Localization of a substrate binding site on the FeMo-cofactor in nitrogenase: trapping propargyl alcohol with an alpha-70-substituted MoFe protein

Analysis of early intermediate states of the nitrogenase reaction by regularization of EPR spectra

Due to the complexity of the catalytic FeMo cofactor site in nitrogenases that mediates the reduction of molecular nitrogen to ammonium, mechanistic details of this reaction remain under debate. In this study, selenium- and sulfur-incorporated FeMo cofactors of the catalytic MoFe protein component from Azotobacter vinelandii are prepared under turnover conditions and investigated by using different EPR methods. Complex signal patterns are observed in the continuous wave EPR spectra of selenium-incorporated samples, which are analyzed by Tikhonov regularization, a method that has not yet been applied to high spin systems of transition metal cofactors, and by an already established grid-of-error approach. Both methods yield similar probability distributions that reveal the presence of at least four other species with different electronic structures in addition to the ground state E0. Two of these species were preliminary assigned to hydrogenated E2 states. In addition, advanced pulsed-EPR experiments are utilized to verify the incorporation of sulfur and selenium into the FeMo cofactor, and to assign hyperfine couplings of 33S and 77Se that directly couple to the FeMo cluster. With this analysis, we report selenium incorporation under turnover conditions as a straightforward approach to stabilize and analyze early intermediate states of the FeMo cofactor.

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.

Dehydrated UiO-66(SH)2 : The Zr-O Cluster and Its Photocatalytic Role Mimicking the Biological Nitrogen Fixation

This work reports the dehydrated Zr-based MOF UiO-66(SH)₂ as a visible-light-driven photocatalyst to mimic the biological N₂ fixation process. The ¹⁵ N₂ and other control experiments demonstrated that the new photocatalyst is highly efficient in converting N₂ to ammonia. In-situ TGA, XPS, and EXAFS as well as first-principles simulations were used to demonstrate the role of the thermal treatment and the changes of the local structures around Zr due to the dehydration. It was shown that the dehydration opened a gate for the entry of N₂ molecules into the [Zr₆ O₆ ] cluster where the strong N≡N bond was broken stepwise by μ-N-Zr type interactions driven by the photoelectrons aided by the protonation. This mechanism was discussed in comparison with the Lowe-Thorneley mechanism proposed for the MoFe nitrogenase, and with emphasis on the [Zr₆ O₆ ] cluster effect and the leading role of photoelectrons over the protonation. The results shed new light on understanding the catalytic mechanism of biological N₂ fixation and open a new way to fix N₂ under mild conditions.

The Spectroscopy of Nitrogenases

Nitrogenases are responsible for biological nitrogen fixation, a crucial step in the biogeochemical nitrogen cycle. These enzymes utilize a two-component protein system and a series of iron-sulfur clusters to perform this reaction, culminating at the FeMco active site (M = Mo, V, Fe), which is capable of binding and reducing N2 to 2NH3. In this review, we summarize how different spectroscopic approaches have shed light on various aspects of these enzymes, including their structure, mechanism, alternative reactivity, and maturation. Synthetic model chemistry and theory have also played significant roles in developing our present understanding of these systems and are discussed in the context of their contributions to interpreting the nature of nitrogenases. Despite years of significant progress, there is still much to be learned from these enzymes through spectroscopic means, and we highlight where further spectroscopic investigations are needed.

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.

Reactivity, Mechanism, and Assembly of the Alternative Nitrogenases

Biological nitrogen fixation is catalyzed by the enzyme nitrogenase, which facilitates the cleavage of the relatively inert triple bond of N₂. Nitrogenase is most commonly associated with the molybdenum-iron cofactor called FeMoco or the M-cluster, and it has been the subject of extensive structural and spectroscopic characterization over the past 60 years. In the late 1980s and early 1990s, two "alternative nitrogenase" systems were discovered, isolated, and found to incorporate V or Fe in place of Mo. These systems are regulated by separate gene clusters; however, there is a high degree of structural and functional similarity between each nitrogenase. Limited studies with the V- and Fe-nitrogenases initially demonstrated that these enzymes were analogously active as the Mo-nitrogenase, but more recent investigations have found capabilities that are unique to the alternative systems. In this review, we will discuss the reactivity, biosynthetic, and mechanistic proposals for the alternative nitrogenases as well as their electronic and structural properties in comparison to the well-characterized Mo-dependent system. Studies over the past 10 years have been particularly fruitful, though key aspects about V- and Fe-nitrogenases remain unexplored.

The influences of carbon donor ligands on biomimetic multi-iron complexes for N2 reduction

The active site clusters of nitrogenase enzymes possess the only examples of carbides in biology. These are the only biological FeS clusters that are capable of reducing N₂ to NH₄⁺, implicating the central carbon and its interaction with Fe as important in the mechanism of N₂ reduction. This biological question motivates study of the influence of carbon donors on the electronic structure and reactivity of unsaturated, high-spin iron centers. Here, we present functional and structural models that test the impacts of carbon donors and sulfide donors in simpler iron compounds. We report the first example of a diiron complex that is bridged by an alkylidene and a sulfide, which serves as a high-fidelity structural and spectroscopic model of a two-iron portion of the active-site cluster (FeMoco) in the resting state of Mo-nitrogenase. The model complexes have antiferromagnetically coupled pairs of high-spin iron centers, and sulfur K-edge X-ray absorption spectroscopy shows comparable covalency of the sulfide for C and S bridged species. The sulfur-bridged compound does not interact with N₂ even upon reduction, but upon removal of the sulfide it becomes capable of reducing N₂ to NH₄⁺ with the addition of protons and electrons. This provides synthetic support for sulfide extrusion in the activation of nitrogenase cofactors.

High-spin diiron alkylidenes give insight into the electronic structure and functional relevance of carbon in the FeMoco active site of nitrogenase.

Mononuclear Fe(I) and Fe(II) Acetylene Adducts and Their Reductive Protonation to Terminal Fe(IV) and Fe(V) Carbynes

The activity of nitrogenase enzymes, which catalyze the conversion of atmospheric dinitrogen to bioavailable ammonia, is most commonly assayed by the reduction of acetylene gas to ethylene. Despite the practical importance of acetylene as a substrate, little is known concerning its binding or activation in the iron-rich active site. "Fischer-Tropsch" type coupling of non-native C1 substrates to higher-order C≥2 products is also known for nitrogenase, though potential metal-carbon multiply bonded intermediates remain underexplored. Here we report the activation of acetylene gas at a mononuclear tris(phosphino)silyl-iron center, (SiP3)Fe, to give Fe(I) and Fe(II) side-on adducts, including S = 1/2 FeI(η2-HCCH); the latter is characterized by pulse EPR spectroscopy and DFT calculations. Reductive protonation reactions with these compounds converge at stable examples of unusual, formally iron(IV) and iron(V) carbyne complexes, as in diamagnetic (SiP3)Fe≡CCH3 and the paramagnetic cation S = 1/2 [(SiP3)Fe≡CCH3]+. Both alkylcarbyne compounds possess short Fe-C triple bonds (approximately 1.7 Å) trans to the anchoring silane. Pulse EPR experiments, X-band ENDOR and HYSCORE, reveal delocalization of the iron-based spin onto the α-carbyne nucleus in carbon p-orbitals. Furthermore, isotropic coupling of the distal β-CH3 protons with iron indicates hyperconjugation with the spin/hole character on the Fe≡CCH3 unit. The electronic structures of (SiP3)Fe≡CCH3 and [(SiP3)Fe≡CCH3]+ are discussed in comparison to previously characterized, but heterosubstituted, iron carbynes, as well as a hypothetical nitride species, (SiP3)Fe≡N. Such comparisons are germane to the consideration of formally high-valent, multiply bonded Fe≡C and/or Fe≡N intermediates in synthetic or biological catalysis by iron.

Nitrogenase-Relevant Reactivity of a Synthetic Iron-Sulfur-Carbon Site

Simple synthetic compounds with only S and C donors offer a ligation environment similar to the active site of nitrogenase (FeMoco) and thus demonstrate reasonable mechanisms and geometries for N₂ binding and reduction in nature. We recently reported the first example of N₂ binding at a mononuclear iron site supported by only S and C donors. In this work, we report experiments that examine the mechanism of N₂ binding in this system. The reduction of an iron(II) tris(thiolate) complex with 1 equiv of KC₈ leads to a thermally unstable intermediate, and a combination of Mössbauer, EPR, and X-ray absorption spectroscopies identifies it as a high-spin (S = 3/2) iron(I) species that maintains coordination of all three sulfur atoms. DFT calculations suggest that this iron(I) intermediate has a pseudotetrahedral geometry that resembles the S₃C iron coordination environment of the belt iron sites in the resting state of the FeMoco. Further reduction to the iron(0) oxidation level under argon causes the dissociation of one of the thiolate donors and gives an η⁶-arene species which reacts with N₂. Thus, in this system the loss of thiolate and binding of N₂ require reduction beyond the iron(I) level to the iron(0) level. Further reduction of the iron(0)-N₂ complex gives a reactive, formally iron(-I) species. Treatment of the putative iron(-I) complex with weak acids gives low yields of ammonia and hydrazine, demonstrating that these nitrogenase products can be generated from N₂ at a synthetic Fe-S-C site. Catalytic N₂ reduction is not observed, which is attributed to protonation of the supporting ligand and degradation of the complex via ligand dissociation. Identification of the challenges in this system gives insight into the design features needed for functional biomimetic complexes.

α-Lys424 Participates in Insertion of FeMoco to MoFe Protein and Maintains Nitrogenase Activity in Klebsiella oxytoca M5al

Our previous investigation of substrates reduction catalyzed by nitrogenase suggested that α-Ile⁴²³ of MoFe protein possibly functions as an electron transfer gate to Mo site of active center-“FeMoco”. Amino acid residue α-Lys⁴²⁴ connects directly to α-Ile⁴²³, and they are located in the same α-helix (α423-431). In the present study, function of α-Lys⁴²⁴ was investigated by replacing it with Arg (alkaline, like Lys), Gln (neutral), Glu (acidic), and Ala (neutral) through site-directed mutagenesis and homologous recombination. The mutants were, respectively, termed 424R, 424Q, 424E, and 424A. Studies of diazotrophic cell growth, cytological, and enzymatic properties indicated that none of the substitutions altered the secondary structure of MoFe protein, or normal expression of nifA, nifL, and nifD. Substitution of alkaline amino acid (i.e., 424R) maintained acetylene (C₂H₂) and proton (H⁺) reduction activities at normal levels similar to that of wild-type (WT), because its FeMoco content did not reduce. In contrast, substitution of acidic or neutral amino acid (i.e., 424Q, 424E, 424A) impaired the catalytic activity of nitrogenase to varying degrees. Combination of MoFe protein structural simulation and the results of a series of experiments, the function of α-Lys⁴²⁴ in ensuring insertion of FeMoco to MoFe protein was further confirmed, and the contribution of α-Lys⁴²⁴ in maintaining low potential of the microenvironment causing efficient catalytic activity of nitrogenase was demonstrated.

Ligand-Based Control of Single-Site vs. Multi-Site Reactivity by a Trichromium Cluster

The trichromium cluster (^tbs L)Cr₃ (thf) ([^tbs L]^6- =[1,3,5-C₆ H₉ (NC₆ H₄ -o-NSi^t BuMe₂ )₃ ]^6- ) exhibits steric- and solvation-controlled reactivity with organic azides to form three distinct products: reaction of (^tbs L)Cr₃ (thf) with benzyl azide forms a symmetrized bridging imido complex (^tbs L)Cr₃ (μ³ -NBn); reaction with mesityl azide in benzene affords a terminally bound imido complex (^tbs L)Cr₃ (μ¹ -NMes); whereas the reaction with mesityl azide in THF leads to terminal N-atom excision from the azide to yield the nitride complex (^tbs L)Cr₃ (μ³ -N). The reactivity of this complex demonstrates the ability of the cluster-templating ligand to produce a well-defined polynuclear transition metal cluster that can access distinct single-site and cooperative reactivity controlled by either substrate steric demands or reaction media.

A Thermodynamic Model for Redox-Dependent Binding of Carbon Monoxide at Site-Differentiated, High Spin Iron Clusters

Binding of N₂ and CO by the FeMo-cofactor of nitrogenase depends on the redox level of the cluster, but the extent to which pure redox chemistry perturbs the affinity of high spin iron clusters for π-acids is not well understood. Here, we report a series of site-differentiated iron clusters that reversibly bind CO in redox states Fe^II₄ through Fe^IIFe^III₃. One electron redox events result in small changes in the affinity for (at most ∼400-fold) and activation of CO (at most 28 cm^-1 for ν_CO). The small influence of redox chemistry on the affinity of these high spin, valence-localized clusters for CO is in stark contrast to the large enhancements (10⁵-10²² fold) in π-acid affinity reported for monometallic and low spin, bimetallic iron complexes, where redox chemistry occurs exclusively at the ligand binding site. While electron-loading at metal centers remote from the substrate binding site has minimal influence on the CO binding energetics (∼1 kcal·mol^-1), it provides a conduit for CO binding at an Fe^III center. Indeed, internal electron transfer from these remote sites accommodates binding of CO at an Fe^III, with a small energetic penalty arising from redox reorganization (∼2.6 kcal·mol^-1). The ease with which these clusters redistribute electrons in response to ligand binding highlights a potential pathway for coordination of N₂ and CO by FeMoco, which may occur on an oxidized edge of the cofactor.

Insight into the Iron-Molybdenum Cofactor of Nitrogenase from Synthetic Iron Complexes with Sulfur, Carbon, and Hydride Ligands

Nitrogenase enzymes are used by microorganisms for converting atmospheric N2 to ammonia, which provides an essential source of N atoms for higher organisms. The active site of the molybdenum-dependent nitrogenase is the unique carbide-containing iron-sulfur cluster called the iron-molybdenum cofactor (FeMoco). On the FeMoco, N2 binding is suggested to occur at one or more iron atoms, but the structures of the catalytic intermediates are not clear. In order to establish the feasibility of different potential mechanistic steps during biological N2 reduction, chemists have prepared iron complexes that mimic various structural aspects of the iron sites in the FeMoco. This reductionist approach gives mechanistic insight, and also uncovers fundamental principles that could be used more broadly for small-molecule activation. Here, we discuss recent results and highlight directions for future research. In one direction, synthetic iron complexes have now been shown to bind N2, break the N-N triple bond, and produce ammonia catalytically. Carbon- and sulfur-based donors have been incorporated into the ligand spheres of Fe-N2 complexes to show how these atoms may influence the structure and reactivity of the FeMoco. Hydrides have been incorporated into synthetic systems, which can bind N2, reduce some nitrogenase substrates, and/or reductively eliminate H2 to generate reduced iron centers. Though some carbide-containing iron clusters are known, none yet have sulfide bridges or high-spin iron atoms like the FeMoco.

Catalysis-dependent selenium incorporation and migration in the nitrogenase active site iron-molybdenum cofactor

Dinitrogen reduction in the biological nitrogen cycle is catalyzed by nitrogenase, a two-component metalloenzyme. Understanding of the transformation of the inert resting state of the active site FeMo-cofactor into an activated state capable of reducing dinitrogen remains elusive. Here we report the catalysis dependent, site-selective incorporation of selenium into the FeMo-cofactor from selenocyanate as a newly identified substrate and inhibitor. The 1.60 Å resolution structure reveals selenium occupying the S2B site of FeMo-cofactor in the Azotobacter vinelandii MoFe-protein, a position that was recently identified as the CO-binding site. The Se2B-labeled enzyme retains substrate reduction activity and marks the starting point for a crystallographic pulse-chase experiment of the active site during turnover. Through a series of crystal structures obtained at resolutions of 1.32-1.66 Å, including the CO-inhibited form of Av1-Se2B, the exchangeability of all three belt-sulfur sites is demonstrated, providing direct insights into unforeseen rearrangements of the metal center during catalysis.

Uncoupling binding of substrate CO from turnover by vanadium nitrogenase

Biocatalysis by nitrogenase, particularly the reduction of N2 and CO by this enzyme, has tremendous significance in environment- and energy-related areas. Elucidation of the detailed mechanism of nitrogenase has been hampered by the inability to trap substrates or intermediates in a well-defined state. Here, we report the capture of substrate CO on the resting-state vanadium-nitrogenase in a catalytically competent conformation. The close resemblance of this active CO-bound conformation to the recently described structure of CO-inhibited molybdenum-nitrogenase points to the mechanistic relevance of sulfur displacement to the activation of iron sites in the cofactor for CO binding. Moreover, the ability of vanadium-nitrogenase to bind substrate in the resting-state uncouples substrate binding from subsequent turnover, providing a platform for generation of defined intermediate(s) of both CO and N2 reduction.

Ligand binding to the FeMo-cofactor: structures of CO-bound and reactivated nitrogenase

The mechanism of nitrogenase remains enigmatic, with a major unresolved issue concerning how inhibitors and substrates bind to the active site. We report a crystal structure of carbon monoxide (CO)-inhibited nitrogenase molybdenum-iron (MoFe)-protein at 1.50 angstrom resolution, which reveals a CO molecule bridging Fe2 and Fe6 of the FeMo-cofactor. The μ2 binding geometry is achieved by replacing a belt-sulfur atom (S2B) and highlights the generation of a reactive iron species uncovered by the displacement of sulfur. The CO inhibition is fully reversible as established by regain of enzyme activity and reappearance of S2B in the 1.43 angstrom resolution structure of the reactivated enzyme. The substantial and reversible reorganization of the FeMo-cofactor accompanying CO binding was unanticipated and provides insights into a catalytically competent state of nitrogenase.

Multimetallic Cooperativity in Activation of Dinitrogen at Iron-Potassium Sites

The reaction of soluble iron-oxygen-potassium assemblies with N₂ gives insight into the mechanisms of multimetallic N₂ coordination. We report a series of very electron-rich three-coordinate, β-diketiminate-supported iron(I) phenoxide complexes, which are metastable but have been characterized under Ar by both crystallography and solution methods. Both monomeric and dimeric Fe-OPh-K compounds have been characterized, and their iron environments are very similar in the solid and solution states. In the dimer, potassium ions hold together the phenoxide oxygens and aryl rings of the two halves, to give a flexible diiron core. The reactions of the monomeric and dimeric iron(I) compounds with N₂ are surprisingly different: the mononuclear iron(I) complexes give no reaction with N₂, but the dimeric Fe₂K₂ complex reacts rapidly to give a diiron-N₂ product. Computational studies show that the key to the rapid N₂ reaction of the dimer is the preorganization of the two iron atoms. Thus, cooperation between Fe (which weakens the N-N bond) and K (which orients the Fe atoms) can be used to create a low-energy pathway for N₂ reactions.

Role of Azotobacter vinelandii FdxN in FeMo-co biosynthesis

Biosynthesis of metal clusters for the nitrogenase component proteins NifH and NifDK involves electron donation events. Yet, electron donors specific to the biosynthetic pathways of the [4Fe-4S] cluster of NifH, or the P-cluster and the FeMo-co of NifDK, have not been identified. Here we show that an Azotobacter vinelandii mutant lacking fdxN was specifically impaired in FeMo-co biosynthesis. The ΔfdxN mutant produced 5-fold less NifB-co, an early FeMo-co biosynthetic intermediate, than wild type. As a consequence, it accumulated FeMo-co-deficient apo-NifDK and was impaired in NifDK activity. We conclude that FdxN plays a role in FeMo-co biosynthesis, presumably by donating electrons to support NifB-co synthesis by NifB. This is the first role in nitrogenase biosynthesis unequivocally assigned to any A. vinelandii ferredoxin.

Multiple amino acid sequence alignment nitrogenase component 1: insights into phylogenetics and structure-function relationships

Amino acid residues critical for a protein's structure-function are retained by natural selection and these residues are identified by the level of variance in co-aligned homologous protein sequences. The relevant residues in the nitrogen fixation Component 1 α- and β-subunits were identified by the alignment of 95 protein sequences. Proteins were included from species encompassing multiple microbial phyla and diverse ecological niches as well as the nitrogen fixation genotypes, anf, nif, and vnf, which encode proteins associated with cofactors differing at one metal site. After adjusting for differences in sequence length, insertions, and deletions, the remaining >85% of the sequence co-aligned the subunits from the three genotypes. Six Groups, designated Anf, Vnf , and Nif I-IV, were assigned based upon genetic origin, sequence adjustments, and conserved residues. Both subunits subdivided into the same groups. Invariant and single variant residues were identified and were defined as “core” for nitrogenase function. Three species in Group Nif-III, Candidatus Desulforudis audaxviator, Desulfotomaculum kuznetsovii, and Thermodesulfatator indicus, were found to have a seleno-cysteine that replaces one cysteinyl ligand of the 8Fe:7S, P-cluster. Subsets of invariant residues, limited to individual groups, were identified; these unique residues help identify the gene of origin (anf, nif, or vnf) yet should not be considered diagnostic of the metal content of associated cofactors. Fourteen of the 19 residues that compose the cofactor pocket are invariant or single variant; the other five residues are highly variable but do not correlate with the putative metal content of the cofactor. The variable residues are clustered on one side of the cofactor, away from other functional centers in the three dimensional structure. Many of the invariant and single variant residues were not previously recognized as potentially critical and their identification provides the bases for new analyses of the three-dimensional structure and for mutagenesis studies.

Classifying the metal dependence of uncharacterized nitrogenases

Nitrogenase enzymes have evolved complex iron–sulfur (Fe–S) containing cofactors that most commonly contain molybdenum (MoFe, Nif) as a heterometal but also exist as vanadium (VFe, Vnf) and heterometal-independent (Fe-only, Anf) forms. All three varieties are capable of the reduction of dinitrogen (N₂) to ammonia (NH₃) but exhibit differences in catalytic rates and substrate specificity unique to metal type. Recently, N₂ reduction activity was observed in archaeal methanotrophs and methanogens that encode for nitrogenase homologs which do not cluster phylogenetically with previously characterized nitrogenases. To gain insight into the metal cofactors of these uncharacterized nitrogenase homologs, predicted three-dimensional structures of the nitrogenase active site metal-cofactor binding subunits NifD, VnfD, and AnfD were generated and compared. Dendrograms based on structural similarity indicate nitrogenase homologs cluster based on heterometal content and that uncharacterized nitrogenase D homologs cluster with NifD, providing evidence that the structure of the enzyme has evolved in response to metal utilization. Characterization of the structural environment of the nitrogenase active site revealed amino acid variations that are unique to each class of nitrogenase as defined by heterometal cofactor content; uncharacterized nitrogenases contain amino acids near the active site most similar to NifD. Together, these results suggest that uncharacterized nitrogenase homologs present in numerous anaerobic methanogens, archaeal methanotrophs, and firmicutes bind FeMo-co in their active site, and add to growing evidence that diversification of metal utilization likely occurred in an anoxic habitat.

Structure and spectroscopy of a bidentate bis-homocitrate dioxo-molybdenum(VI) complex: insights relevant to the structure and properties of the FeMo-cofactor in nitrogenase

Direct reaction of potassium molybdate (with natural abundance Mo or enriched with (92)Mo or (100)Mo) with excess hydrolyzed homocitric acid-γ-lactone in acidic solution resulted in the isolation of a cis-dioxo bis-homocitrato molybdenum(VI) complex, K(2)[*MoO(2)(R,S-H(2)homocit)(2)]·2H(2)O (1) (*Mo=Mo, 1; (92)Mo, 2; (100)Mo, 3; H(4)homocit=homocitric acid-γ-lactone·H(2)O) and K(2)[MoO(2)((18)O-R,S-H(2)homocit)(2)]·2H(2)O (4). The complex has been characterized by elemental analysis, FT-IR, solid and solution (13)C NMR, and single crystal x-ray diffraction analysis. The molybdenum atom in (1) is quasi-octahedrally coordinated by two cis oxo groups and two bidentate homocitrate ligands. The latter coordinates via its α-alkoxy and α-carboxy groups, while the β- and γ-carboxylic acid groups remain uncomplexed, similar to the coordination mode of homocitrate in the Mo-cofactor of nitrogenase. In the IR spectra, the MoO stretching modes near 900 cm(-1) show 2-3 cm(-1) red- and blue-shifts for the (92)Mo-complex (2) and (100)Mo-complex (3) respectively compared with the natural abundance version (1). At lower frequencies, bands at 553 and 540 cm(-1) are assigned to ν(Mo-O) vibrations involving the alkoxide ligand. At higher frequencies, bands in the 1700-1730 cm(-1) region are assigned to stretching modes of protonated carboxylates. In addition, a band at 1675 cm(-1) was observed that may be analogous to a band seen at 1677 cm(-1) in nitrogenase photolysis studies. The solution behavior of (1) in D(2)O was probed with (1)H and (13)C NMR spectra. An obvious dissociation of homocitrate was found, even though bound to the high valent Mo(VI). This suggests the likely lability of coordinated homocitrate in the FeMo-cofactor with its lower valence Mo(IV).

Reduction of N2 by supported tungsten clusters gives a model of the process by nitrogenase

Metalloenzymes catalyze difficult chemical reactions under mild conditions. Mimicking their functions is a challenging task and it has been investigated using homogeneous systems containing metal complexes. The nitrogenase that converts N(2) to NH(3) under mild conditions is one of such enzymes. Efforts to realize the biological function have continued for more than four decades, which has resulted in several reports of reduction of N(2), ligated to metal complexes in solutions, to NH(3) by protonation under mild conditions. Here, we show that seemingly distinct supported small tungsten clusters in a dry environment reduce N(2) under mild conditions like the nitrogenase. N(2) is reduced to NH(3) via N(2)H(4) by addition of neutral H atoms, which agrees with the mechanism recently proposed for the N(2) reduction on the active site of nitrogenase. The process on the supported clusters gives a model of the biological N(2) reduction.

Electron transfer in nitrogenase catalysis

Nitrogenase is a two-component enzyme that catalyzes the nucleotide-dependent reduction of N2 to 2NH3. This process involves three redox-active metal-containing cofactors including a [4Fe-4S] cluster, an eight-iron P cluster and a seven-iron plus molybdenum FeMo-cofactor, the site of substrate reduction. A deficit-spending model for electron transfer has recently been proposed that incorporates protein conformational gating that favors uni-directional electron transfer among the metalloclusters for the activation of the substrate-binding site. Also reviewed is a proposal that each of the metal clusters cycles through only two redox states of the metal-sulfur core as the system accumulates the multiple electrons required for substrate binding and reduction. In particular, it was suggested that as FeMo-cofactor acquires the four electrons necessary for optimal binding of N2, each successive pair of electrons is stored as an Fe-H--Fe bridging hydride, with the FeMo-cofactor metal-ion core retaining its resting redox state. We here broaden the discussion of stable intermediates that might form when FeMo-cofactor receives an odd number of electrons.

EXAFS and NRVS reveal a conformational distortion of the FeMo-cofactor in the MoFe nitrogenase propargyl alcohol complex

We have used EXAFS and NRVS spectroscopies to examine the structural changes in the FeMo-cofactor active site of the α-70(Ala) variant of Azotobacter vinelandii nitrogenase on binding and reduction of propargyl alcohol (PA). The Mo K-edge near-edge and EXAFS spectra are very similar in the presence and absence of PA, suggesting PA does not bind at Mo. By contrast, Fe EXAFS spectra show a clear and reproducible change in the long Fe-Fe interaction at ~3.7 Å on PA binding with the apparent appearance of a new Fe-Fe interaction at 3.99 Å. An analogous change in the long Mo-Fe 5.1 Å interaction is not seen. The NRVS spectra exclude the possibility of large-scale structural change of the FeMo-cofactor involving breaking the μ(2) Fe-S-Fe bonds of the Fe(6)S(9)X core. The simplest chemically consistent structural change is that the bound form of PA is coordinated at Fe atoms (Fe6 or Fe7) adjacent to the Mo terminus, with a concomitant movement of the Fe away from the central atom X and along the Fe-X bond by about 0.35 Å. This study comprises the first experimental evidence of the conformational changes of the FeMo-cofactor active site on binding a substrate or product.

Electron paramagnetic resonance spectroscopy

EPR spectroscopy has been an important tool in nitrogenase research for the last 50 years. The three metalloclusters in nitrogenase, the Fe protein [4Fe-4S] cluster, and the MoFe protein P-cluster, and FeMo-cofactor, all have EPR spectra when poised in the appropriate paramagnetic states. EPR spectroscopy can probe changes in the electronic properties of each metal cluster, such as when substrates bind, and can provide a definitive method for observing changes in the redox states of the clusters. In this chapter, the methods for analysis of the three metal clusters of nitrogenase by EPR spectroscopy are described, along with methods for trapping substrate-derived intermediates on the active site that are amenable to characterization by EPR and other magnetic resonance spectroscopy techniques.

Mechanism of Mo-dependent nitrogenase

Nitrogenase is the enzyme responsible for biological reduction of dinitrogen (N(2)) to ammonia, a form usable for life. Playing a central role in the global biogeochemical nitrogen cycle, this enzyme has been the focus of intensive research for over 60 years. This chapter provides an overview of the features of nitrogenase as a background to the subsequent chapters of this volume that detail the many methods that have been applied in an attempt to gain a deeper understanding of this complex enzyme.

Formation of {[HIPTN(3)N]Mo(III)H}(-) by heterolytic cleavage of H(2) as established by EPR and ENDOR spectroscopy

MoN(2) (Mo = [(HIPTNCH(2)CH(2))(3)N]Mo, where HIPT = 3,5-(2,4,6-i-Pr(3)C(6)H(2))(2)C(6)H(3)) is the first stage in the reduction of N(2) to NH(3) by Mo. Its reaction with dihydrogen in fluid solution yields "MoH(2)", a molybdenum-dihydrogen compound. In this report, we describe a comprehensive electron paramagnetic resonance (EPR) and (1/2)H/(14)N electron nuclear double resonance (ENDOR) study of the product of the reaction between MoN(2) and H(2) that is trapped in frozen solution, 1. EPR spectra of 1 show that it has a near-axial g tensor, g = [2.086, 1.961, 1.947], with dramatically reduced g anisotropy relative to MoN(2). Analysis of the g values reveal that this anion has the Mo(III), [d(xz), d(yz)](3) orbital configuration, as proposed for the parent MoN(2) complex, and that it undergoes a strong pseudo-Jahn-Teller (PJT) distortion. Simulations of the 2D 35 GHz (1)H ENDOR pattern comprised of spectra taken at multiple fields across the EPR envelope (2 K) show that 1 is the [MoH](-) anion. The 35 GHz Mims pulsed (2)H ENDOR spectra of 1 prepared with (2)H(2) show the corresponding (2)H(-) signal, with a substantial deuterium isotope effect in a(iso). Radiolytic reduction of a structural analogue, Mo(IV)H, at 77 K, confirms the assignment of 1. Analysis of the 2D (14)N ENDOR pattern for the ligand amine nitrogen further reveals the presence of a linear N(ax)-Mo-H(-) molecular axis that is parallel to the unique magnetic direction (g(1)). The ENDOR pattern of the three equatorial nitrogens is well-reproduced by a model in which the Mo-N(eq) plane has undergone a static, not dynamic, PJT distortion, leading to a range of hyperfine couplings for the three N(eq)'s. The finding of a nearly axial hyperfine coupling tensor for the terminal hydride bound Mo supports the earlier proposal that the two exchangeable hydrogenic species bound to the FeMo cofactor of the nitrogense turnover intermediate, which has accumulated four electrons/protons (E(4)), are hydrides that bridge two metal ions, not terminal hydrides.

Trapping an intermediate of dinitrogen (N2) reduction on nitrogenase

Nitrogenase reduces dinitrogen (N2) by six electrons and six protons at an active-site metallocluster called FeMo cofactor, to yield two ammonia molecules. Insights into the mechanism of substrate reduction by nitrogenase have come from recent successes in trapping and characterizing intermediates generated during the reduction of protons as well as nitrogenous and alkyne substrates by MoFe proteins with amino acid substitutions. Here, we describe an intermediate generated at a high concentration during reduction of the natural nitrogenase substrate, N2, by wild-type MoFe protein, providing evidence that it contains N2 bound to the active-site FeMo cofactor. When MoFe protein was frozen at 77 K during steady-state turnover with N2, the S = 3/2 EPR signal (g = [4.3, 3.64, 2.00]) arising from the resting state of FeMo cofactor was observed to convert to a rhombic, S = 1/2, signal (g = [2.08, 1.99, 1.97]). The intensity of the N2-dependent EPR signal increased with increasing N2 partial pressure, reaching a maximum intensity of approximately 20% of that of the original FeMo cofactor signal at > or = 0.2 atm N2. An almost complete loss of resting FeMo cofactor signal in this sample implies that the remainder of the enzyme has been reduced to an EPR-silent intermediate state. The N2-dependent EPR signal intensity also varied with the ratio of Fe protein to MoFe protein (electron flux through nitrogenase), with the maximum signal intensity observed with a ratio of 2:1 (1:1 Fe protein:FeMo cofactor) or higher. The pH optimum for the signal was 7.1. The N2-dependent EPR signal intensity exhibited a linear dependence on the square root of the EPR microwave power in contrast to the nonlinear response of signal intensity observed for hydrazine-, diazene-, and methyldiazene-trapped states. 15N ENDOR spectroscopic analysis of MoFe protein captured during turnover with 15N2 revealed a 15N nuclear spin coupled to the FeMo cofactor with a hyperfine tensor A = [0.9, 1.4, 0.45] MHz establishing that an N2-derived species was trapped on the FeMo cofactor. The observation of a single type of 15N-coupled nucleus from the field dependence, along with the absence of an associated exchangeable 1H ENDOR signal, is consistent with an N2 molecule bound end-on to the FeMo cofactor.

Catalytic activities of NifEN: implications for nitrogenase evolution and mechanism

NifEN is a key player in the biosynthesis of nitrogenase MoFe protein. It not only shares a considerable degree of sequence homology with the MoFe protein, but also contains clusters that are homologous to those found in the MoFe protein. Here we present an investigation of the catalytic activities of NifEN. Our data show that NifEN is catalytically competent in acetylene (C(2)H(2)) and azide (N(3)(-)) reduction, yet unable to reduce dinitrogen (N(2)) or evolve hydrogen (H(2)). Upon turnover, C(2)H(2) gives rise to an additional S = 1/2 signal, whereas N(3)(-) perturbs the signal originating from the NifEN-associated FeMoco homolog. Combined biochemical and spectroscopic studies reveal that N(3)(-) can act as either an inhibitor or an activator for the binding and/or reduction of C(2)H(2), while carbon monoxide (CO) is a potent inhibitor for the binding and/or reduction of both N(3)(-) and C(2)H(2). Taken together, our results suggest that NifEN is a catalytic homolog of MoFe protein; however, it is only a "skeleton" version of the MoFe protein, as its associated clusters are simpler in structure and less versatile in function, which, in turn, may account for its narrower range of substrates and lower activities of substrate reduction. The resemblance of NifEN to MoFe protein in catalysis points to a plausible, sequential appearance of the two proteins in nitrogenase evolution. More importantly, the discrepancy between the two systems may provide useful insights into nitrogenase mechanism and allow reconstruction of a fully functional nitrogenase from the "skeleton" enzyme, NifEN.

Mechanism of Mo-dependent nitrogenase

Nitrogen-fixing bacteria catalyze the reduction of dinitrogen (N(2)) to two ammonia molecules (NH(3)), the major contribution of fixed nitrogen to the biogeochemical nitrogen cycle. The most widely studied nitrogenase is the molybdenum (Mo)-dependent enzyme. The reduction of N(2) by this enzyme involves the transient interaction of two component proteins, designated the iron (Fe) protein and the MoFe protein, and minimally requires 16 magnesium ATP (MgATP), eight protons, and eight electrons. The current state of knowledge on how these proteins and small molecules together effect the reduction of N(2) to ammonia is reviewed. Included is a summary of the roles of the Fe protein and MgATP hydrolysis, information on the roles of the two metal clusters contained in the MoFe protein in catalysis, insights gained from recent success in trapping substrates and inhibitors at the active-site metal cluster FeMo cofactor, and finally, considerations of the mechanism of N(2) reduction catalyzed by nitrogenase.