The catalytic cycle of nitrous oxide reductase - The enzyme that catalyzes the last step of denitrification

N2O recovery from wastewater and flue gas via microbial denitrification: Processes and mechanisms

Nitrous oxide (N2O) is increasingly regarded as a significant greenhouse gas implicated in global warming and the depletion of the ozone layer, yet it is also recognized as a valuable resource. This paper comprehensively reviews innovative microbial denitrification techniques for recovering N2O from nitrogenous wastewater and flue gas. Critical analysis is carried out on cutting-edge processes such as the coupled aerobic-anoxic nitrous decomposition operation (CANDO) process, semi-artificial photosynthesis, and the selective utilization of microbial strains, as well as flue gas absorption coupled with heterotrophic/autotrophic denitrification. These processes are highlighted for their potential to facilitate denitrification and enhance the recovery rate of N2O. The review integrates feasible methods for process control and optimization, and presents the underlying mechanisms for N2O recovery through denitrification, primarily achieved by suppressing nitrous oxide reductase (Nos) activity and intensifying competition for electron donors. The paper concludes by recognizing the shortcomings in existing technologies and proposing future research directions, with an emphasis on prioritizing the collection and utilization of N2O while considering environmental sustainability and economic feasibility. Through this review, we aim to inspire interest in the recovery and utilization of N2O, as well as the development and application of related technologies.

Enhancing biological conversion of NO to N2O by utilizing thermophiles instead of mesophiles

The production of nitrous oxide (N2O) through the biological denitrification of nitric oxide (NO) from flue gases has recently been achieved. Although the temperature of flue gas after desulphurization is usually 45-70 °C, all previous studies conducted microbial denitrification of NO under mesophilic conditions (22-35 °C). This study investigated the biological conversion of NO to N2O in both mesophilic (35-45 °C) and thermophilic conditions (45-50 °C). The results showed that temperature has a great impact on N2O production, with a maximum conversion efficiency (from NO to N2O) of 82% achieved at 45 °C, which is obviously higher than the reported conversion efficiencies (24-71%) under mesophilic conditions. Additionally, high-throughput sequencing result showed that the genera Enterococcus, Clostridium, Romboutsia, and Streptococcus were closely related to NO denitrification and N2O production. Microbial communities at 40 and 45 °C had greater metabolizing capacities for polymeric carbon sources. This study suggests that thermophilic condition (45 °C) is more suitable for biological production of N2O from NO.

Triazenide-supported [Cu4S] structural mimics of CuZ that mediate N2O disproportionation rather than reduction

As part of the nitrogen cycle, environmental nitrous oxide (N2O) undergoes the N2O reduction reaction (N2ORR) catalyzed by nitrous oxide reductase, a metalloenzyme whose catalytic active site is a tetranuclear copper-sulfide cluster (CuZ). On the other hand, heterogeneous Cu catalysts on oxide supports are known to mediate decomposition of N2O (deN2O) by disproportionation. In this study, a CuZ model system supported by triazenide ligands is characterized by X-ray crystallography, NMR and EPR spectroscopies, and electronic structure calculations. Although the triazenide-ligated Cu4(μ4-S) clusters are closely related to previous formamidinate derivatives, which differ only in replacement of a remote N atom for a CH group, divergent reactivity with N2O is observed. Whereas the formamidinate-ligated clusters were previously shown to mediate single-turnover N2ORR, the triazenide-ligated clusters are found to mediate deN2O, behavior that was previously unknown to natural or synthetic copper-sulfide clusters. The reaction pathway for deN2O by this model system, including previously unidentified transition state models for N2O activation in N-O cleavage and O-O coupling steps, are included. The divergent reactivity of these two related but subtly different systems point to key factors influencing behavior of Cu-based catalysts for N2ORR (i.e., CuZ) and deN2O (e.g., CuO/CeO2).

Cu4S Cluster in "0-Hole" and "1-Hole" States: Geometric and Electronic Structure Variations for the Active CuZ* Site of N2O Reductase

The active site of nitrous oxide reductase (N2OR), a key enzyme in denitrification, features a unique μ4-sulfido-bridged tetranuclear Cu cluster (the so-called CuZ or CuZ* site). Details of the catalytic mechanism have remained under debate and, to date, synthetic model complexes of the CuZ*/CuZ sites are extremely rare due to the difficulty in building the unique {Cu4(μ4-S)} core structure. Herein, we report the synthesis and characterization of [Cu4(μ4-S)]n+ (n = 2, 2; n = 3, 3) clusters, supported by a macrocyclic {py2NHC4} ligand (py = pyridine, NHC = N-heterocyclic carbene), in both their 0-hole (2) and 1-hole (3) states, thus mimicking the two active states of the CuZ* site during enzymatic N2O reduction. Structural and electronic properties of these {Cu4(μ4-S)} clusters are elucidated by employing multiple methods, including X-ray diffraction (XRD), nuclear magnetic resonance (NMR), UV/vis, electron paramagnetic resonance (EPR), Cu/S K-edge X-ray emission spectroscopy (XES), and Cu K-edge X-ray absorption spectroscopy (XAS) in combination with time-dependent density functional theory (TD-DFT) calculations. A significant geometry change of the {Cu4(μ4-S)} core occurs upon oxidation from 2 (τ4(S) = 0.46, seesaw) to 3 (τ4(S) = 0.03, square planar), which has not been observed so far for the biological CuZ(*) site and is unprecedented for known model complexes. The single electron of the 1-hole species 3 is predominantly delocalized over two opposite Cu ions via the central S atom, mediated by a π/π superexchange pathway. Cu K-edge XAS and Cu/S K-edge XES corroborate a mixed Cu/S-based oxidation event in which the lowest unoccupied molecular orbital (LUMO) has a significant S-character. Furthermore, preliminary reactivity studies evidence a nucleophilic character of the central μ4-S in the fully reduced 0-hole state.

Does the aging behavior of microplastics affect the process of denitrification by the difference of copper ion adsorption?

Riparian sediment is a hot zone for denitrification that can withhold copper and microplastics (MPs) from outside. It has been proven that MPs affect denitrification and the existing forms of copper in the environment. However, the impact of copper on sediment denitrification under exposure to MPs remains unclear. This study revealed the response of sediment denitrification to copper availability under the adsorption of MPs and the complexation of MP-derived dissolved organic matter (DOM). These results showed that MP accumulation inhibited denitrification. However, aged MPs increased the activity of nitrite reductase (12.64%), nitrogen dioxide reductase (37.68%), and electron transport (28.93%) compared with pristine MPs. The aging behavior of MPs alleviated 28.18% nitrite accumulation and 16.41-118.35% nitrous oxide emissions. Thus, the aging behavior of MPs alleviated the inhibition of denitrification. Notably, we resolved the copper ion adsorption and complexation by MPs, MP-derived DOM contributed to the denitrification process, and we found that the key nitrogen removal factors were affected by K_L, K_M, and K₂. These results fill a gap in our understanding of biochemical synthesis of MPs during denitrification. Furthermore, it can be used to build a predictive understanding of the long-term effects of MPs on the sediment nitrogen cycle.

Orchestrating copper binding: structure and variations on the cupredoxin fold

A large number of copper binding proteins coordinate metal ions using a shared three-dimensional fold called the cupredoxin domain. This domain was originally identified in Type 1 "blue copper" centers but has since proven to be a common domain architecture within an increasingly large and diverse group of copper binding domains. The cupredoxin fold has a number of qualities that make it ideal for coordinating Cu ions for purposes including electron transfer, enzyme catalysis, assembly of other copper sites, and copper sequestration. The structural core does not undergo major conformational changes upon metal binding, but variations within the coordination environment of the metal site confer a range of Cu-binding affinities, reduction potentials, and spectroscopic properties. Here, we discuss these proteins from a structural perspective, examining how variations within the overall cupredoxin fold and metal binding sites are linked to distinct spectroscopic properties and biological functions. Expanding far beyond the blue copper proteins, cupredoxin domains are used by a growing number of proteins and enzymes as a means of binding copper ions, with many more likely remaining to be identified.

NosZ gene cloning, reduction performance and structure of Pseudomonas citronellolis WXP-4 nitrous oxide reductase

Nitrous oxide reductase (N₂OR) is the only known enzyme that can reduce the powerful greenhouse gas nitrous oxide (N₂O) to harmless nitrogen at the final step of bacterial denitrification. To alleviate the N₂O emission, emerging approaches aim at microbiome biotechnology. In this study, the genome sequence of facultative anaerobic bacteria Pseudomonas citronellolis WXP-4, which efficiently degrades N₂O, was obtained by de novo sequencing for the first time, and then, four key reductase structure coding genes related to complete denitrification were identified. The single structural encoding gene nosZ with a length of 1914 bp from strain WXP-4 was cloned in Escherichia coli BL21(DE3), and the N₂OR protein (76 kDa) was relatively highly efficiently expressed under the optimal inducing conditions of 1.0 mM IPTG, 5 h, and 30 °C. Denitrification experiment results confirmed that recombinant E. coli had strong denitrification ability and reduced 10 mg L⁻¹ of N₂O to N₂ within 15 h under the optimal conditions of pH 7.0 and 40 °C, its corresponding N₂O reduction rate was almost 2.3 times that of Alcaligenes denitrificans strain TB, but only 80% of that of wild strain WXP-4, meaning that nos gene cluster auxiliary gene deletion decreased the activity of N₂OR. The 3D structure of N₂OR predicted on the basis of sequence homology found that electron transfer center CuA had only five amino acid ligands, and the S2 of the catalytically active center CuZ only bound one Cu_I atom. The unique 3D structure was different from previous reports and may be closely related to the strong N₂O reduction ability of strain WXP-4 and recombinant E. coli. The findings show a potential application of recombinant E. coli in alleviating the greenhouse effect and provide a new perspective for researching the relationship between structure and function of N₂OR.

Nitrous oxide reductase (N₂OR) is the only known enzyme that can reduce the powerful greenhouse gas nitrous oxide (N₂O) to harmless nitrogen at the final step of bacterial denitrification. The recombinant E. coli and wild strain WXP-4 demonstrate strong N₂O reduction ability.

Sulfur-driven autotrophic denitrification of nitric oxide for efficient nitrous oxide recovery

Nitrous oxide (N₂ O) was previously deemed as a potent greenhouse gas but is actually an untapped energy source, which can accumulate during the microbial denitrification of nitric oxide (NO). Compared with the organic electron donor required in heterotrophic denitrification, elemental sulfur (S⁰ ) is a promising electron donor alternative due to its cheap cost and low biomass yield in sulfur-driven autotrophic denitrification. However, no effort has been made to test N₂ O recovery from sulfur-driven denitrification of NO so far. Therefore, in this study, batch and continuous experiments were carried out to investigate the NO removal performance and N₂ O recovery potential via sulfur-driven NO-based denitrification under various Fe(II)EDTA-NO concentrations. Efficient energy recovery was achieved, as up to 35.5%-40.9% of NO was converted to N₂ O under various NO concentrations. N₂ O recovery from Fe(II)EDTA-NO could be enhanced by the low bioavailability of sulfur and the acid environment caused by sulfur oxidation. The NO reductase (NOR) and N₂ O reductase (N₂ OR) were inhibited distinctively at relatively low NO levels, leading to efficient N₂ O accumulation, but were suppressed irreversibly at NO level beyond 15 mM in continuous experiments. Such results indicated that the regulation of NO at a relatively low level would benefit the system stability and NO removal capacity during long-term system operation. The continuous operation of the sulfur-driven Fe(II)EDTA-NO-based denitrification reduced the overall microbial diversity but enriched several key microbial community. Thauera, Thermomonas, and Arenimonas that are able to carry out sulfur-driven autotrophic denitrification became the dominant organisms with their relative abundance increased from 25.8% to 68.3%, collectively.

In Silico Analysis of the Enzymes Involved in Haloarchaeal Denitrification

During the last century, anthropogenic activities such as fertilization have led to an increase in pollution in many ecosystems by nitrogen compounds. Consequently, researchers aim to reduce nitrogen pollutants following different strategies. Some haloarchaea, owing to their denitrifier metabolism, have been proposed as good model organisms for the removal of not only nitrate, nitrite, and ammonium, but also (per)chlorates and bromate in brines and saline wastewater. Bacterial denitrification has been extensively described at the physiological, biochemical, and genetic levels. However, their haloarchaea counterparts remain poorly described. In previous work the model structure of nitric oxide reductase was analysed. In this study, a bioinformatic analysis of the sequences and the structural models of the nitrate, nitrite and nitrous oxide reductases has been described for the first time in the haloarchaeon model Haloferax mediterranei. The main residues involved in the catalytic mechanism and in the coordination of the metal centres have been explored to shed light on their structural characterization and classification. These results set the basis for understanding the molecular mechanism for haloarchaeal denitrification, necessary for the use and optimization of these microorganisms in bioremediation of saline environments among other potential applications including bioremediation of industrial waters.

Bacterial nitric oxide metabolism: Recent insights in rhizobia

Nitric oxide (NO) is a reactive gaseous molecule that has several functions in biological systems depending on its concentration. At low concentrations, NO acts as a signaling molecule, while at high concentrations, it becomes very toxic due to its ability to react with multiple cellular targets. Soil bacteria, commonly known as rhizobia, have the capacity to establish a N₂-fixing symbiosis with legumes inducing the formation of nodules in their roots. Several reports have shown NO production in the nodules where this gas acts either as a signaling molecule which regulates gene expression, or as a potent inhibitor of nitrogenase and other plant and bacteria enzymes. A better understanding of the sinks and sources of NO in rhizobia is essential to protect symbiotic nitrogen fixation from nitrosative stress. In nodules, both the plant and the microsymbiont contribute to the production of NO. From the bacterial perspective, the main source of NO reported in rhizobia is the denitrification pathway that varies significantly depending on the species. In addition to denitrification, nitrate assimilation is emerging as a new source of NO in rhizobia. To control NO accumulation in the nodules, in addition to plant haemoglobins, bacteroids also contribute to NO detoxification through the expression of a NorBC-type nitric oxide reductase as well as rhizobial haemoglobins. In the present review, updated knowledge about the NO metabolism in legume-associated endosymbiotic bacteria is summarized.

Coordination chemistry of the CuZ site in nitrous oxide reductase and its synthetic mimics

Atmospheric nitrous oxide (N2O) has garnered significant attention recently due to its dual roles as an ozone depletion agent and a potent greenhouse gas. Anthropogenic N2O emissions occur primarily through agricultural disruption of nitrogen homeostasis causing N2O to build up in the atmosphere. The enzyme responsible for N2O fixation within the geochemical nitrogen cycle is nitrous oxide reductase (N2OR), which catalyzes 2H+/2e- reduction of N2O to N2 and H2O at a tetranuclear active site, CuZ. In this review, the coordination chemistry of CuZ is reviewed. Recent advances in the understanding of biological CuZ coordination chemistry is discussed, as are significant breakthroughs in synthetic modeling of CuZ that have emerged in recent years. The latter topic includes both structurally faithful, synthetic [Cu4(µ4-S)] clusters that are able to reduce N2O, as well as dicopper motifs that shed light on reaction pathways available to the critical CuI-CuIV cluster edge of CuZ. Collectively, these advances in metalloenzyme studies and synthetic model systems provide meaningful knowledge about the physiologically relevant coordination chemistry of CuZ but also open new questions that will pose challenges in the near future.

Biological Reduction of Nitric Oxide for Efficient Recovery of Nitrous Oxide as an Energy Source

Chemical absorption-biological reduction based on Fe(II)EDTA is a promising technology to remove nitric oxide (NO) from flue gases. However, limited effort has been made to enable direct energy recovery from NO through production of nitrous oxide (N₂O) as a potential renewable energy rather than greenhouse gas. In this work, the enhanced energy recovery in the form of N₂O via biological NO reduction was investigated by conducting short-term and long-term experiments at different Fe(II)EDTA-NO and organic carbon levels. The results showed both NO reductase and N₂O reductase were inhibited at Fe(II)EDTA-NO concentration up to 20 mM, with the latter being inhibited more significantly, thus facilitating N₂O accumulation. Furthermore, N₂O accumulation was enhanced under carbon-limiting conditions because of electron competition during short-term experiments. Up to 47.5% of NO-N could be converted to gaseous N₂O-N, representing efficient N₂O recovery. Fe(II)EDTA-NO reduced microbial diversity and altered the community structure toward Fe(II)EDTA-NO-reducing bacteria-dominated culture during long-term experiments. The most abundant bacterial genus Pseudomonas, which was able to resist the toxicity of Fe(II)EDTA-NO, was significantly enriched, with its relative abundance increased from 1.0 to 70.3%, suggesting Pseudomonas could be the typical microbe for the energy recovery technology in NO-based denitrification.

Cu Homeostasis in Bacteria: The Ins and Outs

Copper (Cu) is an essential trace element for all living organisms and used as cofactor in key enzymes of important biological processes, such as aerobic respiration or superoxide dismutation. However, due to its toxicity, cells have developed elaborate mechanisms for Cu homeostasis, which balance Cu supply for cuproprotein biogenesis with the need to remove excess Cu. This review summarizes our current knowledge on bacterial Cu homeostasis with a focus on Gram-negative bacteria and describes the multiple strategies that bacteria use for uptake, storage and export of Cu. We furthermore describe general mechanistic principles that aid the bacterial response to toxic Cu concentrations and illustrate dedicated Cu relay systems that facilitate Cu delivery for cuproenzyme biogenesis. Progress in understanding how bacteria avoid Cu poisoning while maintaining a certain Cu quota for cell proliferation is of particular importance for microbial pathogens because Cu is utilized by the host immune system for attenuating pathogen survival in host cells.

nosX is essential for whole-cell N2O reduction in Paracoccus denitrificans but not for assembly of copper centres of nitrous oxide reductase

Nitrous oxide (N₂O) is a potent greenhouse gas that is produced naturally as an intermediate during the process of denitrification carried out by some soil bacteria. It is consumed by nitrous oxide reductase (N₂OR), the terminal enzyme of the denitrification pathway, which catalyses a reduction reaction to generate dinitrogen. N₂OR contains two important copper cofactors (Cu_A and Cu_Z centres) that are essential for activity, and in copper-limited environments, N₂OR fails to function, contributing to rising levels of atmospheric N₂O and a major environmental challenge. Here we report studies of nosX, one of eight genes in the nos cluster of the soil dwelling α-proteobaterium Paraccocus denitrificans. A P. denitrificans ΔnosX deletion mutant failed to reduce N₂O under both copper-sufficient and copper-limited conditions, demonstrating that NosX plays an essential role in N₂OR activity. N₂OR isolated from nosX-deficient cells was found to be unaffected in terms of the assembly of its copper cofactors, and to be active in in vitro assays, indicating that NosX is not required for the maturation of the enzyme; in particular, it plays no part in the assembly of either of the Cu_A and Cu_Z centres. Furthermore, quantitative Reverse Transcription PCR (qRT-PCR) studies showed that NosX does not significantly affect the expression of the N₂OR-encoding nosZ gene. NosX is a homologue of the FAD-binding protein ApbE from Pseudomonas stutzeri, which functions in the flavinylation of another N₂OR accessory protein, NosR. Thus, it is likely that NosX is a system-specific maturation factor of NosR, and so is indirectly involved in maintaining the reaction cycle of N₂OR and cellular N₂O reduction.

The effect of pH on Marinobacter hydrocarbonoclasticus denitrification pathway and nitrous oxide reductase

Increasing atmospheric concentration of N₂O has been a concern, as it is a potent greenhouse gas and promotes ozone layer destruction. In the N-cycle, release of N₂O is boosted upon a drop of pH in the environment. Here, Marinobacter hydrocarbonoclasticus was grown in batch mode in the presence of nitrate, to study the effect of pH in the denitrification pathway by gene expression profiling, quantification of nitrate and nitrite, and evaluating the ability of whole cells to reduce NO and N₂O. At pH 6.5, accumulation of nitrite in the medium occurs and the cells were unable to reduce N₂O. In addition, the biochemical properties of N₂O reductase isolated from cells grown at pH 6.5, 7.5 and 8.5 were compared for the first time. The amount of this enzyme at acidic pH was lower than that at pH 7.5 and 8.5, pinpointing to a post-transcriptional regulation, though pH did not affect gene expression of N₂O reductase accessory genes. N₂O reductase isolated from cells grown at pH 6.5 has its catalytic center mainly as CuZ(4Cu1S), while that from cells grown at pH 7.5 or 8.5 has it as CuZ(4Cu2S). This study evidences that an in vivo secondary level of regulation is required to maintain N₂O reductase in an active state.

Biochar as electron donor for reduction of N2O by Paracoccus denitrificans

Biochar (BC) has been shown to influence microbial denitrification and mitigate soil N2O emissions. However, it is unclear if BC is able to directly stimulate the microbial reduction of N2O to N2. We hypothesized that the ability of BC to lower N2O emissions could be related not only to its ability to store electrons, but to donate them to bacteria that enzymatically reduce N2O. Therefore, we carried out anoxic incubations with Paracoccus denitrificans, known amounts of N2O, and nine contrasting BCs, in the absence of any other electron donor or acceptor. We found a strong and direct correlation between the extent and rates of N2O reduction with BC's EDC/EEC (electron donating capacity/electron exchange capacity). Apart from the redox capacity, other BC properties were found to regulate the BC's ability to increase N2O reduction by P. denitrificans. For this specific BC series, we found that a high H/C and ash content, low surface area and poor lignin feedstocks favored N2O reduction. This provides valuable information for producing tailored BCs with the potential to assist and promote the reduction of N2O in the pursuit of reducing this greenhouse gas emissions.

Impact of Electronic and Steric Changes of Ligands on the Assembly, Stability, and Redox Activity of Cu4(μ4-S) Model Compounds of the CuZ Active Site of Nitrous Oxide Reductase (N2OR)

Model compounds have been widely utilized in understanding the structure and function of the unusual Cu₄(μ₄-S) active site (Cu_Z) of nitrous oxide reductase (N₂OR). However, only a limited number of model compounds that mimic both structural and functional features of Cu_Z are available, limiting insights about Cu_Z that can be gained from model studies. Our aim has been to construct Cu₄(μ₄-S) clusters with tailored redox activity and chemical reactivity via modulating the ligand environment. Our synthetic approach uses dicopper(I) precursor complexes (Cu₂L₂) that assemble into a Cu₄(μ₄-S)L₄ cluster with the addition of an appropriate sulfur source. Here, we summarize the features of the ligands L that stabilize precursor and Cu₄(μ₄-S) clusters, along with the alternative products that form with inappropriate ligands. The precursors are more likely to rearrange to Cu₄(μ₄-S) clusters when the Cu(I) ions are supported by bidentate ligands with 3-atom bridges, but steric and electronic features of the ligand also play crucial roles. Neutral phosphine donors have been found to stabilize Cu₄(μ₄-S) clusters in the 4Cu(I) oxidation state, while neutral nitrogen donors could not stabilize Cu₄(μ₄-S) clusters. Anionic formamidinate ligands have been found to stabilize Cu₄(μ₄-S) clusters in the 2Cu(I):2Cu(II) and 3Cu(I):1Cu(II) states, with both the formation of the dicopper(I) precursors and subsequent assembly of clusters being governed by the steric factor at the ortho positions of the N-aryl substituents. Phosphaamidinates, which combine a neutral phosphine donor and an anionic nitrogen donor in the same ligand, form multinuclear Cu(I) clusters unless the negative charge is valence-trapped on nitrogen, in which case the resulting dicopper precursor is unable to rearrange to a multinuclear cluster. Taken together, the results presented in this study provide design criteria for successful assembly of synthetic model clusters for the Cu_Z active site of N₂OR, which should enable future insights into the chemical behavior of Cu_Z.

Proton-coupled electron transfer mechanisms of the copper centres of nitrous oxide reductase from Marinobacter hydrocarbonoclasticus - An electrochemical study

Reduction of N₂O to N₂ is catalysed by nitrous oxide reductase in the last step of the denitrification pathway. This multicopper enzyme has an electron transferring centre, CuA, and a tetranuclear copper-sulfide catalytic centre, "CuZ", which exists as CuZ*(4Cu1S) or CuZ(4Cu2S). The redox behaviour of these metal centres in Marinobacter hydrocarbonoclasticus nitrous oxide reductase was investigated by potentiometry and for the first time by direct electrochemistry. The reduction potential of CuA and CuZ(4Cu2S) was estimated by potentiometry to be +275 ± 5 mV and +65 ± 5 mV vs SHE, respectively, at pH 7.6. A proton-coupled electron transfer mechanism governs CuZ(4Cu2S) reduction potential, due to the protonation/deprotonation of Lys397 with a pK_ox of 6.0 ± 0.1 and a pK_red of 9.2 ± 0.1. The reduction potential of CuA, in enzyme samples with CuZ*(4Cu1S), is controlled by protonation of the coordinating histidine residues in a two-proton coupled electron transfer process. In the cyclic voltammograms, two redox pairs were identified corresponding to CuA and CuZ(4Cu2S), with no additional signals being detected that could be attributed to CuZ*(4Cu1S). However, an enhanced cathodic signal for the activated enzyme was observed under turnover conditions, which is explained by the binding of nitrous oxide to CuZ⁰(4Cu1S), an intermediate species in the catalytic cycle.

Effects of cobalt-histidine absorbent on aerobic denitrification by Paracoccus versutus LYM

To overcome the problem that ferrous complexes are easily oxidized by O₂ and then lose NO binding ability in the chemical absorption-biological reduction (CABR) process, cobalt(II)-histidine [Co(II)His] was proposed as an alternative. To evaluate the applicability of Co(II)His, the effects of CoHis absorbent on the aerobic denitrification by Paracoccus versutus LYM were investigated. Results indicated that His significantly promoted nitrite reduction. The inhibition effects of CoHis absorbent could be substantially alleviated by increasing the initial His/Co²⁺ to 4 or higher. CoHis with concentrations of 4, 8, 12, 16 and 20 mM presented no distinct effect on nitrite reduction, but slightly inhibited the reduction of nitrate, resulting in longer lag of nitrate reduction, and obviously promoted the growth of strain LYM. In the presence of 5, 10, 15 and 20 mM CoHis absorbent, the main denitrification product was N₂ (not less than 95.0%). This study is of significance in verifying the applicability of Co(II)His in the CABR process, and provides a referable CoHis absorbent concentration as 20 mM with an initial His/Co²⁺ of 4 for the future experiments.

Catalytic M Center of Copper Monooxygenases Probed by Rational Design. Effects of Selenomethionine and Histidine Substitution on Structure and Reactivity

The M centers of the mononuclear monooxygenases peptidylglycine monooxygenase (PHM) and dopamine β-monooxygenase bind and activate dioxygen en route to substrate hydroxylation. Recently, we reported the rational design of a protein-based model in which the CusF metallochaperone was repurposed via a His to Met mutation to act as a structural and spectroscopic biomimic. The PHM M site exhibits a number of unusual attributes, including a His₂Met ligand set, a fluxional Cu(I)-S(Met) bond, tight binding of exogenous ligands CO and N₃^-, and complete coupling of oxygen reduction to substrate hydroxylation even at extremely low turnover rates. In particular, mutation of the Met ligand to His completely eliminates the catalytic activity despite the propensity of Cu^I-His₃ centers to bind and activate dioxygen in other metalloenzyme systems. Here, we further develop the CusF-based model to explore methionine variants in which Met is replaced by selenomethionine (SeM) and histidine. We examine the effects on coordinate structure and exogenous ligand binding via X-ray absorption spectroscopy and electron paramagnetic resonance and probe the consequences of mutations on redox chemistry via studies of the reduction by ascorbate and oxidation via molecular oxygen. The M-site model is three-coordinate in the Cu(I) state and binds CO to form a four-coordinate carbonyl. In the oxidized forms, the coordination changes to tetragonal five-coordinate with a long axial Met ligand that like the enzymes is undetectable at either the Cu or Se K edges. The EXAFS data at the Se K edge of the SeM variant provide unique information about the nature of the Cu-methionine bond that is likewise weak and fluxional. Kinetic studies document the sluggish reactivity of the Cu(I) complexes with molecular oxygen and rapid rates of reduction of the Cu(II) complexes by ascorbate, indicating a remarkable stability of the Cu(I) state in all three derivatives. The results show little difference between the Met ligand and its SeM and His congeners and suggest that the Met contributes to catalysis in ways that are more complex than simple perturbation of the redox chemistry. Overall, the results stimulate a critical re-examination of the canonical reaction mechanisms of the mononuclear copper monooxygenases.

Bacterial nitrous oxide respiration: electron transport chains and copper transfer reactions

Biologically catalyzed nitrous oxide (N₂O, laughing gas) reduction to dinitrogen gas (N₂) is a desirable process in the light of ever-increasing atmospheric concentrations of this important greenhouse gas and ozone depleting substance. A diverse range of bacterial species produce the copper cluster-containing enzyme N₂O reductase (NosZ), which is the only known enzyme that converts N₂O to N₂. Based on phylogenetic analyses, NosZ enzymes have been classified into clade I or clade II and it has turned out that this differentiation is also applicable to nos gene clusters (NGCs) and some physiological traits of the corresponding microbial cells. The NosZ enzyme is the terminal reductase of anaerobic N₂O respiration, in which electrons derived from a donor substrate are transferred to NosZ by means of an electron transport chain (ETC) that conserves energy through proton motive force generation. This chapter presents models of the ETCs involved in clade I and clade II N₂O respiration as well as of the respective NosZ maturation and maintenance processes. Despite differences in NGCs and growth yields of N₂O-respiring microorganisms, the deduced bioenergetic framework in clade I and clade II N₂O respiration is assumed to be equivalent. In both cases proton motive quinol oxidation by N₂O is thought to be catalyzed by the Q cycle mechanism of a membrane-bound Rieske/cytochrome bc complex. However, clade I and clade II organisms are expected to differ significantly in terms of auxiliary electron transport processes as well as NosZ active site maintenance and repair.

NosL is a dedicated copper chaperone for assembly of the CuZ center of nitrous oxide reductase

Nitrous oxide reductase (N₂OR) is the terminal enzyme of the denitrification pathway of soil bacteria that reduces the greenhouse gas nitrous oxide (N₂O) to dinitrogen. In addition to a binuclear Cu_A site that functions in electron transfer, the active site of N₂OR features a unique tetranuclear copper cluster bridged by inorganic sulfide, termed Cu_Z. In copper-limited environments, N₂OR fails to function, resulting in truncation of denitrification and rising levels of N₂O released by cells to the atmosphere, presenting a major environmental challenge. Here we report studies of nosL from Paracoccus denitrificans, which is part of the nos gene cluster, and encodes a putative copper binding protein. A Paracoccus denitrificans ΔnosL mutant strain had no denitrification phenotype under copper-sufficient conditions but failed to reduce N₂O under copper-limited conditions. N₂OR isolated from ΔnosL cells was found to be deficient in copper and to exhibit attenuated activity. UV-visible absorbance spectroscopy revealed that bands due to the Cu_A center were unaffected, while those corresponding to the Cu_Z center were significantly reduced in intensity. In vitro studies of a soluble form of NosL without its predicted membrane anchor showed that it binds one Cu(i) ion per protein with attomolar affinity, but does not bind Cu(ii). Together, the data demonstrate that NosL is a copper-binding protein specifically required for assembly of the Cu_Z center of N₂OR, and thus represents the first characterised assembly factor for the Cu_Z active site of this key environmental enzyme, which is globally responsible for the destruction of a potent greenhouse gas.

HYSCORE Insights into the Distribution of the Unpaired Spin Density in an Engineered CuA Site in Azurin and Its His120Gly Variant

A comparative study of the ¹H and ¹⁴N hyperfine interactions between the Cu_A site in an engineered Cu_A center in azurin (WT-Cu_AAz) and its His120Gly variant (H120G-Cu_AAz) using the two-dimensional ESEEM technique, HYSCORE, is reported. HYSCORE spectroscopy has clarified conflicting results in previous electron paramagnetic resonance (EPR) and electron nuclear double resonance (ENDOR) studies and found clear differences between the two Cu_A azurins. Specifically, a hyperfine coupling A_N⊥ of 15.3 MHz was determined for the first time from the frequencies of double-quantum transitions of ¹⁴N histidine nitrogens coordinated to Cu_A in WT-Cu_AAz. In contrast, such coupling was not observed in the spectra of H120G-Cu_AAz, indicating at least a several megahertz increase in A_N⊥ for the coordinated nitrogen in this variant. In addition, ¹⁴N HYSCORE spectra of WT-Cu_AAz show interaction with only one type of weakly coupled nitrogen assigned to the remote N_ε atom of coordinated imidazole residues based on the quadrupole coupling constant ( e² Qq/4 h) of ∼0.4 MHz. The spectrum of H120G-Cu_AAz resolves additional features typical for backbone peptide nitrogens with larger e² Qq/4 h values of ∼0.7 MHz. Hyperfine couplings with these nitrogens vary between ∼0.4 and 0.7 MHz. In addition, the two resolved cross-peaks from C_β protons in H120G-Cu_AAz display only ∼1 MHz shifts relative to the corresponding peaks in WT-Cu_AAz. These new findings have provided the first experimental evidence of the previous density functional theory analysis that predicted changes in the delocalized electron spin population of ∼0.02-0.03 (i.e., ∼10%) on copper and sulfur atoms of the Cu_A center in H120 variants relative to WT-Cu_AAz and resolved contradicting results between EPR and ENDOR studies of the valence distribution in Cu_AAz and its variants.

Lewis Acid-Mediated One-Electron Reduction of Nitrous Oxide

The one-electron reduction of nitrous oxide (N₂ O) was achieved using strong Lewis acids E(C₆ F₅ )₃ (E=B or Al) in combination with metallocenes. In the case of B(C₆ F₅ )₃ , electron transfer to N₂ O required a powerful reducing agent such as Cp*₂ Co (Cp*=pentamethylcyclopentadienyl). In the presence of Al(C₆ F₅ )₃ , on the other hand, the reactions could be performed with weaker reducing agents such as Cp*₂ Fe or Cp₂ Fe (Cp=cyclopentadienyl). The Lewis acid-mediated electron transfer from the metallocene to N₂ O resulted in cleavage of the N-O bond, generating N₂ and the oxyl radical anion [OE(C₆ F₅ )₃ ]^⋅- . The latter is highly reactive and engages in C-H activation reactions. It was possible to trap the radical by addition of the Gomberg dimer, which acts as a source of the trityl radical.