Nitrite Binding Research Articles

Exploring hydrodynamic cavitation for citrus waste valorisation in Malta: from beverage enhancement to potato sprouting suppression and water remediation.

Introduction: The endorsement of circular economy, zero-waste, and sustainable development by the EU and UN has promoted non-thermal technologies in agro-food and health industries. While northern European countries rapidly integrate these technologies, their implementation in Mediterranean food-supply chains remains uncertain. Aims: We evaluated the usefulness of hydrodynamic cavitation (HC) for valorizing orange peel waste in the fresh orange juice supply chain of the Maltese Islands. Method: We assessed: a) the effectiveness of HC in extracting bioactive compounds from orange peels (Citrus sinensis) in water (35°C) and 70% (v/v) ethanol (-10°C) over time, compared to conventional maceration, and b) the potato sprouting-suppression and biosorbent potential of the processed peel for copper, nitrate, and nitrite binding. Results: Prolonged HC-assisted extractions in water (high cavitation numbers), damaged and/or oxidized bioactive compounds, with flavonoids and ascorbic acid being more sensitive, whereas cold ethanolic extractions preserved the compounds involved in radical scavenging. HC-processing adequately modified the peel, enabling its use as a potato suppressant and biosorbent for copper, nitrate, and nitrite. Conclusion: Coupling HC-assisted bioactive compound extractions with using leftover peel for potato-sprouting prevention and as biosorbent for water pollutant removal offers a straightforward approach to promoting circular economic practices and sustainable agriculture in Malta.

Study of NIT domain-containing chemoreceptors from two global phytopathogens and identification of NIT domains in eukaryotes.

Bacterial signal transduction systems are typically activated by the binding of signal molecules to receptor ligand binding domains (LBDs), such as the NIT LBD. We report here the identification of the NIT domain in more than 15,000 receptors that were present in 30 bacterial phyla, but also in 19 eukaryotic phyla, expanding its known phylogenetic distribution. The NIT domain formed part of seven receptor families that either control transcription, mediate chemotaxis or regulate second messenger levels. We have produced the NIT domains from chemoreceptors of the bacterial phytopathogens Pectobacterium atrosepticum (PacN) and Pseudomonas savastanoi (PscN) as individual purified proteins. High-throughput ligand screening using compound libraries revealed a specificity for nitrate and nitrite binding. Isothermal titration calorimetry experiments showed that PacN-LBD bound preferentially nitrate ( K D = 1.9 μM), whereas the affinity of PscN-LBD for nitrite ( K D = 2.1 μM) was 22 times higher than that for nitrate. Analytical ultracentrifugation experiments indicated that PscN-LBD is monomeric in the presence and absence of ligands. The R182A mutant of PscN did not bind nitrate or nitrite. This residue is not conserved in the NIT domain of the Pseudomonas aeruginosa chemoreceptor PA4520, which may be related to its failure to bind nitrate/nitrite. The magnitude of P. atrosepticum chemotaxis towards nitrate was significantly greater than that of nitrite and pacN deletion almost abolished responses to both compounds. This study highlights the important role of nitrate and nitrite as signal molecules in life and advances our knowledge on the NIT domain as universal nitrate/nitrite sensor module.

The effect of pH and nitrite on the haem pocket of GLB-33, a globin-coupled neuronal transmembrane receptor of Caenorhabditis elegans

Out of the 34 globins in Caenorhabditis elegans, GLB-33 is a putative globin-coupled transmembrane receptor with a yet unknown function. The globin domain (GD) contains a particularly hydrophobic haem pocket, that rapidly oxidizes to a low-spin hydroxide-ligated haem state at physiological pH. Moreover, the GD has one of the fastest nitrite reductase activity ever reported for globins. Here, we use a combination of electronic circular dichroism, resonance Raman and electron paramagnetic resonance (EPR) spectroscopy with mass spectrometry to study the pH dependence of the ferric form of the recombinantly over-expressed GD in the presence and absence of nitrite. The competitive binding of nitrite and hydroxide is examined as well as nitrite-induced haem modifications at acidic pH. Comparison of the spectroscopic results with data from other haem proteins allows to deduce the important effect of Arg at position E10 in stabilization of exogenous ligands. Furthermore, continuous-wave and pulsed EPR indicate that ligation of nitrite occurs in a nitrito mode at pH 5.0 and above. At pH 4.0, an additional formation of a nitro-bound haem form is observed along with fast formation of a nitri-globin.

Effects of steam explosion on phenolic compounds and dietary fiber of grape pomace

Steam explosion (SE), as a high-efficient and environment-friendly pretreatment technology, was applied to pretreat the grape pomace. The results showed that SE increased the yield of free phenolics and flavonoids, but decreased the yield of bound phenolics and flavonoids. The content of total phenolics from grape pomace was much higher than that of total flavonoids. SE significantly decreased the contents of total monomeric anthocyanins and non-extractable proanthocyanins. (−)-Epicatechin and catechin were the most abundant ingredients in free extracts. After SE, most phenolic acids and flavonoids in the free extracts showed an increasing trend, while it is opposite in the bound extracts. SE increased the antioxidant activity of free extracts, but decreased the antioxidant activity of the bound extracts. SE can convert insoluble dietary fiber (IDF) into soluble dietary fiber (SDF) from grape pomace, and increase the oil-holding capacity (OHC) and sodium nitrite binding capacity (SNBC) of SDF. It can be concluded that an optimal SE condition at 1.2 MPa for 1 min could maximally increase the release of the phenolic compounds and enhance the antioxidant capacity; and the optimal SE condition for the extraction, OHC and SNBC of SDF in grape pomace was at 0.8 MPa for 3 min.

PdCu Electrocatalysts for Selective Nitrate and Nitrite Reduction to Nitrogen

Electrocatalytic conversion of nitrate in waste can enable efficient waste remediation (NO3– to N2) or waste valorization (NO3– to NH4+) depending on the selectivity of the catalyst. Palladium and copper electrocatalysts typically exhibit ideal nitrate and nitrite binding properties, allowing for effective destruction of nitrate. However, rational steering of selectivity through material design remains a critical challenge for PdCu electrocatalyst. Here, we use the electrochemical underpotential deposition method to synthesize palladium nanocube electrocataysts with controlled copper surface coverage (e.g., partial and full copper coatings). We then examine the potential for NO3– destruction (conversion) and NO2– reduction reaction. We identify that partial copper-coated Pd nanocubes not only effectively facilitate the reduction of 95% of NO3– but also increase the reduction of NO2– to N2 with 89% selectivity over 20 consecutive cycles (80 h). We also show that under these conditions, the Pd(100) surface facet is exposed. Complete copper-covered Pd nanocubes effectively facilitate the reduction of ∼99% of NO3–. Complete coverage of copper; however, prevented exposure of Pd(100) surface facet, promoting the selective reduction of NO2– to NH4+ with a 70% selectivity over 20 consecutive cycles (80 h). Density functional theory (DFT) calculations show that NO3– and NO2– adsorb more strongly on the Cu(100) surface compared to the Pd(100) surface, while the NO* intermediate generated from NO3– or NO2– reduction adsorbs more strongly on the Pd surface. Barrier calculations show that NO* can readily migrate from the Cu domain to the Pd domain and that the N–N coupling barrier on Pd is significantly diminished at high NO* coverage. Together, these results suggest that the high N2 selectivity observed on the PdCu electrocatalyst is caused by the spillover of NO* from the Cu domains to the Pd domains.

Role of Electronic Structure on Nitrate Reduction to Ammonium: A Periodic Journey.

Electrocatalysis is a promising approach to convert waste nitrate to ammonia and help close the nitrogen cycle. This renewably powered ammonia production process sources hydrogen from water (as opposed to methane in the thermal Haber-Bosch process) but requires a delicate balance between a catalyst's activity for the hydrogen evolution reaction (HER) and the nitrate reduction reaction (NO3RR), influencing the Faradaic efficiency (FE) and selectivity to ammonia/ammonium over other nitrogen-containing products. We measure ammonium FEs ranging from 3.6 ± 6.6% (on Ag) to 93.7 ± 0.9% (on Co) across a range of transition metals (TMs; Ti, Fe, Co, Ni, Ni0.68Cu0.32, Cu, and Ag) in buffered neutral media. To better understand these competing reaction kinetics, we develop a microkinetic model that captures the voltage-dependent nitrate rate order and illustrates its origin as competitive adsorption between nitrate and hydrogen adatoms (H*). NO3RR FE can be described via competition for electrons with the HER, decreasing sharply for TMs with a high work function and a correspondingly high HER activity (e.g., Ni). Ammonium selectivity nominally increases as the TM d-band center energy (Ed) approaches and overcomes the Fermi level (EF), but is exceptionally high for Co compared to materials with similar Ed. Density functional theory (DFT) calculations indicate Co maximizes ammonium selectivity via (1) strong nitrite binding enabling subsequent reduction and (2) promotion of nitric oxide dissociation, leading to selective reduction of the nitrogen adatom (N*) to ammonium.

Influence of heme propionates on the nitrite reductase activity of myoglobin

The heme propionates in myoglobin (Mb) form a H-bonding network among several residues within its second-sphere coordination, providing a key structural role towards Mb's functional properties. Our work aims to understand the role of the heme propionates on the nitrite reductase (NiR) activity (e.g. reduction of NO2− to NO) of this globin by studying an artificial dimethylester heme-substituted horse heart Mb (DME-Mb). The minor structural change brought about by esterification of the heme propionates causes the NiR rate to increase by more than over two-fold (5.6 ± 0.1 M−1 s−1) relative to wildtype (wt) Mb (2.3 ± 0.1 M−1 s−1). The lower pKa observed in DME-Mb may enhance the tendency of His64 towards protonation, therefore increasing the NiR rate. In addition, the nitrite binding constant (Knitrite) for DME-MbIII is greater than wt MbIII (350 M−1 versus 120 M−1). The disparity in the NiR activity correlates with the differences in electrostatic behavior, which influences the system's reactivity towards the approaching NO2− ion, and thus the formation of the FeII-NO2− intermediate.

QM/MM Simulations of Protein Crystal Reactivity Guided by MSOX Crystallography: A Copper Nitrite Reductase Case Study.

The recently developed multiple structures from one crystal (MSOX) serial crystallography method can be used to provide multiple snapshots of the progress of enzymatic reactions taking place within a protein crystal. Such MSOX snapshots can be used as a reference for combined quantum mechanical/molecular mechanical (QM/MM) simulations of enzyme reactivity within the crystal. QM/MM calculations are used to identify details of reference states that cannot be directly observed by X-ray diffraction experiments, such as protonation and oxidation states. These reference states are then used as known fixed endpoints for the modeling of reaction paths. We investigate the mechanism of nitrite reduction in an Achromobacter cycloclastes copper nitrite reductase crystal using MSOX-guided QM/MM calculations, identifying the change in nitrite binding orientation with a change in copper oxidation state, and determining the reaction path to the final NO-bound MSOX structure. The results are compared with QM/MM simulations performed in a solvated environment.

Influence of the heme distal pocket on nitrite binding orientation and reactivity in Sperm Whale myoglobin.

Nitrite binding to recombinant wild-type Sperm Whale myoglobin (SWMb) was studied using a combination of spectroscopic methods including room-temperature magnetic circular dichroism. These revealed that the reactive species is free nitrous acid and the product of the reaction contains a nitrite ion bound to the ferric heme iron in the nitrito- (O-bound) orientation. This exists in a thermal equilibrium with a low-spin ground state and a high-spin excited state and is spectroscopically distinct from the purely low-spin nitro- (N-bound) species observed in the H64V SWMb variant. Substitution of the proximal heme ligand, histidine-93, with lysine yields a novel form of myoglobin (H93K) with enhanced reactivity towards nitrite. The nitrito-mode of binding to the ferric heme iron is retained in the H93K variant again as a thermal equilibrium of spin-states. This proximal substitution influences the heme distal pocket causing the pKa of the alkaline transition to be lowered relative to wild-type SWMb. This change in the environment of the distal pocket coupled with nitrito-binding is the most likely explanation for the 8-fold increase in the rate of nitrite reduction by H93K relative to WT SWMb.

Modification of insoluble dietary fiber from ginger residue through enzymatic treatments to improve its bioactive properties

To add value ginger residues containing insoluble dietary fiber (IDF), multiple enzymes were used to obtain modified insoluble dietary fiber (MIDF). The water retention capacity (WRC), water swelling capacity (WSC) and oil binding capacity (OBC) for lard of MIDF were 22.45%, 33.85% and 36.26% higher than those of IDF, respectively. Meanwhile, MIDF showed higher cation exchange capacity (CEC) than that of IDF. Cholesterol, sodium cholate and sodium nitrite binding capacity (CBC, SCBC, SNBC) of MIDF were 70.28%, 42.07% and 15.9% higher than those of IDF at pH 7, respectively. And CBC and SNBC were 21.18% and 12.17% higher than those of IDF at pH 2, respectively. Compared to IDF, MIDF exposed more hydrophilic groups and more specific surface areas. The oral administration showed that MIDF significantly reduced total cholesterol (TC), triglyceride (TG) and atherogenic index (AI) by 12.23%, 25.15% and 60.63%, respectively (P < 0.05), but significantly increased the high density lipoprotein-cholesterol (HDL-C) by 32.93% to the normal level (P < 0.05). Furthermore, histopathology of liver also indicated that MIDF could reduce the risk of fatty liver. These properties demonstrated that MIDF showed better physicochemical and functional properties than IDF. Thus MIDF would be a potentially available food ingredient in weight-loss functional food processing.

Europium (III) complexes of amino acid-derived bis-imine-substituted phenanthroline ligands for phosphate recognition

Phenanthroline-based chiral hexadentate ligands L1, L2 and L3, as well as their europium (III) complexes 1–3 are synthesized and characterized. The coordination compounds show strong red emission typical for europium (III) derivatives. Various anionic species, F−, Cl−, Br−, I−, SO42−, NO3−, NO2−, HPO42−, CO32−, HCO3− and OAc−, are employed to evaluate the chemo-sensor properties of the complexes using fluorescence spectroscopy. For complex 1, only the addition of HPO42− leads to quenching of luminescence. For the other complexes 2 and 3, NO2− and HPO42− exhibit a strong response in the emission properties. However, complexes 2 and 3 are found to be more sensitive for HPO42− than for NO2−. The corresponding binding constants (logKβ) of the adducts are determined using the Benesi-Hildebrand method. The described studies show that the europium(III) complexes of the hexadentate ligands L1-3 can be considered as highly specific sensors for the recognition of phosphates with some competition by NO2− ions. While phosphate binding is strong in all three examples, the sensitivity for nitrite increases in the order 1 < 2 < 3. The obtained results are remarkable because the differences are due to less sterically hindered substituents in the periphery of the ligand of 2 and 3, which enable the binding of the small nitrite while the bigger phosphate is bound less tightly.

The dual roles of a V(III) centre for substrate binding and oxygen atom abstraction; nitrite reduction mediated by a V(III) complex.

A V(iii) complex bearing a tris(thiolato)phoshine derivative mediates the reduction of nitrite without the assistance of external protons or oxophilic substrates. The metal site plays dual roles for nitrite binding and deoxygenation. The reaction is monitored by spectroscopy combined with isotopic labeling experiments. The formed product, a {VNO}4 species, is isolated and characterized.

Nitrosyl Myoglobins and Their Nitrite Precursors: Crystal Structural and Quantum Mechanics and Molecular Mechanics Theoretical Investigations of Preferred Fe -NO Ligand Orientations in Myoglobin Distal Pockets.

The globular dioxygen binding heme protein myoglobin (Mb) is present in several species. Its interactions with the simple nitrogen oxides, namely, nitric oxide (NO) and nitrite, have been known for decades, but the physiological relevance has only recently become more fully appreciated. We previously reported the O-nitrito mode of binding of nitrite to ferric horse heart wild-type (wt) MbIII and human hemoglobin. We have expanded on this work and report the interactions of nitrite with wt sperm whale (sw) MbIII and its H64A, H64Q, and V68A/I107Y mutants whose dissociation constants increase in the following order: H64Q < wt < V68A/I107Y < H64A. We also report their X-ray crystal structures that reveal the O-nitrito mode of binding of nitrite to these derivatives. The MbII-mediated reductions of nitrite to NO and structural data for the wt and mutant MbII-NOs are described. We show that their FeNO orientations vary with distal pocket identity, with the FeNO moieties pointing toward the hydrophobic interiors when the His64 residue is present but toward the hydrophilic exterior when this His64 residue is absent in this set of mutants. This correlates with the nature of H-bonding to the bound NO ligand (nitrosyl O vs N atom). Quantum mechanics and hybrid quantum mechanics and molecular mechanics calculations help elucidate the origin of the experimentally preferred NO orientations. In a few cases, the calculations reproduce the experimentally observed orientations only when the whole protein is taken into consideration.

The Reaction of Oxy Hemoglobin with Nitrite: Mechanism, Antioxidant-Modulated Effect, and Implications for Blood Substitute Evaluation.

The autocatalytic reaction between nitrite and the oxy form of globins involves free radicals. For myoglobin (Mb), an initial binding of nitrite to the iron-coordinated oxygen molecule was proposed; the resulting ferrous-peroxynitrate species was not detected, but its decay product, the high-valent ferryl form, was demonstrated in stopped-flow experiments. Reported here are the stopped flow spectra recorded upon mixing oxy Hb (native, as well as chemically-derivatized in the form of several candidates of blood substitutes) with a supraphysiological concentration of nitrite. The data may be fitted to a simple kinetic model involving a transient met-aqua form, in contrast to the ferryl detected in the case of Mb in a similar reaction sequence. These data are in line with a previous observation of a transient accumulation of ferryl Hb under auto-catalytic conditions at much lower concentrations of nitrite (Grubina, R. et al. J. Biol. Chem. 2007, 282, 12916). The simple model for fitting the stopped-flow data leaves a small part of the absorbance changes unaccounted for, unless a fourth species is invoked displaying features similar to the oxy and tentatively assigned as ferrous-peroxynitrate. Density functional theory (DFT) calculations support this latter assignment. The reaction allows for differentiating between the reactivities of various chemically modified hemoglobins, including candidates for blood substitutes. Polymerization of hemoglobin slows the nitrite-induced oxidation, in sharp contrast to oxidative-stress type reactions which are generally accelerated, not inhibited. Sheep hemoglobin is found to be distinctly more resistant to reaction with nitrite compared to bovine Hb, at large nitrite concentrations (stopped-flow experiments directly observing the oxy + nitrite reaction) as well as under auto-catalytic conditions. Copolymerization of Hb with bovine serum albumin (BSA) using glutaraldehyde leads to a distinct increase of the lag time compared to native Hb as well as to any other form of derivatization examined in the present study. The Hb-BSA copolymer also displays a slower initial reaction with nitrite under stopped-flow conditions, compared to native Hb.

A Copper(II) Nitrite That Exhibits Change of Nitrite Binding Mode and Formation of Copper(II) Nitrosyl Prior to Nitric Oxide Evolution.

The proton-coupled reduction of CuII-bound nitrite (NO2-) to nitric oxide (NO2- + 2H+ + e- → NO(g) + H2O), such as occurs in the enzyme copper nitrite reductase, is investigated in this work. Our studies focus on the copper(II/I) model complexes [(L2)Cu(H2O)Cl] (1), [(L2)Cu(ONO)] (2), [(L2)Cu(CH3CO2)] (3), and [Co(Cp)2][(L2)Cu(NO2)(CH3CN] (4), where HL2 = N-[2-(methylthio)ethyl]-2'-pyridinecarboxamide. Complex 1 readily reacts with a NO2- anion to form the nitrito-O-bound copper(II) complex 2. Electrochemical reduction of CuII → CuI indicates coordination isomerization from asymmetric nitrito-κ2-O,O to nitro-κ1-N. Isolation and spectroscopic characterization of 4 support this notion of nitrite coordination isomerization (νCu-N ∼ 460 cm-1). A reduction of 2, followed by reaction with acetic acid, causes evolution of stoichiometric NO via the transient copper(II) nitrosyl species and subsequent formation of the acetate-bound complex 3. The probable copper nitrosyl intermediate [(L2)Cu(NO)(CH3CN)]+ of the {CuNO}10 type is evident from low-temperature UV-vis absorption (λmax = 722 nm) and electron paramagnetic resonance spectroscopy. A density functional theory (DFT)-optimized model of [(L2)Cu(NO)(CH3CN)]+ shows end-on NO binding to Cu with Cu-N(NO) and N-O distances of 1.989 and 1.140 Å, respectively, and a Cu-N-O angle of 119.25°, consistent with the formulation of CuII-NO•. A spin-state change that triggers NO release is observed. Considering singlet- and triplet-state electronic configurations of this model, DFT-calculated νNO values of 1802 and 1904 cm-1, respectively, are obtained. We present here important mechanistic aspects of the copper-mediated nitrite reduction pathway with the use of model complexes employing the ligand HL2 and an analogous phenyl-based ligand, N-[2-(methylthio)phenyl]-2'-pyridinecarboxamide (HL1).

Potential for aerobic NO2- reduction and corresponding key enzyme genes involved in Alcaligenes faecalis strain NR.

The potential for aerobic NO2- removal by Alcaligenes faecalis strain NR was investigated. 35mg/L of NO2--N was removed by strain NR under aerobic conditions in the presence of NH4+. 15N-labeling experiment demonstrated that N2O and N2 were possible products during the aerobic nitrite removal process by strain NR. The key enzyme genes of nirK, norB and nosZ, which regulate the aerobic nitrite denitrification process, were successfully amplified from strain NR. The gene sequence analysis indicates that copper-containing nitrite reductase (NIRK) and periplasmic nitrous oxide reductase (NOSZ) were both hydrophilic protein and the transmembrane structures were absent, while nitric oxide reductase large subunit (NORB) was a hydrophobic and transmembrane protein. According to the three-dimensional structure and binding site analysis, the bulky and hydrophobic methionine residue proximity to the nitrite binding sites of NIRK was speculated to be related to the oxygen tolerance of NIRK from strain NR.

DFT Study on Enzyme Turnover Including Proton and Electron Transfers of Copper-Containing Nitrite Reductase.

The reaction mechanism of copper-containing nitrite reductase (CuNiR) has been proposed to include two important events, an intramolecular electron transfer and a proton transfer. The two events have been suggested to be coupled, but the order of these events is currently under debate. We investigated the entire enzyme reaction mechanism of nitrite reduction at the T2 Cu site in thermophilic Geobacillus CuNiR from Geobacillus thermodenitrificans NG80-2 (GtNiR) using density functional theory calculations. We found significant conformational changes of His ligands coordinated to the T2 Cu site upon nitrite binding during the catalytic reaction. The reduction potentials and pKa values calculated for the relevant protonation and reduction states show two possible routes, A and B. Reduction of the T2 Cu site in the resting state is followed by endothermic nitrite binding in route A, while exothermic nitrite binding occurs prior to reduction of the T2 Cu site in route B. We concluded that our results support the random-sequential mechanism rather than the ordered mechanism.

Cooperative binding and extraction of sodium nitrite by a ditopic receptor incorporated into a polymeric resin.

Simple ion pair receptors were synthesised and characterized in solution. The modular design of these receptors facilitated the preparation of a functionally analogous polymeric material able to extract sodium nitrite from acetonitrile solution.

The functional role of the structure of the dioxo-isobacteriochlorin in the catalytic site of cytochrome cd1 for the reduction of nitrite.

Cytochrome cd1 is a key enzyme in bacterial denitrification and catalyzes one-electron reduction of nitrite (NO2-) to nitric oxide (NO) at the heme d1 center under anaerobic conditions. The heme d1 has a unique dioxo-isobacteriochlorin structure and is present only in cytochrome cd1. To reveal the functional role of the unique heme d1 in the catalytic nitrite reduction, we studied effect of the porphyrin macrocycle on each reaction step of the catalytic cycle of cytochrome cd1 using synthetic model complexes. The complexes investigated are iron complexes of dioxo-octaethylisobacteriochlorin (1), mono-oxo-octaethylchlorin (2) and octaethylporphyrin (3). We show here that the reduction potential for the transition from the ferric state to the ferrous state and the binding constant for binding of NO2- to the ferrous complex increases with a trend of 3 < 2 < 1. However, the reactivity of the ferrous nitrite complex with protons increases in the reversed order, 1 < 2 < 3. We also show that the iron bound NO of the ferric NO complex is readily replaced by addition of 1 equiv. of p-nitrophenolate. These results indicate that the dioxo-isobacteriochlorin structure is superior to porphyrin and mono-oxo-chlorin structures in the first iron reduction step, the second nitrite binding step, and the NO dissociation step, but inferior in the third nitrite reduction step. These results suggest that the heme d1 has evolved as the catalytic site of cytochrome cd1 to catalyze the nitrite reduction at the highest possible redox potential while maintaining its catalytic activity.

DFT Study on Nitrite Reduction Mechanism in Copper-Containing Nitrite Reductase.

Dissimilatory reduction of nitrite by copper-containing nitrite reductase (CuNiR) is an important step in the geobiochemical nitrogen cycle. The proposed mechanisms for the reduction of nitrite by CuNiRs include intramolecular electron and proton transfers, and these two events are understood to couple. Proton-coupled electron transfer is one of the key processes in enzyme reactions. We investigated the geometric structure of bound nitrite and the mechanism of nitrite reduction on CuNiR using density functional theory calculations. Also, the proton transfer pathway, the key residues, and their roles in the reaction mechanism were clarified in this study. In our results, the reduction of T2 Cu site promotes the proton transfer, and the hydrogen bond network around the binding site has an important role not only to stabilize the nitrite binding but also to promote the proton transfer to nitrite.