Duplication and extension of the Thorneley and Lowe kinetic model for Klebsiella pneumoniae nitrogenase catalysis using a MATHEMATICA software platform

The activating capture of N2 at the active site of Mo-nitrogenase

Dinitrogen is inherently inert. This report describes detailed density functional calculations (with a 485+ atom model) of mechanistic steps by which the enzyme nitrogenase activates unreactive N2 at the intact active site FeMo-co, to form a key intermediate with bound HNNH. This mechanism does not bind N2 first and then add H atoms, but rather captures N2 ('N2-ready') that diffuses in through the substrate channel and enters a strategic gallery of H atom donors in the reaction zone, between Fe2 and Fe6. This occurs at the E4 stage of the complete mechanism. Exploration of possible reactions of N2 in this space leads to the conclusion that the first reaction step is transfer of H on Fe7 to one end of N2-ready, soon followed by Fe-N bond formation, and then a second H transfer from bridging S2BH to the other N. Two H-N bonds and one or two N-Fe bonds are formed, in some cases with a single transition state. The variable positions and orientations of N2-ready lead to various reaction trajectories and products. The favourable products resulting from this capture, judged by the criteria of reaction energies, reaction barriers, and mechanistic competence for further hydrogenation reactions in the nitrogenase cycle, have Fe2-NH-NH bonding. The trajectory of one N2 capture reaction is described in detail, and calculations that separate the H atom component and the 'heavy atom' components of the classical activation energy are described, in the context of possible H atom tunneling in the activation of N2-ready. I present arguments for the activation of N2 by the pathway of concerted hydrogenation and binding of N2-ready, alternative to the commonly assumed pathway of binding N2 first, with subsequent hydrogenation. The active site of nitrogenase is well primed for the thermodynamic and kinetic advantages of N2 capture.

The binding of reducible N2 in the reaction domain of nitrogenase

The binding of N₂ to FeMo-co, the catalytic site of the enzyme nitrogenase, is central to the conversion to NH₃, but also has a separate role in promoting the N₂-dependent HD reaction (D₂ + 2H⁺ + 2e^- → 2HD). The protein surrounding FeMo-co contains a clear channel for ingress of N₂, directly towards the exo-coordination position of Fe2, a position which is outside the catalytic reaction domain. This led to the hypothesis [I. Dance, Dalton Trans., 2022, 51, 12717] of 'promotional' N₂ bound at exo-Fe2, and a second 'reducible' N₂ bound in the reaction domain, specifically the endo-coordination position of Fe2 or Fe6. The range of possibilities for the binding of reducible N₂ in the presence of bound promotional N₂ is described here, using density functional simulations with a 486 atom model of the active site and surrounding protein. The pathway for ingress of the second N₂ through protein, past the first N₂ at exo-Fe2, and tumbling into the binding domain between Fe2 and Fe6, is described. The calculations explore 24 structures involving 6 different forms of hydrogenated FeMo-co, including structures with S2BH unhooked from Fe2 but tethered to Fe6. The calculations use the most probable electronic states. End-on (η¹) binding of N₂ at the endo position of either Fe2 or Fe6 is almost invariably exothermic, with binding potential energies ranging up to -18 kcal mol^-1. Many structures have binding energies in the range -6 to -14 kcal mol^-1. The relevant entropic penalty for N₂ binding from a diffusible position within the protein is estimated to be 4 kcal mol^-1, and so the binding free energies for reducible N₂ are suitably negative. N₂ binding at endo-Fe2 is stronger than at endo-Fe6 in three of the six structure categories. In many cases the reaction domain containing reducible N₂ is expanded. These results inform computational simulation of the subsequent steps in which surrounding H atoms transfer to reducible N₂.

Biological nitrogen fixation in theory, practice, and reality: a perspective on the molybdenum nitrogenase system

Nitrogenase is the sole enzyme responsible for the ATP-dependent conversion of atmospheric dinitrogen into the bioavailable form of ammonia (NH₃ ), making this protein essential for the maintenance of the nitrogen cycle and thus life itself. Despite the widespread use of the Haber-Bosch process to industrially produce NH₃ , biological nitrogen fixation still accounts for half of the bioavailable nitrogen on Earth. An important feature of nitrogenase is that it operates under physiological conditions, where the equilibrium strongly favours ammonia production. This biological, multielectron reduction is a complex catalytic reaction that has perplexed scientists for decades. In this review, we explore the current understanding of the molybdenum nitrogenase system based on experimental and computational research, as well as the limitations of the crystallographic, spectroscopic, and computational techniques employed. Finally, essential outstanding questions regarding the nitrogenase system will be highlighted alongside suggestions for future experimental and computational work to elucidate this essential yet elusive process.

13C ENDOR Characterization of the Central Carbon within the Nitrogenase Catalytic Cofactor Indicates That the CFe6 Core Is a Stabilizing "Heart of Steel"

Substrates and inhibitors of Mo-dependent nitrogenase bind and react at Fe ions of the active-site FeMo-cofactor [7Fe-9S-C-Mo-homocitrate] contained within the MoFe protein α-subunit. The cofactor contains a CFe6 core, a carbon centered within a trigonal prism of six Fe, whose role in catalysis is unknown. Targeted 13C labeling of the carbon enables electron-nuclear double resonance (ENDOR) spectroscopy to sensitively monitor the electronic properties of the Fe-C bonds and the spin-coupling scheme adopted by the FeMo-cofactor metal ions. This report compares 13CFe6 ENDOR measurements for (i) the wild-type protein resting state (E0; α-Val70) to those of (ii) α-Ile70, (iii) α-Ala70-substituted proteins; (iv) crystallographically characterized CO-inhibited "hi-CO" state; (v) E4(4H) Janus intermediate, activated for N2 binding/reduction by accumulation of 4[e-/H+]; (vi) E4(2H)* state containing a doubly reduced FeMo-cofactor without Fe-bound substrates; and (vii) propargyl alcohol reduction intermediate having allyl alcohol bound as a ferracycle to FeMo-cofactor Fe6. All states examined, both S = 1/2 and 3/2 exhibited near-zero 13C isotropic hyperfine coupling constants, Ca = [-1.3 ↔ +2.7] MHz. Density functional theory computations and natural bond orbital analysis of the Fe-C bonds show that this occurs because a (3 spin-up/3 spin-down) spin-exchange configuration of CFe6 Fe-ion spins produces cancellation of large spin-transfers to carbon in each Fe-C bond. Previous X-ray diffraction and DFT both indicate that trigonal-prismatic geometry around carbon is maintained with high precision in all these states. The persistent structure and Fe-C bonding of the CFe6 core indicate that it does not provide a functionally dynamic (hemilabile) "beating heart"─instead it acts as "a heart of steel", stabilizing the structure of the FeMo-cofactor-active site during nitrogenase catalysis.

Structures and reaction dynamics of N2 and H2 binding at FeMo-co, the active site of nitrogenase

The chemical reactions occurring at the Fe₇MoS₉C(homocitrate) cluster, FeMo-co, the active site of the enzyme nitrogenase (N₂ → NH₃), are enigmatic. Experimental information collected over a long period reveals aspects of the roles of N₂ and H₂, each with more than one type of reactivity. This paper reports investigations of the binding of H₂ and N₂ at intact FeMo-co, using density functional simulations of a large 486 atom relevant portion of the protein, resulting in 27 new structures containing H₂ and/or N₂ bound at the exo and endo coordination sites of the participating Fe atoms, Fe2 and Fe6. Binding energies and transition states for association/dissociation are determined, and trajectories for the approach, binding and separation of H₂/N₂ are described, including diffusion of these small molecules through proximal protein. Influences of surrounding amino acids are identified. FeMo-co deforms geometrically when binding H₂ or N₂, and a procedure for calculating the energy cost involved, the adaptation energy, is introduced here. Adaptation energies, which range from 7 to 36 kcal mol^-1 for the reported structures, are influenced by the protonation state of the His195 side chain. Seven N₂ structures and three H₂ structures have negative binding free energies, which include the estimated entropy penalties for binding of N₂, H₂ from proximal protein. These favoured structures have N₂ bound end-on at exo-Fe2, exo-Fe6 and endo-Fe2 positions of FeMo-co, and H₂ bound at the endo-Fe2 position. Various postulated structures with N₂ bridging Fe2 and Fe6 revert to end-on-N₂ at endo positions. The structures are also assessed via the calculated potential energy barriers for association and dissociation. Barriers to the binding of H₂ range from 1 to 20 kcal mol^-1 and barriers to dissociation of H₂ range from 3 to 18 kcal mol^-1. Barriers to the binding of N₂, in either side-on or end-on mode, range from 2 to 18 kcal mol^-1, while dissociation of bound N₂ encounters barriers of 3 to 8 kcal mol^-1 for side-on bonding and 7 to 18 kcal mol^-1 for end-on bonding. These results allow formulation of mechanisms for the H₂/N₂ exchange reaction, and three feasible mechanisms for associative exchange and three for dissociative exchange are identified. Consistent electronic structures and potential energy surfaces are maintained throughout. Changes in the spin populations of Fe2 and Fe6 connected with cluster deformation and with metal-ligand bond formation are identified.

Positive cooperativity during Azotobacter vinelandii nitrogenase-catalyzed acetylene reduction

The MoFe protein component of the nitrogenase enzyme complex is the substrate reducing site and contains two sets of symmetrically arrayed metallo centers called the P (Fe8S7) and the FeMoco (MoFe7S9-C-homocitrate) centers. The ATP-binding Fe protein is the specific reductant for the MoFe protein. Both symmetrical halves of the MoFe protein are thought to function independently during nitrogenase catalysis. Forming [AlF4]- transition-state complexes between the MoFe protein and the Fe protein of Azotobacter vinelandii ranging from 0 to 2 Fe protein/MoFe protein produced a series of complexes whose specific activity decreases with increase in bound Fe protein/MoFe protein ratio. Reduction of 2H+ to H2 was inhibited in a linear manner with an x-intercept at 2.0 with increasing Fe protein binding, whereas acetylene reduction to ethylene decreased more rapidly with an x-intercept near 1.5. H+ reduction is a distinct process occurring independently at each half of the MoFe protein but acetylene reduction decreases more rapidly than H+ reduction with increasing Fe protein/MoFe protein ratio, suggesting that a response is transmitted between the two αβ halves of the MoFe protein for acetylene reduction as Fe protein is bound. A mechanistic model is derived to investigate this behavior. The model predicts that each site functions independently for 2H+ reduction to H2. For acetylene reduction, the model predicts positive (synchronous) not negative cooperativity arising from acetylene binding to both sites before substrate reduction occurs. When this model is applied to inhibition by Cp2 and modified Av2 protein (L127∆) that form strong, non-dissociable complexes, positive cooperativity is absent and each site acts independently. The results suggest a new paradigm for the catalytic function of the MoFe protein during nitrogenase catalysis.

Reduction of Substrates by Nitrogenases

Nitrogenase is the enzyme that catalyzes biological N₂ reduction to NH₃. This enzyme achieves an impressive rate enhancement over the uncatalyzed reaction. Given the high demand for N₂ fixation to support food and chemical production and the heavy reliance of the industrial Haber-Bosch nitrogen fixation reaction on fossil fuels, there is a strong need to elucidate how nitrogenase achieves this difficult reaction under benign conditions as a means of informing the design of next generation synthetic catalysts. This Review summarizes recent progress in addressing how nitrogenase catalyzes the reduction of an array of substrates. New insights into the mechanism of N₂ and proton reduction are first considered. This is followed by a summary of recent gains in understanding the reduction of a number of other nitrogenous compounds not considered to be physiological substrates. Progress in understanding the reduction of a wide range of C-based substrates, including CO and CO₂, is also discussed, and remaining challenges in understanding nitrogenase substrate reduction are considered.

Rethinking the Nitrogenase Mechanism: Activating the Active Site

Metalloenzymes called nitrogenases (N₂ases) harness the reactivity of transition metals to reduce N₂ to NH₃. Specifically, N₂ases feature a multimetallic active site, called a cofactor, which binds and reduces N₂. The seven Fe centers and one additional metal center (Mo, V, or Fe) that make up the cofactor are all potential substrate binding sites. Unraveling the mechanism by which the cofactor binds N₂ and reduces N₂ to NH₃ represents a multifaceted challenge because cofactor activation is required for N₂ binding and functionalization to NH₃. Despite decades of fascinating contributions, the nature of N₂ binding to the active site and the structure of the activated cofactor remain unknown. Herein, we discuss the challenges associated with N₂ reduction and how transition metal complexes facilitate N₂ functionalization by coordinating N₂. We also review the activation and/or reaction mechanisms reported for small molecule catalysts and the Haber-Bosch catalyst and discuss their potential relevance to biological N₂ fixation. Finally, we survey what is known about the mechanism of N₂ase and highlight recent X-ray crystallographic studies supporting Fe-S bond cleavage at the active site to generate reactive Fe centers as a potential, underexplored route for cofactor activation. We propose that structural rearrangements, beyond electron and proton transfers, are key in generating the catalytically active state(s) of the cofactor. Understanding the mechanism of activation will be key to understanding N₂ binding and reduction.

High-Resolution ENDOR Spectroscopy Combined with Quantum Chemical Calculations Reveals the Structure of Nitrogenase Janus Intermediate E4(4H)

We have shown that the key state in N₂ reduction to two NH₃ molecules by the enzyme nitrogenase is E₄(4H), the "Janus" intermediate, which has accumulated four [e^-/H⁺] and is poised to undergo reductive elimination of H₂ coupled to N₂ binding and activation. Initial ¹H and ⁹⁵Mo ENDOR studies of freeze-trapped E₄(4H) revealed that the catalytic multimetallic cluster (FeMo-co) binds two Fe-bridging hydrides, [Fe-H-Fe]. However, the analysis failed to provide a satisfactory picture of the relative spatial relationships of the two [Fe-H-Fe]. Our recent density functional theory (DFT) study yielded a lowest-energy form, denoted as E₄(4H)^(a), with two parallel Fe-H-Fe planes bridging pairs of "anchor" Fe on the Fe2,3,6,7 face of FeMo-co. However, the relative energies of structures E₄(4H)^(b), with one bridging and one terminal hydride, and E₄(4H)^(c), with one pair of anchor Fe supporting two bridging hydrides, were not beyond the uncertainties in the calculation. Moreover, a structure of V-dependent nitrogenase resulted in a proposed structure analogous to E₄(4H)^(c), and additional structures have been proposed in the DFT studies of others. To resolve the nature of hydride binding to the Janus intermediate, we performed exhaustive, high-resolution CW-stochastic ¹H-ENDOR experiments using improved instrumentation, Mims ²H ENDOR, and a recently developed pulsed-ENDOR protocol ("PESTRE") to obtain absolute hyperfine interaction signs. These measurements are coupled to DFT structural models through an analytical point-dipole Hamiltonian for the hydride electron-nuclear dipolar coupling to its "anchoring" Fe ions, an approach that overcomes limitations inherent in both experimental interpretation and computational accuracy. The result is the freeze-trapped, lowest-energy Janus intermediate structure, E₄(4H)^(a).

Distribution of cyanobacteria and their interactions with pesticides in paddy field: A comprehensive review

Cyanobacteria, also known as blue green algae are one of the important ubiquitous oxygen evolving photosynthetic prokaryotes and ultimate source of nitrogen for paddy fields since decades. In past two decades, indiscriminated use of pesticides led to biomagnification that intensively harm the structure and soil functions of soil microbes including cyanobacteria. Cyanobacterial abundance biomass, short generation, water holding capacity, mineralizing capacity and more importantly nitrogen fixing have enormous potential to abate the negative effects of pesticides. Therefore, investigation of the ecotoxicological effects of pesticides on the structure and function of the tropical paddy field associated cyanobacteria is urgent and need to estimate the fate of interaction of pesticides over nitrogen fixations and other attributes. In this regard, comprehensive survey over cyanobacterial distribution patterns and their interaction with pesticides in Indian context has been deeply reviewed. In addition, the present paper also deals the molecular docking pattern of pesticides with the nitrogen fixing proteins, which helps in revealing the functional interpretation over nitrogen fixation process.

Kinetic Understanding of N2 Reduction versus H2 Evolution at the E4(4H) Janus State in the Three Nitrogenases

The enzyme nitrogenase catalyzes the reduction of N₂ to ammonia but also that of protons to H₂. These reactions compete at the mechanistically central 'Janus' intermediate, denoted E₄(4H), which has accumulated 4e^-/4H⁺ as two bridging Fe-H-Fe hydrides on the active-site cofactor. This state can lose e^-/H⁺ by hydride protonolysis (HP) or become activated by reductive elimination ( re) of the two hydrides and bind N₂ with H₂ loss, yielding an E₄(2N2H) state that goes on to generate two NH₃ molecules. Thus, E₄(4H) represents the key branch point for these competing reactions. Here, we present a steady-state kinetic analysis that precisely describes this competition. The analysis demonstrates that steady-state, high-electron flux turnover overwhelmingly populates the E₄ states at the expense of less reduced states, quenching HP at those states. The ratio of rate constants for E₄(4H) hydride protonolysis ( k_HP) versus reductive elimination ( k_re) provides a sensitive measure of competition between these two processes and thus is a central parameter of nitrogenase catalysis. Analysis of measurements with the three nitrogenase variants (Mo-nitrogenase, V-nitrogenase, and Fe-nitrogenase) reveals that at a fixed N₂ pressure their tendency to productively react with N₂ to produce two NH₃ molecules and an accompanying H₂, rather than diverting electrons to the side reaction, HP production of H₂, decreases with their ratio of rate constants, k _re/ k_HP: Mo-nitrogenase, 5.1 atm^-1; V-nitrogenase, 2 atm^-1; and Fe-nitrogenase, 0.77 atm^-1 (namely, in a 1:0.39:0.15 ratio). Moreover, the lower catalytic effectiveness of the alternative nitrogenases, with more H₂ production side reaction, is not caused by a higher k_HP but by a significantly lower k _re.

Hydride Conformers of the Nitrogenase FeMo-cofactor Two-Electron Reduced State E2(2H), Assigned Using Cryogenic Intra Electron Paramagnetic Resonance Cavity Photolysis

Early studies in which nitrogenase was freeze-trapped during enzymatic turnover revealed the presence of high-spin ( S = ³/₂) electron paramagnetic resonance (EPR) signals from the active-site FeMo-cofactor (FeMo-co) in electron-reduced intermediates of the MoFe protein. Historically denoted as 1b and 1c, each of the signals is describable as a fictitious spin system, S' = ¹/₂, with anisotropic g' tensor, 1b with g' = [4.21, 3.76, ?] and 1c with g' = [4.69, ∼3.20, ?]. A clear discrepancy between the magnetic properties of 1b and 1c and the kinetic analysis of their appearance during pre-steady-state turnover left their identities in doubt, however. We subsequently associated 1b with the state having accumulated 2[e^-/H⁺], denoted as E₂(2H), and suggested that the reducing equivalents are stored on the catalytic FeMo-co cluster as an iron hydride, likely an [Fe-H-Fe] hydride bridge. Intra-EPR cavity photolysis (450 nm; temperature-independent from 4 to 12 K) of the E₂(2H)/1b state now corroborates the identification of this state as storing two reducing equivalents as a hydride. Photolysis converts E₂(2H)/1b to a state with the same EPR spectrum, and thus the same cofactor structure as pre-steady-state turnover 1c, but with a different active-site environment. Upon annealing of the photogenerated state at temperature T = 145 K, it relaxes back to E₂(2H)/1b. This implies that the 1c signal comes from an E₂(2H) hydride isomer of E₂(2H)/1b that stores its two reducing equivalents either as a hydride bridge between a different pair of iron atoms or an Fe-H terminal hydride.

Negative cooperativity in the nitrogenase Fe protein electron delivery cycle

Nitrogenase catalyzes the ATP-dependent reduction of dinitrogen (N₂) to two ammonia (NH₃) molecules through the participation of its two protein components, the MoFe and Fe proteins. Electron transfer (ET) from the Fe protein to the catalytic MoFe protein involves a series of synchronized events requiring the transient association of one Fe protein with each αβ half of the α₂β₂ MoFe protein. This process is referred to as the Fe protein cycle and includes binding of two ATP to an Fe protein, association of an Fe protein with the MoFe protein, ET from the Fe protein to the MoFe protein, hydrolysis of the two ATP to two ADP and two P_i for each ET, P_i release, and dissociation of oxidized Fe protein-(ADP)₂ from the MoFe protein. Because the MoFe protein tetramer has two separate αβ active units, it participates in two distinct Fe protein cycles. Quantitative kinetic measurements of ET, ATP hydrolysis, and P_i release during the presteady-state phase of electron delivery demonstrate that the two halves of the ternary complex between the MoFe protein and two reduced Fe protein-(ATP)₂ do not undergo the Fe protein cycle independently. Instead, the data are globally fit with a two-branch negative-cooperativity kinetic model in which ET in one-half of the complex partially suppresses this process in the other. A possible mechanism for communication between the two halves of the nitrogenase complex is suggested by normal-mode calculations showing correlated and anticorrelated motions between the two halves.

Conformationally Gated Electron Transfer in Nitrogenase. Isolation, Purification, and Characterization of Nitrogenase From Gluconacetobacter diazotrophicus

Nitrogenase is a complex, bacterial enzyme that catalyzes the ATP-dependent reduction of dinitrogen (N₂) to ammonia (NH₃). In its most prevalent form, it consists of two proteins, the catalytic molybdenum-iron protein (MoFeP) and its specific reductase, the iron protein (FeP). A defining feature of nitrogenase is that electron and proton transfer processes linked to substrate reduction are synchronized by conformational changes driven by ATP-dependent FeP-MoFeP interactions. Yet, despite extensive crystallographic, spectroscopic, and biochemical information on nitrogenase, the structural basis of the ATP-dependent synchronization mechanism is not understood in detail. In this chapter, we summarize some of our efforts toward obtaining such an understanding. Experimental investigations of the structure-function relationships in nitrogenase are challenged by the fact that it cannot be readily expressed heterologously in nondiazotrophic bacteria, and the purification protocols for nitrogenase are only known for a small number of diazotrophic organisms. Here, we present methods for purifying and characterizing nitrogenase from a new model organism, Gluconacetobacter diazotrophicus. We also describe procedures for observing redox-dependent conformational changes in G. diazotrophicus nitrogenase by X-ray crystallography and electron paramagnetic resonance spectroscopy, which have provided new insights into the redox-dependent conformational gating processes in nitrogenase.

Unraveling the interactions of the physiological reductant flavodoxin with the different conformations of the Fe protein in the nitrogenase cycle

Nitrogenase reduces dinitrogen (N₂) to ammonia in biological nitrogen fixation. The nitrogenase Fe protein cycle involves a transient association between the reduced, MgATP-bound Fe protein and the MoFe protein and includes electron transfer, ATP hydrolysis, release of P_i, and dissociation of the oxidized, MgADP-bound Fe protein from the MoFe protein. The cycle is completed by reduction of oxidized Fe protein and nucleotide exchange. Recently, a kinetic study of the nitrogenase Fe protein cycle involving the physiological reductant flavodoxin reported a major revision of the rate-limiting step from MoFe protein and Fe protein dissociation to release of P_i Because the Fe protein cannot interact with flavodoxin and the MoFe protein simultaneously, knowledge of the interactions between flavodoxin and the different nucleotide states of the Fe protein is critically important for understanding the Fe protein cycle. Here we used time-resolved limited proteolysis and chemical cross-linking to examine nucleotide-induced structural changes in the Fe protein and their effects on interactions with flavodoxin. Differences in proteolytic cleavage patterns and chemical cross-linking patterns were consistent with known nucleotide-induced structural differences in the Fe protein and indicated that MgATP-bound Fe protein resembles the structure of the Fe protein in the stabilized nitrogenase complex structures. Docking models and cross-linking patterns between the Fe protein and flavodoxin revealed that the MgADP-bound state of the Fe protein has the most complementary docking interface with flavodoxin compared with the MgATP-bound state. Together, these findings provide new insights into the control mechanisms in protein-protein interactions during the Fe protein cycle.

Reversible Protonated Resting State of the Nitrogenase Active Site

Protonated states of the nitrogenase active site are mechanistically significant since substrate reduction is invariably accompanied by proton uptake. We report the low pH characterization by X-ray crystallography and EPR spectroscopy of the nitrogenase molybdenum iron (MoFe) proteins from two phylogenetically distinct nitrogenases (Azotobacter vinelandii, Av, and Clostridium pasteurianum, Cp) at pHs between 4.5 and 8. X-ray data at pHs of 4.5–6 reveal the repositioning of side chains along one side of the FeMo-cofactor, and the corresponding EPR data shows a new S = 3/2 spin system with spectral features similar to a state previously observed during catalytic turnover. The structural changes suggest that FeMo-cofactor belt sulfurs S3A or S5A are potential protonation sites. Notably, the observed structural and electronic low pH changes are correlated and reversible. The detailed structural rearrangements differ between the two MoFe proteins, which may reflect differences in potential protonation sites at the active site among nitrogenase species. These observations emphasize the benefits of investigating multiple nitrogenase species. Our experimental data suggest that reversible protonation of the resting state is likely occurring, and we term this state “E₀H⁺”, following the Lowe–Thorneley naming scheme.

Photoinduced Reductive Elimination of H2 from the Nitrogenase Dihydride (Janus) State Involves a FeMo-cofactor-H2 Intermediate

N₂ reduction by nitrogenase involves the accumulation of four reducing equivalents at the active site FeMo-cofactor to form a state with two [Fe-H-Fe] bridging hydrides (denoted E₄(4H), the Janus intermediate), and we recently demonstrated that the enzyme is activated to cleave the N≡N triple bond by the reductive elimination (re) of H₂ from this state. We are exploring a photochemical approach to obtaining atomic-level details of the re activation process. We have shown that, when E₄(4H) at cryogenic temperatures is subjected to 450 nm irradiation in an EPR cavity, it cleanly undergoes photoinduced re of H₂ to give a reactive doubly reduced intermediate, denoted E₄(2H)*, which corresponds to the intermediate that would form if thermal dissociative re loss of H₂ preceded N₂ binding. Experiments reported here establish that photoinduced re primarily occurs in two steps. Photolysis of E₄(4H) generates an intermediate state that undergoes subsequent photoinduced conversion to [E₄(2H)* + H₂]. The experiments, supported by DFT calculations, indicate that the trapped intermediate is an H₂ complex on the ground adiabatic potential energy suface that connects E₄(4H) with [E₄(2H)* + H₂]. We suggest that this complex, denoted E₄(H₂; 2H), is a thermally populated intermediate in the catalytically central re of H₂ by E₄(4H) and that N₂ reacts with this complex to complete the activated conversion of [E₄(4H) + N₂] into [E₄(2N2H) + H₂].

Reductive Elimination of H2 Activates Nitrogenase to Reduce the N≡N Triple Bond: Characterization of the E4(4H) Janus Intermediate in Wild-Type Enzyme

We proposed a reductive elimination/oxidative addition (re/oa) mechanism for reduction of N2 to 2NH3 by nitrogenase, based on identification of a freeze-trapped intermediate of the α-70(Val→Ile) MoFe protein as the Janus intermediate that stores four reducing equivalents on FeMo-co as two [Fe-H-Fe] bridging hydrides (denoted E4(4H)). The mechanism postulates that obligatory re of the hydrides as H2 drives reduction of N2 to a state (denoted E4(2N2H)) with a moiety at the diazene (HN═NH) reduction level bound to the catalytic FeMo-co. EPR/ENDOR/photophysical measurements on wild type (WT) MoFe protein now establish this mechanism. They show that a state freeze-trapped during N2 reduction by WT MoFe is the same Janus intermediate, thereby establishing the α-70(Val→Ile) intermediate as a reliable guide to mechanism. Monitoring the Janus state in WT MoFe during N2 reduction under mixed-isotope condition, H2O buffer/D2, and the converse, establishes that the bridging hydrides/deuterides do not exchange with solvent during enzymatic turnover, thereby solving longstanding puzzles. Relaxation of E4(2N2H) to the WT resting-state is shown to occur via oa of H2 and release of N2 to form Janus, followed by sequential release of two H2, demonstrating the kinetic reversibility of the re/oa equilibrium. Relative populations of E4(2N2H)/E4(4H) freeze-trapped during WT turnover furthermore show that the reversible re/oa equilibrium between [E4(4H) + N2] and [E4(2N2H) + H2] is ∼ thermoneutral (ΔreG(0) ∼ -2 kcal/mol), whereas, by itself, hydrogenation of N2(g) is highly endergonic. These findings demonstrate that (i) re/oa accounts for the historical Key Constraints on mechanism, (ii) that Janus is central to N2 reduction by WT enzyme, which (iii) indeed occurs via the re/oa mechanism. Thus, emerges a picture of the central mechanistic steps by which nitrogenase carries out one of the most challenging chemical transformations in biology.

Tyrosine-Coordinated P-Cluster in G. diazotrophicus Nitrogenase: Evidence for the Importance of O-Based Ligands in Conformationally Gated Electron Transfer

The P-cluster is a unique iron-sulfur center that likely functions as a dynamic electron (e(-)) relay site between the Fe-protein and the catalytic FeMo-cofactor in nitrogenase. The P-cluster has been shown to undergo large conformational changes upon 2-e(-) oxidation which entail the coordination of two of the Fe centers to a Ser side chain and a backbone amide N, respectively. Yet, how and if this 2-e(-) oxidized state (P(OX)) is involved in catalysis by nitrogenase is not well established. Here, we present the crystal structures of reduced and oxidized MoFe-protein (MoFeP) from Gluconacetobacter diazotrophicus (Gd), which natively possesses an Ala residue in the position of the Ser ligand to the P-cluster. While reduced Gd-MoFeP is structurally identical to previously characterized counterparts around the FeMo-cofactor, oxidized Gd-MoFeP features an unusual Tyr coordination to its P-cluster along with ligation by a backbone amide nitrogen. EPR analysis of the oxidized Gd-MoFeP P-cluster confirmed that it is a 2-e(-) oxidized, integer-spin species. Importantly, we have found that the sequence positions corresponding to the Ser and Tyr ligands are almost completely covariant among Group I nitrogenases. These findings strongly support the possibility that the P(OX) state is functionally relevant in nitrogenase catalysis and that a hard, O-based anionic ligand serves to stabilize this state in a switchable fashion.

Exploring Electron/Proton Transfer and Conformational Changes in the Nitrogenase MoFe Protein and FeMo-cofactor Through Cryoreduction/EPR Measurements

We combine cryoreduction/annealing/EPR measurements of nitrogenase MoFe protein with results of earlier investigations to provide a detailed view of the electron/proton transfer events and conformational changes that occur during early stages of [e^-/H⁺] accumulation by the MoFe protein. This includes reduction of (i) the non-catalytic state of the iron-molybdenum cofactor (FeMo-co) active site that is generated by chemical oxidation of the resting-state cofactor (S = 3/2)) within resting MoFe (E₀), and (ii) the catalytic state that has accumulated n =1 [e^-/H⁺] above the resting-state level, denoted E₁(1H) (S ≥ 1) in the Lowe-Thorneley kinetic scheme. FeMo-co does not undergo a major change of conformation during reduction of oxidized FeMo-co. In contrast, FeMo-co undergoes substantial conformational changes during the reduction of E₀ to E₁(1H), and of E₁(1H) to E₂(2H) (n = 2; S = 3/2). The experimental results further suggest that the E₁(1H) → E₂(2H) step involves coupled delivery of a proton and electron (PCET) to FeMo-co of E₁(H) to generate a non-equilibrium S = ½ form E₂(2H)*. This subsequently undergoes conformational relaxation and attendant change in FeMo-co spin state, to generate the equilibrium E₂(2H) (S = 3/2) state. Unexpectedly, these experiments also reveal conformational coupling between FeMo-co and P-cluster, and between Fe protein binding and FeMo-co, which might play a role in gated ET from reduced Fe protein to FeMo-co.

Evidence That the Pi Release Event Is the Rate-Limiting Step in the Nitrogenase Catalytic Cycle

Nitrogenase reduction of dinitrogen (N2) to ammonia (NH3) involves a sequence of events that occur upon the transient association of the reduced Fe protein containing two ATP molecules with the MoFe protein that includes electron transfer, ATP hydrolysis, Pi release, and dissociation of the oxidized, ADP-containing Fe protein from the reduced MoFe protein. Numerous kinetic studies using the nonphysiological electron donor dithionite have suggested that the rate-limiting step in this reaction cycle is the dissociation of the Fe protein from the MoFe protein. Here, we have established the rate constants for each of the key steps in the catalytic cycle using the physiological reductant flavodoxin protein in its hydroquinone state. The findings indicate that with this reductant, the rate-limiting step in the reaction cycle is not protein-protein dissociation or reduction of the oxidized Fe protein, but rather events associated with the Pi release step. Further, it is demonstrated that (i) Fe protein transfers only one electron to MoFe protein in each Fe protein cycle coupled with hydrolysis of two ATP molecules, (ii) the oxidized Fe protein is not reduced when bound to MoFe protein, and (iii) the Fe protein interacts with flavodoxin using the same binding interface that is used with the MoFe protein. These findings allow a revision of the rate-limiting step in the nitrogenase Fe protein cycle.

Reversible Photoinduced Reductive Elimination of H2 from the Nitrogenase Dihydride State, the E(4)(4H) Janus Intermediate

We recently demonstrated that N2 reduction by nitrogenase involves the obligatory release of one H2 per N2 reduced. These studies focus on the E4(4H) "Janus intermediate", which has accumulated four reducing equivalents as two [Fe-H-Fe] bridging hydrides. E4(4H) is poised to bind and reduce N2 through reductive elimination (re) of the two hydrides as H2, coupled to the binding/reduction of N2. To obtain atomic-level details of the re activation process, we carried out in situ 450 nm photolysis of E4(4H) in an EPR cavity at temperatures below 20 K. ENDOR and EPR measurements show that photolysis generates a new FeMo-co state, denoted E4(2H)*, through the photoinduced re of the two bridging hydrides of E4(4H) as H2. During cryoannealing at temperatures above 175 K, E4(2H)* reverts to E4(4H) through the oxidative addition (oa) of the H2. The photolysis quantum yield is temperature invariant at liquid helium temperatures and shows a rather large kinetic isotope effect, KIE = 10. These observations imply that photoinduced release of H2 involves a barrier to the combination of the two nascent H atoms, in contrast to a barrierless process for monometallic inorganic complexes, and further suggest that H2 formation involves nuclear tunneling through that barrier. The oa recombination of E4(2H)* with the liberated H2 offers compelling evidence for the Janus intermediate as the point at which H2 is necessarily lost during N2 reduction; this mechanistically coupled loss must be gated by N2 addition that drives the re/oa equilibrium toward reductive elimination of H2 with N2 binding/reduction.

Evidence for Functionally Relevant Encounter Complexes in Nitrogenase Catalysis

Nitrogenase is the only enzyme that can convert atmospheric dinitrogen (N2) into biologically usable ammonia (NH3). To achieve this multielectron redox process, the nitrogenase component proteins, MoFe-protein (MoFeP) and Fe-protein (FeP), repeatedly associate and dissociate in an ATP-dependent manner, where one electron is transferred from FeP to MoFeP per association. Here, we provide experimental evidence that encounter complexes between FeP and MoFeP play a functional role in nitrogenase catalysis. The encounter complexes are stabilized by electrostatic interactions involving a positively charged patch on the β-subunit of MoFeP. Three single mutations (βAsn399Glu, βLys400Glu, and βArg401Glu) in this patch were generated in Azotobacter vinelandii MoFeP. All of the resulting variants displayed decreases in specific catalytic activity, with the βK400E mutation showing the largest effect. As simulated by the Thorneley-Lowe kinetic scheme, this single mutation lowered the rate constant for FeP-MoFeP association 5-fold. We also found that the βK400E mutation did not affect the coupling of ATP hydrolysis with electron transfer (ET) between FeP and MoFeP. These data suggest a mechanism where FeP initially forms encounter complexes on the MoFeP β-subunit surface en route to the ATP-activated, ET-competent complex over the αβ-interface.

Identification of a key catalytic intermediate demonstrates that nitrogenase is activated by the reversible exchange of N₂ for H₂

Freeze-quenching nitrogenase during turnover with N2 traps an S = ½ intermediate that was shown by ENDOR and EPR spectroscopy to contain N2 or a reduction product bound to the active-site molybdenum-iron cofactor (FeMo-co). To identify this intermediate (termed here EG), we turned to a quench-cryoannealing relaxation protocol. The trapped state is allowed to relax to the resting E0 state in frozen medium at a temperature below the melting temperature; relaxation is monitored by periodically cooling the sample to cryogenic temperature for EPR analysis. During -50 °C cryoannealing of EG prepared under turnover conditions in which the concentrations of N2 and H2 ([H2], [N2]) are systematically and independently varied, the rate of decay of EG is accelerated by increasing [H2] and slowed by increasing [N2] in the frozen reaction mixture; correspondingly, the accumulation of EG is greater with low [H2] and/or high [N2]. The influence of these diatomics identifies EG as the key catalytic intermediate formed by reductive elimination of H2 with concomitant N2 binding, a state in which FeMo-co binds the components of diazene (an N-N moiety, perhaps N2 and two [e(-)/H(+)] or diazene itself). This identification combines with an earlier study to demonstrate that nitrogenase is activated for N2 binding and reduction through the thermodynamically and kinetically reversible reductive-elimination/oxidative-addition exchange of N2 and H2, with an implied limiting stoichiometry of eight electrons/protons for the reduction of N2 to two NH3.

A confirmation of the quench-cryoannealing relaxation protocol for identifying reduction states of freeze-trapped nitrogenase intermediates

We have advanced a mechanism for nitrogenase catalysis that rests on the identification of a low-spin EPR signal (S = 1/2) trapped during turnover of a MoFe protein as the E4 state, which has accumulated four reducing equivalents as two [Fe-H-Fe] bridging hydrides. Because electrons are delivered to the MoFe protein one at a time, with the rate-limiting step being the off-rate of oxidized Fe protein, it is difficult to directly control, or know, the degree of reduction, n, of a trapped intermediate, denoted En, n = 1-8. To overcome this previously intractable problem, we introduced a quench-cryoannealing relaxation protocol for determining n of an EPR-active trapped En turnover state. The trapped "hydride" state was allowed to relax to the resting E0 state in frozen medium, which prevents additional accumulation of reducing equivalents; binding of reduced Fe protein and release of oxidized protein from the MoFe protein both are abolished in a frozen solid. Relaxation of En was monitored by periodic EPR analysis at cryogenic temperature. The protocol rests on the hypothesis that an intermediate trapped in the frozen solid can relax toward the resting state only by the release of a stable reduction product from FeMo-co. In turnover under Ar, the only product that can be released is H2, which carries two reducing equivalents. This hypothesis implicitly predicts that states that have accumulated an odd number of electrons/protons (n = 1, 3) during turnover under Ar cannot relax to E0: E3 can relax to E1, but E1 cannot relax to E0 in the frozen state. The present experiments confirm this prediction and, thus, the quench-cryoannealing protocol and our assignment of E4, the foundation of the proposed mechanism for nitrogenase catalysis. This study further gives insights into the identity of the En intermediates with high-spin EPR signals, 1b and 1c, trapped under high electron flux.

On reversible H2 loss upon N2 binding to FeMo-cofactor of nitrogenase

Nitrogenase is activated for N2 reduction by the accumulation of four electrons/protons on its active site FeMo-cofactor, yielding a state, designated as E4, which contains two iron-bridging hydrides [Fe-H-Fe]. A central puzzle of nitrogenase function is an apparently obligatory formation of one H2 per N2 reduced, which would "waste" two reducing equivalents and four ATP. We recently presented a draft mechanism for nitrogenase that provides an explanation for obligatory H2 production. In this model, H2 is produced by reductive elimination of the two bridging hydrides of E4 during N2 binding. This process releases H2, yielding N2 bound to FeMo-cofactor that is doubly reduced relative to the resting redox level, and thereby is activated to promptly generate bound diazene (HN=NH). This mechanism predicts that during turnover under D2/N2, the reverse reaction of D2 with the N2-bound product of reductive elimination would generate dideutero-E4 [E4(2D)], which can relax with loss of HD to the state designated E2, with a single deuteride bridge [E2(D)]. Neither of these deuterated intermediate states could otherwise form in H2O buffer. The predicted E2(D) and E4(2D) states are here established by intercepting them with the nonphysiological substrate acetylene (C2H2) to generate deuterated ethylenes (C2H3D and C2H2D2). The demonstration that gaseous H2/D2 can reduce a substrate other than H(+) with N2 as a cocatalyst confirms the essential mechanistic role for H2 formation, and hence a limiting stoichiometry for biological nitrogen fixation of eight electrons/protons, and provides direct experimental support for the reductive elimination mechanism.

Electron transfer precedes ATP hydrolysis during nitrogenase catalysis

The biological reduction of N2 to NH3 catalyzed by Mo-dependent nitrogenase requires at least eight rounds of a complex cycle of events associated with ATP-driven electron transfer (ET) from the Fe protein to the catalytic MoFe protein, with each ET coupled to the hydrolysis of two ATP molecules. Although steps within this cycle have been studied for decades, the nature of the coupling between ATP hydrolysis and ET, in particular the order of ET and ATP hydrolysis, has been elusive. Here, we have measured first-order rate constants for each key step in the reaction sequence, including direct measurement of the ATP hydrolysis rate constant: kATP = 70 s(-1), 25 °C. Comparison of the rate constants establishes that the reaction sequence involves four sequential steps: (i) conformationally gated ET (kET = 140 s(-1), 25 °C), (ii) ATP hydrolysis (kATP = 70 s(-1), 25 °C), (iii) Phosphate release (kPi = 16 s(-1), 25 °C), and (iv) Fe protein dissociation from the MoFe protein (kdiss = 6 s(-1), 25 °C). These findings allow completion of the thermodynamic cycle undergone by the Fe protein, showing that the energy of ATP binding and protein-protein association drive ET, with subsequent ATP hydrolysis and Pi release causing dissociation of the complex between the Fe(ox)(ADP)2 protein and the reduced MoFe protein.

Nitrogenase: a draft mechanism

Biological nitrogen fixation, the reduction of N(2) to two NH(3) molecules, supports more than half the human population. The predominant form of the enzyme nitrogenase, which catalyzes this reaction, comprises an electron-delivery Fe protein and a catalytic MoFe protein. Although nitrogenase has been studied extensively, the catalytic mechanism has remained unknown. At a minimum, a mechanism must identify and characterize each intermediate formed during catalysis and embed these intermediates within a kinetic framework that explains their dynamic interconversion. The Lowe-Thorneley (LT) model describes nitrogenase kinetics and provides rate constants for transformations among intermediates (denoted E(n), where n is the number of electrons (and protons), that have accumulated within the MoFe protein). Until recently, however, research on purified nitrogenase had not characterized any E(n) state beyond E(0). In this Account, we summarize the recent characterization of three freeze-trapped intermediate states formed during nitrogenase catalysis and place them within the LT kinetic scheme. First we discuss the key E(4) state, which is primed for N(2) binding and reduction and which we refer to as the "Janus intermediate" because it lies halfway through the reaction cycle. This state has accumulated four reducing equivalents stored as two [Fe-H-Fe] bridging hydrides bound to the active-site iron-molybdenum cofactor ([7Fe-9S-Mo-C-homocitrate]; FeMo-co) at its resting oxidation level. The other two trapped intermediates contain reduced forms of N(2). One, intermediate, designated I, has S = 1/2 FeMo-co. Electron nuclear double resonance/hyperfine sublevel correlation (ENDOR/HYSCORE) measurements indicate that I is the final catalytic state, E(8), with NH(3) product bound to FeMo-co at its resting redox level. The other characterized intermediate, designated H, has integer-spin FeMo-co (non-Kramers; S ≥ 2). Electron spin echo envelope modulation (ESEEM) measurements indicate that H contains the [-NH(2)] fragment bound to FeMo-co and therefore corresponds to E(7). These assignments in the context of previous studies imply a pathway in which (i) N(2) binds at E(4) with liberation of H(2), (ii) N(2) is promptly reduced to N(2)H(2), (iii) the two N's are reduced in two steps to form hydrazine-bound FeMo-co, and (iv) two NH(3) are liberated in two further steps of reduction. This proposal identifies nitrogenase as following a "prompt-alternating (P-A)" reaction pathway and unifies the catalytic pathway with the LT kinetic framework. However, the proposal does not incorporate one of the most puzzling aspects of nitrogenase catalysis: obligatory generation of H(2) upon N(2) binding that apparently "wastes" two reducing equivalents and thus 25% of the total energy supplied by the hydrolysis of ATP. Because E(4) stores its four accumulated reducing equivalents as two bridging hydrides, we propose an answer to this puzzle based on the organometallic chemistry of hydrides and dihydrogen. We propose that H(2) release upon N(2) binding involves reductive elimination of two hydrides to yield N(2) bound to doubly reduced FeMo-co. Delivery of the two available electrons and two activating protons yields cofactor-bound diazene, in agreement with the P-A scheme. This keystone completes a draft mechanism for nitrogenase that both organizes the vast body of data on which it is founded and serves as a basis for future experiments.

Temperature invariance of the nitrogenase electron transfer mechanism

Earlier studies of electron transfer (ET) from the nitrogenase Fe protein to the MoFe protein concluded that the mechanism for ET changed during cooling from 25 to 5 °C, based on the observation that the rate constant for Fe protein to MoFe protein ET decreases strongly, with a nonlinear Arrhenius plot. They further indicated that the ET was reversible, with complete ET at ambient temperature but with an equilibrium constant near unity at 5 °C. These studies were conducted with buffers having a strong temperature coefficient. We have examined the temperature variation in the kinetics of oxidation of the Fe protein by the MoFe protein at a constant pH of 7.4 fixed by the buffer 3-(N-morpholino)propanesulfonic acid (MOPS), which has a very small temperature coefficient. Using MOPS, we also observe temperature-dependent ET rate constants, with nonlinear Arrhenius plots, but we find that ET is gated across the temperature range by a conformational change that involves the binding of numerous water molecules, consistent with an unchanging ET mechanism. Furthermore, there is no solvent kinetic isotope effect throughout the temperature range studied, again consistent with an unchanging mechanism. In addition, the nonlinear Arrhenius plots are explained by the change in heat capacity caused by the binding of waters in an invariant gating ET mechanism. Together, these observations contradict the idea of a change in ET mechanism with cooling. Finally, the extent of ET at constant pH does not change significantly with temperature, in contrast to the previously proposed change in ET equilibrium.

Unification of reaction pathway and kinetic scheme for N2 reduction catalyzed by nitrogenase

Nitrogenase catalyzes the reduction of N(2) and protons to yield two NH(3) and one H(2). Substrate binding occurs at a complex organo-metallocluster called FeMo-cofactor (FeMo-co). Each catalytic cycle involves the sequential delivery of eight electrons/protons to this cluster, and this process has been framed within a kinetic scheme developed by Lowe and Thorneley. Rapid freezing of a modified nitrogenase under turnover conditions using diazene, methyldiazene (HN = N-CH(3)), or hydrazine as substrate recently was shown to trap a common S = ½ intermediate, designated I. It was further concluded that the two N-atoms of N(2) are hydrogenated alternately ("Alternating" (A) pathway). In the present work, Q-band CW EPR and (95)Mo ESEEM spectroscopy reveal such samples also contain a common intermediate with FeMo-co in an integer-spin state having a ground-state "non-Kramers" doublet. This species, designated H, has been characterized by ESEEM spectroscopy using a combination of (14,15)N isotopologs plus (1,2)H isotopologs of methyldiazene. It is concluded that: H has NH(2) bound to FeMo-co and corresponds to the penultimate intermediate of N(2) hydrogenation, the state formed after the accumulation of seven electrons/protons and the release of the first NH(3); I corresponds to the final intermediate in N(2) reduction, the state formed after accumulation of eight electrons/protons, with NH(3) still bound to FeMo-co prior to release and regeneration of resting-state FeMo-co. A proposed unification of the Lowe-Thorneley kinetic model with the "prompt" alternating reaction pathway represents a draft mechanism for N(2) reduction by nitrogenase.

57Fe ENDOR spectroscopy and 'electron inventory' analysis of the nitrogenase E4 intermediate suggest the metal-ion core of FeMo-cofactor cycles through only one redox couple

N(2) binds to the active-site metal cluster in the nitrogenase MoFe protein, the FeMo-cofactor ([7Fe-9S-Mo-homocitrate-X]; FeMo-co) only after the MoFe protein has accumulated three or four electrons/protons (E(3) or E(4) states), with the E(4) state being optimally activated. Here we study the FeMo-co (57)Fe atoms of E(4) trapped with the α-70(Val→Ile) MoFe protein variant through use of advanced ENDOR methods: 'random-hop' Davies pulsed 35 GHz ENDOR; difference triple resonance; the recently developed Pulse-Endor-SaTuration and REcovery (PESTRE) protocol for determining hyperfine-coupling signs; and Raw-DATA (RD)-PESTRE, a PESTRE variant that gives a continuous sign readout over a selected radiofrequency range. These methods have allowed experimental determination of the signed isotropic (57)Fe hyperfine couplings for five of the seven iron sites of the reductively activated E(4) FeMo-co, and given the magnitude of the coupling for a sixth. When supplemented by the use of sum-rules developed to describe electron-spin coupling in FeS proteins, these (57)Fe measurements yield both the magnitude and signs of the isotropic couplings for the complete set of seven Fe sites of FeMo-co in E(4). In light of the previous findings that FeMo-co of E(4) binds two hydrides in the form of (Fe-(μ-H(-))-Fe) fragments, and that molybdenum has not become reduced, an 'electron inventory' analysis assigns the formal redox level of FeMo-co metal ions in E(4) to that of the resting state (M(N)), with the four accumulated electrons residing on the two Fe-bound hydrides. Comparisons with earlier (57)Fe ENDOR studies and electron inventory analyses of the bio-organometallic intermediate formed during the reduction of alkynes and the CO-inhibited forms of nitrogenase (hi-CO and lo-CO) inspire the conjecture that throughout the eight-electron reduction of N(2) plus 2H(+) to two NH(3) plus H(2), the inorganic core of FeMo-co cycles through only a single redox couple connecting two formal redox levels: those associated with the resting state, M(N), and with the one-electron reduced state, M(R). We further note that this conjecture might apply to other complex FeS enzymes.

ENDOR/HYSCORE studies of the common intermediate trapped during nitrogenase reduction of N2H2, CH3N2H, and N2H4 support an alternating reaction pathway for N2 reduction

Enzymatic N(2) reduction proceeds along a reaction pathway composed of a sequence of intermediate states generated as a dinitrogen bound to the active-site iron-molybdenum cofactor (FeMo-co) of the nitrogenase MoFe protein undergoes six steps of hydrogenation (e(-)/H(+) delivery). There are two competing proposals for the reaction pathway, and they invoke different intermediates. In the 'Distal' (D) pathway, a single N of N(2) is hydrogenated in three steps until the first NH(3) is liberated, and then the remaining nitrido-N is hydrogenated three more times to yield the second NH(3). In the 'Alternating' (A) pathway, the two N's instead are hydrogenated alternately, with a hydrazine-bound intermediate formed after four steps of hydrogenation and the first NH(3) liberated only during the fifth step. A recent combination of X/Q-band EPR and (15)N, (1,2)H ENDOR measurements suggested that states trapped during turnover of the α-70(Ala)/α-195(Gln) MoFe protein with diazene or hydrazine as substrate correspond to a common intermediate (here denoted I) in which FeMo-co binds a substrate-derived [N(x)H(y)] moiety, and measurements reported here show that turnover with methyldiazene generates the same intermediate. In the present report we describe X/Q-band EPR and (14/15)N, (1,2)H ENDOR/HYSCORE/ESEEM measurements that characterize the N-atom(s) and proton(s) associated with this moiety. The experiments establish that turnover with N(2)H(2), CH(3)N(2)H, and N(2)H(4) in fact generates a common intermediate, I, and show that the N-N bond of substrate has been cleaved in I. Analysis of this finding leads us to conclude that nitrogenase reduces N(2)H(2), CH(3)N(2)H, and N(2)H(4) via a common A reaction pathway, and that the same is true for N(2) itself, with Fe ion(s) providing the site of reaction.

Conformational gating of electron transfer from the nitrogenase Fe protein to MoFe protein

The nitrogenase Fe protein contains a [4Fe-4S] cluster and delivers one electron at a time to the catalytic MoFe protein. During this electron delivery, the Fe protein in its [4Fe-4S](1+) reduced state (Fe(red)) binds two MgATP and forms a complex with the MoFe protein, with subsequent transfer of one electron to the MoFe protein in a reaction coupled to the hydrolysis of two ATP. Crystal structures with the nitrogenase complex in different nucleotide-bound states show major conformational changes which provide a structural underpinning to suggestions that intercomponent electron transfer (ET) is "gated" by conformational changes of the complex and/or of its component proteins. Although electron delivery is coupled to ATP hydrolysis, their connection is puzzling, for it appears that ET precedes both ATP hydrolysis and Pi release. We here test the gating hypothesis with studies of the intracomplex oxidation of Fe(red) by MoFe protein in the presence of a variety of solutes. Conformational control of this process (gating) is revealed by the finding that it responds to changes in osmotic pressure (but not viscosity), with no fewer than 80 waters being bound during the reaction. The absence of a solvent kinetic isotope effect further implies that ATP hydrolysis does not occur during the rate-limiting step of ET.

Climbing nitrogenase: toward a mechanism of enzymatic nitrogen fixation

"Nitrogen fixation", the reduction of dinitrogen (N2) to two ammonia (NH3) molecules, by the Mo-dependent nitrogenase is essential for all life. Despite four decades of research, a daunting number of unanswered questions about the mechanism of nitrogenase activity make it the "Everest of enzymes". This Account describes our efforts to climb one "face" of this mountain by meeting two interdependent challenges central to determining the mechanism of biological N2 reduction. The first challenge is to determine the reaction pathway: the composition and structure of each of the substrate-derived moieties bound to the catalytic FeMo cofactor (FeMo-co) of the molybdenum-iron (MoFe) protein of nitrogenase. To overcome this challenge, it is necessary to discriminate between the two classes of potential reaction pathways: (1) a "distal" (D) pathway, in which H atoms add sequentially at a single N or (2) an "alternating" (A) pathway, in which H atoms add alternately to the two N atoms of N2. Second, it is necessary to characterize the dynamics of conversion among intermediates within the accepted Lowe-Thorneley kinetic scheme for N2 reduction. That goal requires an experimental determination of the number of electrons and protons delivered to the MoFe protein as well as their "inventory", a partition into those residing on each of the reaction components and released as H2 or NH3. The principal obstacle to this "climb" has been the inability to generate N2 reduction intermediates for characterization. A combination of genetic, biochemical, and spectroscopic approaches recently overcame this obstacle. These experiments identified one of the four-iron Fe-S faces of the active-site FeMo-co as the specific site of reactivity, indicated that the side chain of residue alpha70V controls access to this face, and supported the involvement of the side chain of residue alpha195H in proton delivery. We can now freeze-quench trap N2 reduction pathway intermediates and use electron-nuclear double resonance (ENDOR) and electron spin-echo envelope modulation (ESEEM) spectroscopies to characterize them. However, even successful trapping of a N2 reduction intermediate occurs without synchronous electron delivery to the MoFe protein. As a result, the number of electrons and protons, n, delivered to MoFe during its formation is unknown. To determine n and the electron inventory, we initially employed ENDOR spectroscopy to analyze the substrate moiety bound to the FeMo-co and 57Fe within the cofactor. Difficulties in using that approach led us to devise a robust kinetic protocol for determining n of a trapped intermediate. This Account describes strategies that we have formulated to bring this "face" of the nitrogenase mechanism into view and afford approaches to its climb. Although the summit remains distant, we look forward to continued progress in the ascent.

Competitive 15N Kinetic Isotope Effects of Nitrogenase-Catalyzed Dinitrogen Reduction

Biological N2 fixation is achieved under ambient conditions by enzymatic catalysis. The enzyme nitrogenase has been studied extensively, but the N2 chemical reduction step is, by far, not rate limiting and hard to examine. A new method was developed that allows studying the reduction transition state within the enzyme's complex kinetic cascade by means of the 15N kinetic isotope effect on the reaction's second-order rate constant, V/K. A value of 1.7% +/- 0.2% was measured.

A sulfido-bridged diiron(II) compound and its reactions with nitrogenase-relevant substrates

The active site iron-molybdenum cofactor of nitrogenase has sulfide-bridged pairs of redox-active, trigonal pyramidal iron atoms that are postulated to be the site of N2 transformation. A synthetic compound is described in which two three-coordinate iron(II) ions are bridged similarly by sulfide. The compound binds nitrogen donors to become trigonal pyramidal and cleaves the N-N bond of phenylhydrazine with oxidation of iron(II) to iron(III).