Structure and properties of the catalytic site of nitric oxide reductase at ambient temperature

NO Coupling at Copper to cis-Hyponitrite: N2O Formation via Protonation and H-Atom Transfer

Copper nitrite reductases (CuNIRs) convert NO2- to NO as well as NO to N2O under high NO flux at a mononuclear type 2 Cu center. While model complexes illustrate N-N coupling from NO that results in symmetric trans-hyponitrite [CuII]-ONNO-[CuII] complexes, we report NO assembly at a single Cu site in the presence of an external reductant Cp*2M (M = Co, Fe) to give the first copper cis-hyponitrites [Cp*2M]{[CuII](κ2-O2N2)[CuI]}. Importantly, the κ1-N-bound [CuI] fragment may be easily removed by the addition of mild Lewis bases such as CNAr or pyridine to form the spectroscopically similar anion {[CuII](κ2-O2N2)}-. The addition of electrophiles such as H+ to these anionic copper(II) cis-hyponitrites leads to N2O generation with the formation of the dicopper(II)-bis-μ-hydroxide [CuII]2(μ-OH)2. One-electron oxidation of the {[CuII](κ2-O2N2)}- core turns on H-atom transfer reactivity, enabling the oxidation of 9,10-dihydroanthracene to anthracene with concomitant formation of N2O and [CuII]2(μ-OH)2. These studies illustrate both the reductive coupling of NO at a single copper center and a way to harness the strong oxidizing power of nitric oxide via the neutral cis-hyponitrite [Cu](κ2-O2N2).

Complex Interplay of Heme-Copper Oxidases with Nitrite and Nitric Oxide

Nitrite and nitric oxide (NO), two active and critical nitrogen oxides linking nitrate to dinitrogen gas in the broad nitrogen biogeochemical cycle, are capable of interacting with redox-sensitive proteins. The interactions of both with heme-copper oxidases (HCOs) serve as the foundation not only for the enzymatic interconversion of nitrogen oxides but also for the inhibitory activity. From extensive studies, we now know that NO interacts with HCOs in a rapid and reversible manner, either competing with oxygen or not. During interconversion, a partially reduced heme/copper center reduces the nitrite ion, producing NO with the heme serving as the reductant and the cupric ion providing a Lewis acid interaction with nitrite. The interaction may lead to the formation of either a relatively stable nitrosyl-derivative of the enzyme reduced or a more labile nitrite-derivative of the enzyme oxidized through two different pathways, resulting in enzyme inhibition. Although nitrite and NO show similar biochemical properties, a growing body of evidence suggests that they are largely treated as distinct molecules by bacterial cells. NO seemingly interacts with all hemoproteins indiscriminately, whereas nitrite shows high specificity to HCOs. Moreover, as biologically active molecules and signal molecules, nitrite and NO directly affect the activity of different enzymes and are perceived by completely different sensing systems, respectively, through which they are linked to different biological processes. Further attempts to reconcile this apparent contradiction could open up possible avenues for the application of these nitrogen oxides in a variety of fields, the pharmaceutical industry in particular.

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.

Activation of O2 and NO in heme-copper oxidases - mechanistic insights from computational modelling

Heme-copper oxidases are transmembrane enzymes involved in aerobic and anaerobic respiration. The largest subgroup contains the cytochrome c oxidases (CcO), which reduce molecular oxygen to water. A significant part of the free energy released in this exergonic process is conserved as an electrochemical gradient across the membrane, via two processes, electrogenic chemistry and proton pumping. A deviant subgroup is the cytochrome c dependent NO reductases (cNOR), which reduce nitric oxide to nitrous oxide and water. This is also an exergonic reaction, but in this case none of the released free energy is conserved. Computational studies applying hybrid density functional theory to cluster models of the bimetallic active sites in the heme-copper oxidases are reviewed. To obtain a reliable description of the reaction mechanisms, energy profiles of the entire catalytic cycles, including the reduction steps have to be constructed. This requires a careful combination of computational results with certain experimental data. Computational studies have elucidated mechanistic details of the chemical parts of the reactions, involving cleavage and formation of covalent bonds, which have not been obtainable from pure experimental investigations. Important insights regarding the mechanisms of energy conservation have also been gained. The computational studies show that the reduction potentials of the active site cofactors in the CcOs are large enough to afford electrogenic chemistry and proton pumping, i.e. efficient energy conservation. These results solve a conflict between different types of experimental data. A mechanism for the proton pumping, involving a specific and crucial role for the active site tyrosine, conserved in all CcOs, is suggested. For the cNORs, the calculations show that the low reduction potentials of the active site cofactors are optimized for fast elimination of the toxic NO molecules. At the same time, the low reduction potentials lead to endergonic reduction steps with high barriers. To prevent even higher barriers, which would lead to a too slow reaction, when the electrochemical gradient across the membrane is present, the chemistry must occur in a non-electrogenic manner. This explains why there is no energy conservation in cNOR.

Molecular understanding of heteronuclear active sites in heme-copper oxidases, nitric oxide reductases, and sulfite reductases through biomimetic modelling

Heme-copper oxidases (HCO), nitric oxide reductases (NOR), and sulfite reductases (SiR) catalyze the multi-electron and multi-proton reductions of O2, NO, and SO32-, respectively. Each of these reactions is important to drive cellular energy production through respiratory metabolism and HCO, NOR, and SiR evolved to contain heteronuclear active sites containing heme/copper, heme/nonheme iron, and heme-[4Fe-4S] centers, respectively. The complexity of the structures and reactions of these native enzymes, along with their large sizes and/or membrane associations, make it challenging to fully understand the crucial structural features responsible for the catalytic properties of these active sites. In this review, we summarize progress that has been made to better understand these heteronuclear metalloenzymes at the molecular level though study of the native enzymes along with insights gained from biomimetic models comprising either small molecules or proteins. Further understanding the reaction selectivity of these enzymes is discussed through comparisons of their similar heteronuclear active sites, and we offer outlook for further investigations.

Biological and Bioinspired Inorganic N-N Bond-Forming Reactions

The metallobiochemistry underlying the formation of the inorganic N-N-bond-containing molecules nitrous oxide (N2O), dinitrogen (N2), and hydrazine (N2H4) is essential to the lifestyles of diverse organisms. Similar reactions hold promise as means to use N-based fuels as alternative carbon-free energy sources. This review discusses research efforts to understand the mechanisms underlying biological N-N bond formation in primary metabolism and how the associated reactions are tied to energy transduction and organismal survival. These efforts comprise studies of both natural and engineered metalloenzymes as well as synthetic model complexes.

Copper(I) Complex Mediated Nitric Oxide Reductive Coupling: Ligand Hydrogen Bonding Derived Proton Transfer Promotes N2O(g) Release

A cuprous chelate bearing a secondary sphere hydrogen bonding functionality, [(PV-tmpa)Cu^I]⁺, transforms ^•NO_(g) to N₂O_(g) in high-yields in methanol. Ligand derived proton transfer facilitates N-O bond cleavage of a putative hyponitrite intermediate releasing N₂O_(g), underscoring the crucial balance between H-bonding capabilities and acidities in (bio)chemical ^•NO_(g) coupling systems.

Mechanisms for enzymatic reduction of nitric oxide to nitrous oxide - A comparison between nitric oxide reductase and cytochrome c oxidase

Cytochrome c oxidases (CcO) reduce O₂ to H₂O in the respiratory chain of mitochondria and many aerobic bacteria. In addition, some species of CcO can also reduce NO to N₂O and water while others cannot. Here, the mechanism for NO-reduction in CcO is investigated using quantum mechanical calculations. Comparison is made to the corresponding reaction in a "true" cytochrome c-dependent NO reductase (cNOR). The calculations show that in cNOR, where the reduction potentials are low, the toxic NO molecules are rapidly reduced, while the higher reduction potentials in CcO lead to a slower or even impossible reaction, consistent with experimental observations. In both enzymes the reaction is initiated by addition of two NO molecules to the reduced active site, forming a hyponitrite intermediate. In cNOR, N₂O can then be formed using only the active-site electrons. In contrast, in CcO, one proton-coupled reduction step most likely has to occur before N₂O can be formed, and furthermore, proton transfer is most likely rate-limiting. This can explain why different CcO species with the same heme a₃-Cu active site differ with respect to NO reduction efficiency, since they have a varying number and/or properties of proton channels. Finally, the calculations also indicate that a conserved active site valine plays a role in reducing the rate of NO reduction in CcO.

Electroanalytical characterization of the direct Marinobacter hydrocarbonoclasticus nitric oxide reductase-catalysed nitric oxide and dioxygen reduction

Understanding the direct electron transfer processes between redox proteins and electrode surface is fundamental to understand the proteins mechanistic properties and for development of novel biosensors. In this study, nitric oxide reductase (NOR) extracted from Marinobacter hydrocarbonoclasticus bacteria was adsorbed onto a pyrolytic graphite electrode (PGE) to develop an unmediated enzymatic biosensor (PGE/NOR)) for characterization of NOR direct electrochemical behaviour and NOR electroanalytical features towards NO and O₂. Square-wave voltammetry showed the reduction potential of all the four NOR redox centers: 0.095 ± 0.002, -0.108 ± 0.008, -0.328 ± 0.001 and -0.635 ± 0.004 V vs. SCE for heme c, heme b, heme b₃ and non-heme Fe_B, respectively. The determined sensitivity (-4.00 × 10^-8 ± 1.84 × 10^-9 A/μM and - 2.71 × 10^-8 ± 1.44 × 10^-9 A/μM for NO and O₂, respectively), limit of detection (0.5 μM for NO and 1.0 μM for O₂) and the Michaelis Menten constant (2.1 and 7.0 μM for NO and O₂, respectively) corroborated the higher affinity of NOR for its natural substrate (NO). No significant interference on sensitivity towards NO was perceived in the presence of O₂, while the O₂ reduction was markedly and negatively impacted (3.6 times lower sensitivity) by the presence of NO. These results clearly demonstrate the high potential of NOR for the design of innovative NO biosensors.

Copper(I)/NO(g) Reductive Coupling Producing a trans-Hyponitrite Bridged Dicopper(II) Complex: Redox Reversal Giving Copper(I)/NO(g) Disproportionation

A copper complex, [CuI(tmpa)(MeCN)]+, effectively reductively couples NO(g) at RT in methanol (MeOH), giving a structurally characterized hyponitrito-dicopper(II) adduct. Hydrogen-bonding from MeOH is critical for the hyponitrite complex formation and stabilization. This complex exhibits the reverse redox process in aprotic solvents, giving CuI + NO(g), leading to CuI-mediated NO(g)-disproportionation. The relationship of this chemistry to biological iron and/or copper mediated NO(g) reductive coupling to give N2O(g) is discussed.

Nitric oxide coupling to generate N2O promoted by a single-heme system as examined by density functional theory

Bacteria utilize a heme/non-heme enzyme system to detoxify nitric oxide (NO) to N₂O. In order to probe the capacity of a single-heme system to mediate this NO-to-N₂O transformation, various scenarios for addition of electrons, protons, and a second NO molecule to a heme nitrosyl to generate N₂O were explored by density functional theory calculations. We describe, utilizing this single-heme system, several stepwise intermediates along pathways that enable the critical N-N bond formation step yielding the desired Fe-N₂O product. We also report a hitherto unreported directional second protonation that results in either productive N₂O formation with loss of water, or formation of a non-productive hyponitrous acid adduct Fe{HONNOH}.

Nitrous Oxide Metabolism in Nitrate-Reducing Bacteria: Physiology and Regulatory Mechanisms

Nitrous oxide (N2O) is an important greenhouse gas (GHG) with substantial global warming potential and also contributes to ozone depletion through photochemical nitric oxide (NO) production in the stratosphere. The negative effects of N2O on climate and stratospheric ozone make N2O mitigation an international challenge. More than 60% of global N2O emissions are emitted from agricultural soils mainly due to the application of synthetic nitrogen-containing fertilizers. Thus, mitigation strategies must be developed which increase (or at least do not negatively impact) on agricultural efficiency whilst decrease the levels of N2O released. This aim is particularly important in the context of the ever expanding population and subsequent increased burden on the food chain. More than two-thirds of N2O emissions from soils can be attributed to bacterial and fungal denitrification and nitrification processes. In ammonia-oxidizing bacteria, N2O is formed through the oxidation of hydroxylamine to nitrite. In denitrifiers, nitrate is reduced to N2 via nitrite, NO and N2O production. In addition to denitrification, respiratory nitrate ammonification (also termed dissimilatory nitrate reduction to ammonium) is another important nitrate-reducing mechanism in soil, responsible for the loss of nitrate and production of N2O from reduction of NO that is formed as a by-product of the reduction process. This review will synthesize our current understanding of the environmental, regulatory and biochemical control of N2O emissions by nitrate-reducing bacteria and point to new solutions for agricultural GHG mitigation.

A bridged di-iron porphyrin hyponitrite complex as a model for biological N2O production from hyponitrite

Heme-hyponitrites are intermediates that form at the bimetallic active sites of bacterial nitric oxide reductases. To probe a possible effect of the Fe-Fe distance on hyponitrite stability, we prepared a bridged bis-porphyrin Fe-hyponitrite compound, namely [(OEP-CH2)Fe]2(μ2,η(1),η(1)-ONNO). Its υNO of 992 cm(-1) (υ15NO of 976 cm(-1)) is close to the υNO of 983 cm(-1) reported previously by us for the crystallographically characterized [(OEP)Fe]2(μ2,η(1),η(1)-ONNO) compound. The bridged bis-porphyrin Fe-hyponitrite complex is unstable with respect to N2O production, supporting the role of the bis-Fe porphyrin system in hyponitrite conversion to N2O. The preparation and crystallographic determination of the bridging sulfato derivative is also reported.

Probing the nitrite and nitric oxide reductase activity of cbb3 oxidase: resonance Raman detection of a six-coordinate ferrous heme-nitrosyl species in the binuclear b3/CuB center

In this work we report the first spectroscopic evidence demonstrating that cbb3 oxidase catalyzes the reduction of nitrite to nitrous oxide under reducing anaerobic conditions. The reaction proceeds through the formation of a ferrous six-coordinate heme b3-nitrosyl species that has been characterized by resonance Raman spectroscopy.