitronates under aerobic condition. Interestingly, under anaerobic condition, only Gt1378 still maintained high activity for 2-nitropropane and nitroethane, indicating that the W-2 strain utilized various pathways to degrade nitronates under aerobic and anaerobic conditions, respectively. Taken together, the first revelation of thermophilic nitroalkane-degrading mechanism under both aerobic and anaerobic conditions provides guidance and platform for biotechnological and industrial applications.

Involvement of NpdA, a Putative 2-Nitropropane Dioxygenase, in the T3SS Expression and Full Virulence in Ralstonia solanacearum OE1-1

Previously, we isolated several genes that potentially affected the expression of type III secretion system (T3SS) in Ralstonia solanacearum OE1-1. Here, we focused on the rsp0316, which encodes a putative 2-nitropropane dioxygenase (hereafter designated NpdA). The deletion of npdA substantially reduced the T3SS expression and virulence in OE1-1, and the complementation with functional NpdA could completely restore its reduced T3SS expression and virulence to that of wild type. The NpdA was highly conserved among diverse R. solanacearum species and the NpdA-dependent expression of T3SS was not specific to OE1-1 strain, but not the virulence. The NpdA was important for the T3SS expression in planta, while it was not required for the bacterial growth in planta. Moreover, the NpdA was not required for the elicitation of hypersensitive response (HR) of R. solanacearum strains in tobacco leaves. The T3SS in R. solanacearum is directly controlled by the AraC-type transcriptional regulator HrpB and regulated by a complex regulation network. The NpdA affected the T3SS expression mediated with HrpB but through some novel pathway. All these results from genetic studies demonstrate that NpdA is a novel factor for the T3SS expression in diverse R. solanacearum species in medium, but specifically for the T3SS expression in strain OE1-1 in planta. And the NpdA-dependent expression of T3SS in planta plays an important role in pathogenicity of R. solanacearum OE1-1 in host plants.

Structural and biochemical characterization of FabK from Thermotoga maritima

TM0800 from Thermotoga maritima is one of the hypothetical proteins with unknown function. The crystal structure determined at 2.3 Å resolution reveals a two domain structure: the N-terminal domain forming a barrel and the C-terminal forming a lid. One FMN is bound between the two domains with the phosphate making intricate hydrogen bonds with protein and three tightly bound water molecules, and the isoalloxazine ring packed against the side chains of Met22 and Met276. The structure is almost identical to that of FabK (enoyl-acyl carrier protein (ACP) reductase, ENR II), a key enzyme in bacterial type II fatty-acid biosynthesis that catalyzes the final step in each elongation cycle; and the enzymatic activity confirms that TM0800 is an ENR. Enzymatic activity was almost completely abolished when the helices connecting the barrel and the lid were deleted. Also, the Met276Ala and Ser280Ala mutants showed a significant reduction in enzymatic activity. The crystal structure of Met276Ala mutant at 1.9 Å resolution showed an absence of FMN suggesting that FMN plays a role in catalysis, and Met276 is important in positioning FMN. TmFabK exists as a dimer in both solution and crystal. Together this study provides molecular basis for the catalytic activity of FabK.

Functional Annotation of a Presumed Nitronate Monoxygenase Reveals a New Class of NADH:Quinone Reductases

The protein PA1024 from Pseudomonas aeruginosa PAO1 is currently classified as 2-nitropropane dioxygenase, the previous name for nitronate monooxygenase in the GenBank^TM and PDB databases, but the enzyme was not kinetically characterized. In this study, PA1024 was purified to high levels, and the enzymatic activity was investigated by spectroscopic and polarographic techniques. Purified PA1024 did not exhibit nitronate monooxygenase activity; however, it displayed NADH:quinone reductase and a small NADH:oxidase activity. The enzyme preferred NADH to NADPH as a reducing substrate. PA1024 could reduce a broad spectrum of quinone substrates via a Ping Pong Bi Bi steady-state kinetic mechanism, generating the corresponding hydroquinones. The reductive half-reaction with NADH showed a k_red value of 24 s^-1 and an apparent K_d value estimated in the low micromolar range. The enzyme was not able to reduce the azo dye methyl red, routinely used in the kinetic characterization of azoreductases. Finally, we revisited and modified the existing six conserved motifs of PA1024, which define a new class of NADH:quinone reductases and are present in more than 490 hypothetical proteins in the GenBank^TM, the vast majority of which are currently misannotated as nitronate monooxygenase.

Functional interactions among filamentous Epsilonproteobacteria and Bacteroidetes in a deep-sea hydrothermal vent biofilm

Little is known about how lithoautotrophic primary production is connected to microbial organotrophic consumption in hydrothermal systems. Using a multifaceted approach, we analysed the structure and metabolic capabilities within a biofilm growing on the surface of a black smoker chimney in the Loki's Castle vent field. Imaging revealed the presence of rod-shaped Bacteroidetes growing as ectobionts on long, sheathed microbial filaments (> 100 μm) affiliated with the Sulfurovum genus within Epsilonproteobacteria. The filaments were composed of a thick (> 200 nm) stable polysaccharide, representing a substantial fraction of organic carbon produced by primary production. An integrated -omics approach enabled us to assess the metabolic potential and in situ metabolism of individual taxonomic and morphological groups identified by imaging. Specifically, we provide evidence that organotrophic Bacteroidetes attach to and glide along the surface of Sulfurovum filaments utilizing organic polymers produced by the lithoautotrophic Sulfurovum. Furthermore, in situ expression of acetyl-CoA synthetase by Sulfurovum suggested the ability to assimilate acetate, indicating recycling of organic matter in the biofilm. This study expands our understanding of the lifestyles of Epsilonproteobacteria in hydrothermal vents, their metabolic properties and co-operative interactions in deep-sea hydrothermal vent food webs.

The combined structural and kinetic characterization of a bacterial nitronate monooxygenase from Pseudomonas aeruginosa PAO1 establishes NMO class I and II

Nitronate monooxygenase (NMO) oxidizes the mitochondrial toxin propionate 3-nitronate (P3N) to malonate semialdehyde. The enzyme has been previously characterized biochemically in fungi, but no structural information is available. Based on amino acid similarity 4,985 genes are annotated in the GenBank(TM) as NMO. Of these, 4,424 (i.e. 89%) are bacterial genes, including several Pseudomonads that have been shown to use P3N as growth substrate. Here, we have cloned and expressed the gene pa4202 of Pseudomonas aeruginosa PAO1, purified the resulting protein, and characterized it. The enzyme is active on P3N and other alkyl nitronates, but cannot oxidize nitroalkanes. P3N is the best substrate at pH 7.5 and atmospheric oxygen with k(cat)(app)/K(m)(app) of 12 × 10(6) M(-1) s(-1), k(cat)(app) of 1300 s(-1), and K(m)(app) of 110 μm. Anerobic reduction of the enzyme with P3N yields a flavosemiquinone, which is formed within 7.5 ms, consistent with this species being a catalytic intermediate. Absorption spectroscopy, mass spectrometry, and x-ray crystallography demonstrate a tightly, non-covalently bound FMN in the active site of the enzyme. Thus, PA4202 is the first NMO identified and characterized in bacteria. The x-ray crystal structure of the enzyme was solved at 1.44 Å, showing a TIM barrel-fold. Four motifs in common with the biochemically characterized NMO from Cyberlindnera saturnus are identified in the structure of bacterial NMO, defining Class I NMO, which includes bacterial, fungal, and two animal NMOs. Notably, the only other NMO from Neurospora crassa for which biochemical evidence is available lacks the four motifs, defining Class II NMO.

Rv1894c is a novel hypoxia-induced nitronate monooxygenase required for Mycobacterium tuberculosis virulence

Tuberculosis is difficult to cure, requiring a minimum of 6 months of treatment with multiple antibiotics. Small numbers of organisms are able to tolerate the antibiotics and persist in the lungs of infected humans, but they still require some metabolic activity to survive. We studied the role of the hypoxia-induced Rv1894c gene in Mycobacterium tuberculosis virulence in guinea pigs, which develop hypoxic, necrotic granulomas histologically resembling those in humans and found this gene to be necessary for full bacillary growth and survival. We characterized the function of the encoded enzyme as a nitronate monooxygenase, which is needed to prevent the buildup of toxic products during hypoxic metabolism and is negatively regulated by the transcriptional repressor KstR. Future studies will focus on developing small-molecule inhibitors that target Rv1894c and its homologs, with the goal of killing persistent bacteria, thereby shortening the time needed to treat tuberculosis.

Cytochrome P450 reductase: a harbinger of diffusible reduced oxygen species

The bi-enzymatic system of cytochrome P450 (CYP, a hemoprotein) and cytochrome P450 reductase (CPR, a diflavoenzyme) mediate the redox metabolism of diverse indigenous and xenobiotic molecules in various cellular and organ systems, using oxygen and NADPH. Curiously, when a 1∶1 ratio is seen to be optimal for metabolism, the ubiquitous CYP:CPR distribution ratio is 10 to 100∶1 or higher. Further, the NADPH equivalents consumed in these in vitro or in situ assemblies usually far exceeded the amount of substrate metabolized. We aimed to find the rationale to explain for these two oddities. We report here that CPR is capable of activating molecular oxygen on its own merit, generating diffusible reduced oxygen species (DROS). Also, in the first instance for a flavoprotein, CPR is shown to deplete peroxide via diffusible radical mediated process, thereby leading to the formation of water (but without significant evolution of oxygen). We also quantitatively demonstrate that the rate of oxygen activation and peroxide depletion by CPR accounts for the major reactivity in the CYP+CPR mixture. We show unambiguously that CPR is able to regulate the concentration of diffusible reduced oxygen species in the reaction milieu. These findings point out that CPR mediated processes are bound to be energetically ‘wasteful’ and potentially ‘hazardous’ owing to the unavoidable nature of the CPR to generate and deplete DROS. Hence, we can understand that CPR is distributed at low densities in cells. Some of the activities that were primarily attributed to the heme-center of CYP are now established to be a facet of the flavins of CPR. The current approach of modeling drugs to minimize “uncoupling” on the basis of erstwhile hypothesis stands questionable, considering the ideas brought forth in this work.

Growth of bacteria on 3-nitropropionic acid as a sole source of carbon, nitrogen, and energy

3-Nitropropionic acid (3NPA) is a widespread nitroaliphatic toxin found in a variety of legumes and fungi. Several enzymes have been reported that can transform the compound, but none led to the mineralization of 3NPA. We report here the isolation of bacteria that grow on 3NPA and its anion, propionate-3-nitronate (P3N), as the sole source of carbon, nitrogen, and energy. Experiments with resting cells, cell extracts, and purified enzymes indicate that the pathway involves conversion of 3NPA to P3N, which upon denitration yields malonic semialdehyde, nitrate, nitrite, and traces of H(2)O(2). Malonic semialdehyde is decarboxylated to acetyl coenzyme A. The gene that encodes the enzyme responsible for the denitration of P3N was cloned and expressed, and the enzyme was purified. Stoichiometry of the reaction indicates that the enzyme is a monooxygenase. The gene sequence is related to a large group of genes annotated as 2-nitropropane dioxygenases, but the P3N monooxygenase and closely related enzymes form a cluster within COG2070 that differs from previously characterized 2-nitropropane dioxygenases by their substrate specificities and reaction products. The results suggest that the P3N monooxygenases enable bacteria to exploit 3NPA in natural habitats as a growth substrate.

Nitronate monooxygenase, a model for anionic flavin semiquinone intermediates in oxidative catalysis

Nitronate monooxygenase (NMO), formerly referred to as 2-nitropropane dioxygenase, is an FMN-dependent enzyme that uses molecular oxygen to oxidize (anionic) alkyl nitronates and, in the case of the enzyme from Neurospora crassa, (neutral) nitroalkanes to the corresponding carbonyl compounds and nitrite. Over the past 5 years, a resurgence of interest on the enzymology of NMO has driven several studies aimed at the elucidation of the mechanistic and structural properties of the enzyme. This review article summarizes the knowledge gained from these studies on NMO, which has been emerging as a model system for the investigation of anionic flavosemiquinone intermediates in the oxidative catalysis of organic molecules, and for the effect that branching of reaction intermediates has on both the kinetic parameters and isotope effects associated with enzymatic reactions. A comparison of the catalytic mechanism of NMO with other flavin-dependent enzymes that oxidize nitroalkane and nitronates is also presented.

Structure-Based Insight into the Asymmetric Bioreduction of the C=C Double Bond of alpha,beta-Unsaturated Nitroalkenes by Pentaerythritol Tetranitrate Reductase

Biocatalytic reduction of alpha- or beta-alkyl-beta-arylnitroalkenes provides a convenient and efficient method to prepare chiral substituted nitroalkanes. Pentaerythritol tetranitrate reductase (PETN reductase) from Enterobacter cloacae st. PB2 catalyses the reduction of nitroolefins such as 1-nitrocyclohexene (1) with steady state and rapid reaction kinetics comparable to other old yellow enzyme homologues. Furthermore, it reduces 2-aryl-1-nitropropenes (4a-d) to their equivalent (S)-nitropropanes 9a-d. The enzyme shows a preference for the (Z)-isomer of substrates 4a-d, providing almost pure enantiomeric products 9a-d (ees up to > 99%) in quantitative yield, whereas the respective (E)-isomers are reduced with lower enantioselectivity (63-89% ee) and lower product yields. 1-Aryl-2-nitropropenes (5a, b) are also reduced efficiently, but the products (R)-10 have lower optical purities. The structure of the enzyme complex with 1-nitrocyclohexene (1) was determined by X-ray crystallography, revealing two substrate-binding modes, with only one compatible with hydride transfer. Models of nitropropenes 4 and 5 in the active site of PETN reductase predicted that the enantioselectivity of the reaction was dependent on the orientation of binding of the (E)- and (Z)-substrates. This work provides a structural basis for understanding the mechanism of asymmetric bioreduction of nitroalkenes by PETN reductase.

Oxidation of alkyl nitronates catalyzed by 2-nitropropane dioxygenase from Hansenula mrakii

2-Nitropropane dioxygenase from Hansenula mrakii was expressed in Escherichia coli cells and purified in active and stable form using 60% saturation of ammonium sulfate and a single chromatographic step onto a DEAE column. MALDI-TOF mass spectrometric and spectrophotometric analyses of the flavin extracted by heat or acid denaturation of the enzyme indicated that FMN, and not FAD as erroneously reported previously, is present in a 1:1 stoichiometry with the protein. Inductively coupled plasma mass spectrometric analysis of the enzyme established that H. mrakii 2-nitropropane dioxygenase contains negligible amounts of iron, manganese, zinc, and copper ions, which are not catalytically relevant. Anaerobic substrate reduction and kinetic data using a Clark oxygen electrode to measure rates of oxygen consumption indicated that the enzyme is active on a broad range of alkyl nitronates, with a marked preference for unbranched substrates over propyl-2-nitronate. Interestingly, the enzyme reacts poorly, if at all, with nitroalkanes, as suggested by lack of both anaerobic reduction of the enzyme-bound flavin and consumption of oxygen with nitroethane, nitrobutane, and 2-nitropropane. Finally, both the tight binding of sulfite (K(d)=90 microM, at pH 8 and 15 degrees C) to the enzyme and the formation of the anionic flavosemiquinone upon anaerobic incubation with alkyl nitronates are consistent with the presence of a positively charged group in proximity of the N1-C2=O atoms of the FMN cofactor.

Crystal structure of 2-nitropropane dioxygenase complexed with FMN and substrate. Identification of the catalytic base

Nitroalkane compounds are widely used in chemical industry and are also produced by microorganisms and plants. Some nitroalkanes have been demonstrated to be carcinogenic, and enzymatic oxidation of nitroalkanes is of considerable interest. 2-Nitropropane dioxygenases from Neurospora crassa and Williopsis mrakii (Hansenula mrakii), members of one family of the nitroalkane-oxidizing enzymes, contain FMN and FAD, respectively. The enzymatic oxidation of nitroalkanes by 2-nitropropane dioxygenase operates by an oxidase-style catalytic mechanism, which was recently shown to involve the formation of an anionic flavin semiquinone. This represents a unique case in which an anionic flavin semiquinone has been experimentally observed in the catalytic pathway for oxidation catalyzed by a flavin-dependent enzyme. Here we report the first crystal structure of 2-nitropropane dioxygenase from Pseudomonas aeruginosa in two forms: a binary complex with FMN and a ternary complex with both FMN and 2-nitropropane. The structure identifies His(152) as the proposed catalytic base, thus providing a structural framework for a better understanding of the catalytic mechanism.