Historic overview of nitrogenase research

Protonated and deprotonated vanadyl imidazole tartrates for the mimics of the vanadium coordination in the FeV-cofactor of V-nitrogenase

Chiral imidazole-based oxidovanadium tartrates (H2im)2[Δ,Λ-VIV2O2(R,R-H2tart)(R,R-tart)(Him)2]·Him (1, H4tart = tartaric acid, Him = imidazole) and [Λ,Λ-VIV2O2(R,R-tart)(Him)6]·4H2O (2) and their corresponding enantiomers (H2im)2[Λ,Δ-VIV2O2(S,S-H2tart)(S,S-tart)(Him)2]·Him (3) and [Δ,Δ-VIV2O2(S,S-tart)(Him)6]·4H2O (4) were obtained in alkaline solutions. Interestingly, the tartrates chelate with vanadium bidentately through α-alkoxy/α-hydroxy and α-carboxy groups and imidazole coordinates monodentately through nitrogen atom. It is worth noting that complexes 1 and 3 contain both protonated α-hydroxy and deprotonated α-alkoxy groups simultaneously, which have short V-Oα-alkoxy distances [1.976(4)av Å in 1-4] and long V-Oα-hydroxy distances [2.237(3)av Å in 1 and 2.230(2)av Å in 3]. There is an interesting strong intramolecular hydrogen bond [O(11)⋯O(1) 2.731(5) Å] between the two parts in 1 and 3. The protonated V-O distances are closer to the average bond distance in reported FeV-cofactors (FeV-cos, V-Oα-alkoxy 2.156av Å) in VFe proteins, which corresponds to the feasible protonation of coordinated α-hydroxy in R-homocitrate in V-nitrogenase, showing the homocitrate in the mechanistic model for nitrogen reduction as a secondary proton donor. Furthermore, vibrational circular dichroism (VCD) and IR spectra of 1-4 pointed out the disparity between the characteristic vibrations of the C-O and C-OH groups clearly. EPR experiment and theoretical calculations support +4 oxidation states for vanadium in 1-4. Solution 13C {1H} NMR spectra and CV analyses exhibited the solution properties for 1 and 2, respectively, which indicates that there should be a rapid exchange equilibrium between the protonated and deprotonated species in solutions.

Two ligand-binding sites in CO-reducing V nitrogenase reveal a general mechanistic principle

Besides its role in biological nitrogen fixation, vanadium-containing nitrogenase also reduces carbon monoxide (CO) to hydrocarbons, in analogy to the industrial Fischer-Tropsch process. The protein yields 93% of ethylene (C₂H₄), implying a C-C coupling step that mandates the simultaneous binding of two CO at the active site FeV cofactor. Spectroscopic data indicated multiple CO binding events, but structural analyses of Mo and V nitrogenase only confirmed a single site. Here, we report the structure of a two CO-bound state of V nitrogenase at 1.05 Å resolution, with one μ-bridging and one terminal CO molecule. This additional, specific ligand binding site suggests a mechanistic route for CO reduction and hydrocarbon formation, as well as a second access pathway for protons required during the reaction. Moreover, carbonyls are strong-field ligands that are chemically similar to mechanistically relevant hydrides that may be formed and used in a fully analogous fashion.

Reactivity patterns of vanadium(iv/v)-oxo complexes with olefins in the presence of peroxides: a computational study

Vanadium porphyrin complexes are naturally occurring substances found in crude oil and have been shown to have medicinal properties as well. Little is known on their activities with substrates; therefore, we decided to perform a detailed density functional theory study on the properties and reactivities of vanadium(iv)- and vanadium(v)-oxo complexes with a TPPCl8 or 2,3,7,8,12,13,17,18-octachloro-meso-tetraphenylporphyrinato ligand system. In particular, we investigated the reactivity of [VV(O)(TPPCl8)]+ and [VIV(O)(TPPCl8)] with cyclohexene in the presence of H2O2 or HCO4-. The work shows that vanadium(iv)-oxo and vanadium(v)-oxo are sluggish oxidants by themselves and react with olefins slowly. However, in the presence of hydrogen peroxide, these metal-oxo species can be transformed into a side-on vanadium-peroxo complex, which reacts with substrates more efficiently. Particularly with anionic axial ligands, the side-on vanadium-peroxo and vanadium-oxo complexes produced epoxides from cyclohexene via small barrier heights. In addition to olefin epoxidation, we investigated aliphatic hydroxylation mechanisms by the same oxidants and some oxidants show efficient and viable cyclohexene hydroxylation mechanisms. The work implies that vanadium-oxo and vanadium-peroxo complexes can react with double bonds through epoxidation, and under certain conditions also undergo hydroxylation, but the overall reactivity is highly dependent on the equatorial ligand, the local environment and the presence or absence of anionic axial ligands.

Survey of the Geometric and Electronic Structures of the Key Hydrogenated Forms of FeMo-co, the Active Site of the Enzyme Nitrogenase: Principles of the Mechanistically Significant Coordination Chemistry

The enzyme nitrogenase naturally hydrogenates N2 to NH3, achieved through the accumulation of H atoms on FeMo-co, the Fe7MoS9C(homocitrate) cluster that is the catalytically active site. Four intermediates, E1H1, E2H2, E3H3, and E4H4, carry these hydrogen atoms. I report density functional calculations of the numerous possibilities for the geometric and electronic structures of these poly-hydrogenated forms of FeMo-co. This survey involves more than 100 structures, including those with bound H2, and assesses their relative energies and most likely electronic states. Twelve locations for bound H atoms in the active domain of FeMo-co, including Fe–H–Fe and Fe–H–S bridges, are studied. A significant result is that transverse Fe–H–Fe bridges (transverse to the pseudo-threefold axis of FeMo-co and shared with triply-bridging S) are not possible geometrically unless the S is hydrogenated to become doubly-bridging. The favourable Fe–H–Fe bridges are shared with doubly-bridging S. ENDOR data for an E4H4 intermediate trapped at low temperature, and interpretations in terms of the geometrical and electronic structure of E4H4, are assessed in conjunction with the calculated possibilities. The results reported here yield a set of 24 principles for the mechanistically significant coordination chemistry of H and H2 on FeMo-co, in the stages prior to N2 binding.

How feasible is the reversible S-dissociation mechanism for the activation of FeMo-co, the catalytic site of nitrogenase?

The active site of the enzyme nitrogenase (N₂→ NH₃) is a Fe₇MoS₉C cluster that contains three doubly-bridging μ-S atoms around a central belt. A vanadium nitrogenase variant has a slightly different cluster, containing two μ-S atoms. Recent crystal structures have revealed substitution of one μ-S (S2B, bridging Fe2 and Fe6), by CO in Mo-nitrogenase and an uncertain light atom in V-nitrogenase. These systems retained catalytic activity, and were able to recover the lost μ-S atom. Electron density attributed to the dissociated S is displaced by 7 Å in the crystal structure of the non-standard V-protein. The hypothesis arising from these observations is that the chemical mechanism of nitrogenase involves reversible dissociation of S2B, leaving Fe2 and Fe6 seriously under-coordinated and reactive in trapping N₂ and binding reaction intermediates. Accumulated experimental evidence points to the Fe2-S2B-Fe6 domain as the centre of catalytic hydrogenation of N₂. Using DFT simulations of a large model (>488 atoms) containing all relevant surrounding protein residues, I have investigated the chemical steps that could allow dissociation of S2B. The participation of H atoms is crucial, as is involvement of the nearby side chain of His195 that can function as proton donor to S2B and hydrogen-bonding supporter of displaced S2B. A significant result is that after ingress and binding of N₂ at Fe2 the breaking of the Fe2-S2B bond can be strongly exergonic with negligible kinetic barrier. Subsequent extension of the Fe6-S2B bond and dissociation as H₂S (or SH^-) is endergonic by 20-25 kcal mol^-1, partly because the separating H₂S is restricted by surrounding amino-acids. I present a number of reaction sequences and energy landscapes, and derive thirteen chemical principles relevant to the postulated S-dissociation mechanism. A key conclusion is that unhooking of S2BH or S2BH₂ from Fe2 is favourable, likely, and propitious for subsequent H transfer to bound N₂ or reaction intermediates. The space between Fe2 and Fe6 supports two bridging ligands, and another H atom on Fe6 can move without kinetic barrier to occupy the bridging position vacated by S2B.

A bound reaction intermediate sheds light on the mechanism of nitrogenase

Reduction of N₂ by nitrogenases occurs at an organometallic iron cofactor that commonly also contains either molybdenum or vanadium. The well-characterized resting state of the cofactor does not bind substrate, so its mode of action remains enigmatic. Carbon monoxide was recently found to replace a bridging sulfide, but the mechanistic relevance was unclear. Here we report the structural analysis of vanadium nitrogenase with a bound intermediate, interpreted as a μ²-bridging, protonated nitrogen that implies the site and mode of substrate binding to the cofactor. Binding results in a flip of amino acid glutamine 176, which hydrogen-bonds the ligand and creates a holding position for the displaced sulfide. The intermediate likely represents state E₆ or E₇ of the Thorneley-Lowe model and provides clues to the remainder of the catalytic cycle.

Nitrogen Reduction to Ammonia on a Biomimetic Mononuclear Iron Centre: Insights into the Nitrogenase Enzyme

Nitrogenases catalyse nitrogen fixation to ammonia on a multinuclear Fe‐Mo centre, but their mechanism and particularly the order of proton and electron transfer processes that happen during the catalytic cycle is still unresolved. Recently, a unique biomimetic mononuclear iron model was developed using tris(phosphine)borate (TPB) ligands that was shown to convert N₂ into NH₃. Herein, we present a computational study on the [(TPB)FeN₂]⁻ complex and describe its conversion into ammonia through the addition of electrons and protons. In particular, we tested the consecutive proton transfer on only the distal nitrogen atom or alternated protonation of the distal/proximal nitrogen. It is found that the lowest energy pathway is consecutive addition of three protons to the same site, which forms ammonia and an iron‐nitrido complex. In addition, the proton transfer step of complexes with the metal in various oxidation and spin states were tested and show that the pK_a values of biomimetic mononuclear nitrogenase intermediates vary little with iron oxidation states. As such, the model gives several possible NH₃ formation pathways depending on the order of electron/proton transfer, and all should be physically accessible in the natural system. These results may have implications for enzymatic nitrogenases and give insight into the catalytic properties of mononuclear iron centres.

Regulation of nitrogenase by reversible mono-ADP-ribosylation

Posttranslational modification of proteins plays a key role in the regulation of a plethora of metabolic functions. Protein modification by mono-ADP-ribosylation was first described as a mechanism of action of bacterial toxins. Since these pioneering studies, the number of pathways regulated by ADP-ribosylation in organisms from all domains of life expanded significantly. However, in only a few cases the full regulatory ADP-ribosylation circuit is known. Here, we review the system where mono-ADP-ribosylation regulates the activity of an enzyme: the regulation of nitrogenase in bacteria. When the nitrogenase product, ammonium, becomes available, the ADP-ribosyltransferase (DraT) covalently links an ADP-ribose moiety to a specific arginine residue on nitrogenase switching-off nitrogenase activity. After ammonium exhaustion, the ADP-ribosylhydrolase (DraG) removes the modifying group, restoring nitrogenase activity. DraT and DraG activities are reversibly regulated through interaction with PII signaling proteins . Bioinformatics analysis showed that DraT homologs are restricted to a few nitrogen-fixing bacteria while DraG homologs are widespread in Nature. Structural comparisons indicated that bacterial DraG is closely related to Archaea and mammalian ADP-ribosylhydrolases (ARH). In all available structures, the ARH active site consists of a hydrophilic cleft carrying a binuclear Mg(2+) or Mn(2+) cluster, which is critical for catalysis.

Misconception of reductive elimination of H2, in the context of the mechanism of nitrogenase

Calculated atom partial charges reveal misconceptions of reductive elimination of H₂.

Molybdenum and Tungsten

Molybdenum (Mo) is an essential micronutrient for the majority of organisms ranging from bacteria to animals. To fulfil its biological role, it is incorporated into a pterin-based Mo-cofactor (Moco) and can be found in the active centre of more than 50 enzymes that are involved in key reactions of carbon, nitrogen and sulfur metabolism. Five of the Mo-enzymes are present in eukaryotes: nitrate reductase (NR), sulfite oxidase (SO), aldehyde oxidase (AO), xanthine oxidase (XO) and the amidoxime-reducing component (mARC). Cells acquire Mo in form of the oxyanion molybdate using specific molybdate transporters. In bacteria, molybdate transport is an extensively studied process and is mediated mainly by the ATP-binding cassette system ModABC. In contrast, in eukaryotes, molybdate transport is poorly understood since specific molybdate transporters remained unknown until recently. Two rather distantly related families of proteins, MOT1 and MOT2, are involved in eukaryotic molybdate transport. They each feature high-affinity molybdate transporters that regulate the intracellular concentration of Mo and thus control activity of Mo-enzymes. The present chapter presents an overview of the biological functions of Mo with special focus on recent data related to its uptake, binding and storage.

The transcriptional activator NrpA is crucial for inducing nitrogen fixation in Methanosarcina mazei Gö1 under nitrogen-limited conditions

With the aim of unraveling their potential involvement in the regulation of nitrogen metabolism in Methanosarcina mazei strain Gö1, we characterized five genes that are differentially transcribed in response to changing nitrogen availability and encoding putative transcriptional regulators. Study of the respective mutant strains under nitrogen-limited conditions revealed a growth delay for M. mazei MM0444::pac and MM1708::pac, and strongly reduced diazotrophic growth for MM0872::pac, whereas the absence of MM2441 or MM2525 did not affect growth behaviour. Transcriptome analyses further demonstrated that only MM1708 - encoding a CxxCG zinc finger protein - plays a regulatory role in nitrogen metabolism, most likely by specifically enhancing transcription of the N2 fixation (nif) operon under nitrogen-limited conditions. In agreement with this, a palindromic binding motif was predicted in silico in the nifH promoter region, nine nucleotides upstream of the BRE box, and confirmed to bind purified maltose-binding protein-MM1708 by electromobility shift assays. As MM1708 itself is under the control of the global nitrogen repressor NrpR, this adds a secondary level to the transcriptional regulation of the nif genes, and is most likely crucial for maximal nif induction under nitrogen-limited conditions. This is in accordance with the finding that protein expression of NifH is highly reduced in the absence of MM1708 under nitrogen-limited conditions. On the basis of our findings, we hypothesize that, in M. mazei, nitrogen fixation is controlled by a hierarchical network of two transcriptional regulators, the global nitrogen repressor NrpR, and the newly identified activator NrpA (MM1708), thereby providing tight control of N2 fixation.

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.