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FeMoco

FeMoco, or the iron-molybdenum cofactor, is a highly complex metallocluster that functions as the catalytic active site of the molybdenum nitrogenase enzyme, enabling the biological fixation of atmospheric dinitrogen (N₂) into ammonia (NH₃) through a multi-electron reduction process that requires ATP hydrolysis.^[1] This cofactor is essential for nitrogen-fixing organisms, such as certain bacteria and archaea, to convert inert N₂ into bioavailable forms, supporting global nitrogen cycles and agriculture without industrial inputs.^[2] Structurally, FeMoco consists of seven iron atoms, one molybdenum atom, nine sulfide ions, a central carbide (C⁴⁻) atom interstitially coordinated within a 6Fe core, and a homocitrate ligand bound to the molybdenum, forming the formula [MoFe₇S₉C·homocitrate].^[3] The central carbon atom, confirmed through X-ray emission spectroscopy, plays a crucial role in stabilizing the cluster and facilitating substrate binding and reduction, distinguishing FeMoco from simpler iron-sulfur clusters.^[3] This intricate architecture allows nitrogenase to perform the energetically demanding N₂ reduction, overcoming the molecule's triple bond with high specificity.^[4] The biosynthesis of FeMoco is a multi-step pathway involving specialized nitrogen fixation (Nif) proteins in prokaryotes, beginning with the assembly of an 8Fe precursor cluster by the radical SAM enzyme NifB, which inserts the central carbon from a methyl group.^[5] This precursor, known as NifB-co, is then transferred to the scaffold proteins NifEN for maturation, where molybdenum and homocitrate—synthesized by homoisocitrate dehydrogenase (NifV)—are incorporated before final insertion into the MoFe protein (NifDK) by NifH, the Fe protein reductase.^[1] Disruptions in this pathway, such as mutations in NifB or NifEN, abolish nitrogenase activity, underscoring the precision required for cofactor assembly.^[5] Beyond nitrogen fixation, FeMoco enables nitrogenase to reduce alternative substrates like protons to hydrogen (H₂), carbon monoxide (CO), and even carbon dioxide (CO₂) to hydrocarbons under specific conditions, revealing its versatility in small-molecule activation.^[6] Recent structural studies using cryo-electron microscopy have captured turnover states of nitrogenase, providing insights into how FeMoco's redox states and conformational changes drive catalysis.^[7] Understanding FeMoco has inspired synthetic modeling efforts to mimic its reactivity, with implications for developing bio-inspired catalysts for sustainable ammonia production.^[8]

Structure

Cluster Composition

The iron-molybdenum cofactor (FeMoco) has the empirical formula [MoFe₇S₉C-(R)-homocitrate], consisting of one molybdenum atom, seven iron atoms, nine sulfide ions, a central carbon atom, and an (R)-homocitrate ligand coordinated to the molybdenum. This composition establishes FeMoco as the largest known fully characterized metal cluster in biology, with the homocitrate providing bidentate oxygen coordination to the Mo atom, stabilizing its position within the nitrogenase MoFe protein.^[3] FeMoco is anchored to the protein matrix through specific amino acid ligands: the sulfur atom of cysteine residue α-Cys-275 coordinates to one peripheral iron atom (Fe1), while the imidazole nitrogen of histidine residue α-His-442 ligates the molybdenum atom. These protein-derived ligands integrate the cluster into the α-subunit of the MoFe protein, facilitating electron transfer and substrate access while maintaining structural integrity. At the core of FeMoco lies an interstitial carbon atom, identified as a carbide (C⁴⁻) centrally coordinated to six iron atoms, which contributes to the cluster's unique reactivity and electronic delocalization. Surrounding this carbide, six sulfide ions serve as bridges between the metal centers, linking the molybdenum-iron framework and enabling the overall connectivity of the cluster. The formal oxidation states in the resting state (E₀) are debated but often described as Mo(III) with three Fe(II) and four Fe(III), or alternatively Mo(IV) with four Fe(II) and three Fe(III), reflecting a mixed-valence system where the electronic structure features delocalized electrons among iron sites, supporting the S = 3/2 ground state observed in electron paramagnetic resonance spectroscopy.^[9]^[10]

Geometric Arrangement

The FeMoco cluster exhibits a distinctive trigonal prismatic geometry, comprising two incomplete Fe₄S₃ cubane motifs linked by three μ₂-bridging sulfide ions and an interstitial carbide (C⁴⁻) atom that coordinates six iron atoms at the core. This architecture positions the molybdenum atom at one apex, coordinated to three sulfides within one cubane, while the opposite apex is formed by three irons from the second cubane, creating a compact, symmetric scaffold essential for its catalytic role.^[3] The overall structure spans approximately 10 Å in diameter, with the central carbon residing equidistant from the bridging sulfides. High-resolution crystallographic analyses, such as the 1.16 Å structure of the Azotobacter vinelandii MoFe protein, reveal precise bond metrics that define this arrangement. The average Fe-S bond length is 2.32 Å across the cluster's sulfide ligands, reflecting strong coordination within the cubanes and bridges. Mo-Fe distances vary between 2.7 and 3.0 Å, with an average of approximately 2.69 Å, indicating flexible yet stable heterometal-iron interactions.^[11] Fe-C bonds are notably shorter, ranging from 1.9 to 2.0 Å (average ~2.00 Å), underscoring the carbide's central, nearly tetrahedral coordination to the iron belt.^[12] In the context of the nitrogenase MoFe protein, FeMoco resides adjacent to the P-cluster (a Fe₈S₇ unit), facilitating electron transfer, though FeMoco maintains its independent trigonal prismatic integrity without direct bonding to the P-cluster. Structural variations occur across redox states; for instance, reduction to the E₁ state induces minor distortions, including expansion of Fe-S distances by ~0.02 Å and select Fe-Fe distances by ~0.02 Å, consistent with electron accumulation and potential belt sulfide protonation.^[13]

Biosynthesis

Genetic and Enzymatic Components

The biosynthesis of the iron-molybdenum cofactor (FeMoco) in nitrogenase is orchestrated by a cluster of nitrogen fixation (nif) genes, primarily nifB, nifE, nifN, nifH, nifV, nifQ, nifY, nifX, nifU, and nifS, which encode proteins essential for assembling the complex metallocluster in diazotrophic bacteria such as Azotobacter vinelandii. These genes are organized in operons and coordinate the provision of iron-sulfur clusters, molybdenum, and organic ligands required for FeMoco maturation.^[14] Among the key enzymes, NifB functions as a radical S-adenosylmethionine (SAM) enzyme that catalyzes the formation of the L-cluster, an eight-iron precursor to FeMoco, by fusing iron-sulfur sub-clusters and inserting a central carbide atom.^[15] The NifEN complex, composed of NifE and NifN proteins, serves as a biosynthetic scaffold that binds the L-cluster intermediate and facilitates the incorporation of molybdenum and homocitrate to yield the mature FeMoco core.^[16] NifH, encoding the iron protein of nitrogenase, delivers electrons during the biosynthetic process and supports the maturation of cofactor precursors on the scaffold. NifV encodes homocitrate synthase, which produces R-homocitrate as the essential organic ligand that coordinates molybdenum in FeMoco, enabling proper cluster assembly and catalytic activity. Accessory proteins such as NifQ provide molybdenum for insertion, NifY and NifX aid in cluster stabilization and transfer, while NifU and NifS assemble and supply iron-sulfur units via NifU's scaffolding and NifS's cysteine desulfurase activity.^[17] Recent advances include the 2025 heterologous expression of a simplified nitrogenase analog in Escherichia coli using nifH, nifE, nifN, nifB, nifU, nifS, and nifM genes from Azotobacter vinelandii and Methanosarcina acetivorans, achieving in vivo N₂ fixation and demonstrating the minimal genetic requirements for L-cluster production.^[18]

Stepwise Assembly Pathway

The biosynthesis of FeMoco begins with the assembly of [4Fe-4S] clusters by the NifU scaffold protein and the NifS cysteine desulfurase, which provide iron and sulfide precursors essential for subsequent cluster fusion.^[2] These [4Fe-4S] clusters are transferred to the NifB radical SAM enzyme, where two such units are fused in an ATP-independent process to generate the 8Fe precursor known as the L-cluster, an [8Fe-9S-C] structure featuring a central carbide atom derived from the 5'-deoxyadenosyl radical generated by SAM cleavage.^[2] This L-cluster formation on NifB represents a critical radical-mediated step in FeMoco maturation, incorporating the ninth sulfide from an external source such as sulfite.^[2] The L-cluster is then transferred from NifB to the NifEN scaffold protein, forming an [8Fe-9S] intermediate cluster designated as the VK-cluster, which lacks molybdenum and homocitrate.^[2] On the NifEN scaffold, molybdenum is incorporated via the NifQ protein, which delivers Mo from a [Mo-3Fe-4S] cluster, while homocitrate—synthesized by NifV (homocitrate synthase)—is added as the organic ligand coordinating the molybdenum atom.^[2] This addition, coupled with further sulfide rearrangements and ATP-dependent maturation facilitated by the NifH Fe protein, completes the FeMoco structure on NifEN.^[2] Mature FeMoco is subsequently transferred from NifEN to the apo-MoFe protein, which already contains P-clusters, with the insertion process chaperoned by the NifY (or NafY) protein to prevent cluster degradation and ensure proper positioning within the protein's alpha subunits.^[2] Throughout the maturation steps on NifEN, including molybdenum and homocitrate incorporation, energy is supplied by the hydrolysis of MgATP catalyzed by the NifH Fe protein, which interacts reductively with the scaffold to drive conformational changes and cluster rearrangements.^[2] This ATP-dependent mechanism underscores the energy-intensive nature of FeMoco assembly, mirroring aspects of the nitrogenase catalytic cycle.^[2]

Central Core

Historical Identification

The structure of the iron-molybdenum cofactor (FeMoco) in nitrogenase was initially probed in the 1970s and 1980s using extended X-ray absorption fine structure (EXAFS) spectroscopy, which suggested a complex arrangement of molybdenum coordinated to iron and sulfur atoms, but without resolving a central light atom. Mössbauer spectroscopy during this period provided insights into the oxidation states and magnetic properties of the iron centers, fueling debates over possible interstitial light atoms such as nitrogen or oxygen to explain the cluster's stability and electronic behavior. By the 1990s and early 2000s, higher-resolution X-ray crystallography confirmed the [MoFe₇S₉] core composition, yet the coordination environment remained ambiguous, with proposals favoring a central nitrogen, carbon, or mixed N/O ligand based on spectroscopic fitting and modeling.^[9]^[19] The presence of an interstitial light atom at the center of FeMoco was first directly observed in 2002 through a high-resolution X-ray crystal structure of the MoFe protein, revealing a low-occupancy electron density peak consistent with a small 2p element, though its identity remained elusive. Pre-2011 evidence increasingly pointed toward carbon, as density functional theory (DFT) calculations on model clusters demonstrated that a central carbide better reproduced the observed Fe-Fe distances, spin states, and Mössbauer isomer shifts compared to nitrogen or oxygen alternatives. For instance, DFT studies in the mid-2000s showed that carbon as the interstitial ligand minimized structural distortions and aligned with EXAFS-derived bond lengths, supporting its role in maintaining the cluster's fused cubane geometry.^[20] A major breakthrough occurred in 2011 when single-crystal X-ray crystallography, combined with biosynthetic incorporation of ¹³C- and ¹⁵N-labeled precursors into Azotobacter vinelandii nitrogenase, unambiguously identified the central atom as a carbide (C⁴⁻) ligand, as the anomalous scattering signal shifted only for carbon-labeled samples. This work by Spatzal et al. resolved longstanding debates by showing the carbide's μ₆-coordination to six central iron atoms. Shortly thereafter, X-ray emission spectroscopy (XES) further corroborated the carbide assignment by matching the Fe Kβ valence-to-core emission spectrum to DFT models with carbon, excluding nitrogen or oxygen.^[3] Post-2011 confirmations refined the carbide's position and dynamics using advanced techniques, such as spatially resolved anomalous dispersion X-ray spectroscopy at the iron K-edge, which mapped the carbide's central location in the resting and substrate-bound states of FeMoco. These studies, including pulsed electron-electron double resonance (PELDOR) and ENDOR spectroscopy, affirmed the carbide's fixed position and its contribution to cluster rigidity, briefly underscoring its stabilizing influence without altering the core topology during catalysis.^[21]^[9]

Role and Implications

The central core of FeMoco consists of an interstitial carbide ion, formally described as C⁴⁻, which is essential for maintaining the structural and functional integrity of the cofactor during nitrogenase catalysis. This carbide coordinates to six iron atoms in a trigonal prismatic arrangement, imparting exceptional stability to the [Fe₆C] subunit and preventing cluster dissociation even amid dynamic Fe–S bond cleavage and reformation.^[22] Such robustness allows FeMoco to accommodate the successive accumulation of electrons and protons required for the multi-electron reduction of N₂ to NH₃, a process demanding up to eight equivalents without compromising the core framework.^[22] The carbide significantly influences the electronic structure of FeMoco by modulating the redox potentials of the iron sites, rendering them more reducing and conducive to N₂ activation. Studies on partial synthetic models reveal that incorporating an interstitial carbyne ligand—mimicking the carbide—shifts cluster reduction potentials to values up to 1 V more negative than those in analogous nitrogen- or sulfur-bridged clusters, thereby enhancing the thermodynamic feasibility of binding and reducing inert substrates like N₂.^[12] This electronic tuning ensures that the Fe sites can achieve the low-valent states necessary for weakening the N≡N triple bond during turnover.^[12] In terms of catalytic implications, the carbide serves as a rigid scaffold that orients the peripheral iron atoms, creating accessible axial coordination sites for substrate approach while preserving overall cluster geometry. This structural role facilitates selective binding at reactive Fe centers, optimizing the pathway for proton-coupled electron transfers in nitrogen fixation.^[12] Although FeVco and FeFeco cofactors in alternative nitrogenases also feature a central carbide, differences in heterometal composition (V or Fe versus Mo) lead to distinct redox behaviors and lower catalytic efficiencies for N₂ reduction compared to FeMoco.^[12]^[23]

Properties

Electronic Structure

The electronic structure of the iron-molybdenum cofactor (FeMoco) in its resting state, denoted as E₀, is characterized by a ground-state spin of S = 3/2, arising from antiferromagnetic coupling among the iron centers.^[9] This spin state reflects a complex interplay of high-spin iron ions with delocalized electrons primarily across the seven Fe sites, while the molybdenum center remains less involved in the redox processes.^[24] Density functional theory (DFT) calculations consistently support this antiferromagnetic coupling, modeling the Fe-Fe interactions as superexchange-mediated through bridging sulfides, which stabilizes the observed S = 3/2 ground state over higher-spin alternatives.^[24] Formal oxidation-state assignments for the resting E₀ state provide a framework for understanding the valence electron distribution, though delocalization complicates strict localization. The accepted assignment based on recent studies is Mo³⁺ with 4Fe³⁺ and 3Fe²⁺, alongside 9S²⁻ and C⁴⁻, yielding an overall cluster charge of [MoFe₇S₉C]¹⁻ and a total of 41 valence d-electrons from the metals.^[9] This configuration highlights the mixed-valence nature of the Fe ions, with electron density delocalized in the Fe₄C subcluster, contributing to the cofactor's reactivity. Spectroscopic studies, such as Mössbauer and ENDOR, corroborate aspects of this electronic description by probing Fe site asymmetries.^[25] Upon activation, FeMoco undergoes sequential reduction to states E₁ through E₄, accumulating up to four electrons and protons relative to E₀, with the full catalytic cycle for N₂ reduction requiring eight electrons total (including two for obligatory H₂ production).^[25] In these reduced states, additional electrons are primarily accommodated by the Fe sites through further delocalization and potential hydride formation, while the Mo³⁺ oxidation state persists with minimal change, underscoring the Fe core's dominant role in redox chemistry.^[26] DFT models of these states reveal progressive antiferromagnetic adjustments and increased electron density on the central carbide, facilitating substrate binding without significant Mo reduction.^[24]

Spectroscopic Characteristics

Electron Paramagnetic Resonance (EPR) spectroscopy reveals the paramagnetic nature of FeMoco in its resting state (E₀), characterized by an S = 3/2 ground state with a rhombic EPR signal at effective g-values of approximately 4.3, 3.7, and 2.0.^[27] This signal arises from the antiferromagnetically coupled iron and molybdenum ions, with the high axial anisotropy (E/D ≈ 0.05) attributed to the molybdenum's influence on the cluster's electronic delocalization.^[27] Upon dithionite reduction, the EPR spectrum evolves, often quenching the S = 3/2 signal or shifting to low-spin integer states, reflecting changes in the spin coupling and oxidation levels within the cluster.^[27] Mössbauer spectroscopy elucidates the distinct electronic environments of the seven iron atoms in FeMoco, primarily through isomer shifts (δ) and quadrupole splittings (ΔE_Q) that indicate mixed Fe²⁺/Fe³⁺ valences.^[27] In the resting state at 4.2 K, the spectra resolve multiple subsites, with Fe1 exhibiting δ = 0.39 mm/s and ΔE_Q = -0.69 mm/s, and Fe7 showing δ = 0.50 mm/s and ΔE_Q = -0.65 mm/s, highlighting their unique positions adjacent to the molybdenum and central carbide.^[28] Other iron sites display similar but varied parameters (δ ≈ 0.33–0.48 mm/s, |ΔE_Q| ≈ 0.56–0.68 mm/s), consistent with four-coordinate sulfur ligation and delocalized valence electrons across the cluster.^[28] X-ray Absorption Spectroscopy (XAS) combined with Extended X-ray Absorption Fine Structure (EXAFS) at the Mo K-edge confirms the octahedral coordination of molybdenum in FeMoco, with Mo–S distances of ~2.3 Å to bridging sulfides and Mo–O distances of ~1.8 Å to the homocitrate ligand's carboxylate and alkoxide groups.^[27] These measurements validate the Mo³⁺ oxidation state and its connectivity to three iron atoms (Fe1, Fe3, Fe7) via sulfide bridges. Fe K-edge XAS/EXAFS further characterizes the iron core, revealing average Fe–Fe distances of ~2.6 Å and Fe–S distances of ~2.3 Å, with pre-edge features indicating heterogeneous oxidation states; for example, Fe1, Fe3, and Fe7 display lower edge energies suggestive of ferrous character, while Fe2, Fe4, Fe5, and Fe6 are more oxidized. Such analyses also detect subtle cluster expansions, with Fe–S bond lengthening up to 0.1 Å in reduced forms, underscoring the structural flexibility of the [7Fe–9S–C] core.^[29] Electron Nuclear Double Resonance (ENDOR) spectroscopy provides site-specific hyperfine couplings to identify ligands and assess core atom interactions in FeMoco.^[27] For instance, ¹⁴N ENDOR signals from the α-442 histidine ligand show hyperfine anisotropy (A ≈ 5–10 MHz), confirming its coordination to Fe6, while ¹H ENDOR from homocitrate protons exhibits couplings of ~1–2 MHz, delineating the bidentate binding mode.^[27] ⁵⁷Fe ENDOR further resolves individual iron sites, with hyperfine tensors varying by position (e.g., larger A for peripheral vs. central irons), enabling mapping of electron density and proximity to the interstitial carbon core through through-space dipolar interactions with nearby sulfurs.

Function

Substrate Interactions

Substrate interactions with the FeMoco active site of nitrogenase primarily occur at the iron atoms, particularly along the Fe2–Fe6 edge adjacent to the central carbide atom, enabling the binding and activation of small molecules such as dinitrogen (N₂), carbon monoxide (CO), and protons. These interactions are facilitated by the cofactor's flexible coordination environment, which allows ligands to access coordinatively unsaturated iron sites upon reduction. Experimental structures and spectroscopic studies have elucidated specific binding modes, highlighting the site's adaptability during catalysis. CO, a potent inhibitor of nitrogenase, binds to the Fe2–Fe6 edge of FeMoco near the central carbon in a reduced state (E₄), where one CO molecule coordinates in a bridging fashion between Fe2 and Fe6 and a second CO binds terminally to Fe6, as revealed by a 1.33 Å resolution crystal structure of the MoFe protein under turnover conditions.^[30] This binding mode occludes the substrate access site, preventing N₂ reduction and demonstrating the cofactor's capacity for multiple ligand coordination at this edge. Earlier spectroscopic evidence supports initial terminal CO binding that rearranges to bridging upon further reduction.^[31] N₂ binds to FeMoco in a reduced state (E₄), adopting a bridging coordination mode between iron atoms along the Fe2–Fe6 edge, as captured in a 1.83 Å crystal structure of the MoFe protein during physiological N₂ turnover, where the edge opens to accommodate the substrate without a central ligand.^[32] Computational and model studies suggest possible bridged N₂ coordination between iron atoms or involving the molybdenum atom in certain activated configurations, though experimental data favor bridging Fe binding as the primary mode for reduction initiation.^[26] Protons interact with FeMoco as hydride ligands during the enzyme's reductive activation, primarily bridging or terminally coordinating to Fe2 and Fe6 sites in early E-state intermediates (E₂–E₃), which prepares the cofactor for substrate binding by increasing site reactivity and spin-state flexibility.^[33] These hydride positions are confirmed by ENDOR spectroscopy, showing protonation enhances electron density at the binding edge without fully saturating it.^[34] Inhibitors like cyanide (CN⁻) bind selectively to iron atoms on FeMoco, occupying substrate-accessible sites and blocking N₂ reduction; kinetic and theoretical studies on extracted FeMoco derivatives indicate multiple binding modes at Fe centers, with association constants reflecting tight coordination that mimics substrate inhibition. This binding alters the cofactor's electronic properties, as observed by EPR spectroscopy, confirming Fe-specific occlusion of the active site.^[35] The flexibility of FeMoco's binding pocket is underscored by studies of variant MoFe proteins with mutations near the cofactor (e.g., α-70, α-195, α-242 residues), which enlarge access channels and reveal hidden coordination sites; for instance, the α-96Arg→Gln variant traps acetylene in a pocket adjacent to FeMoco, demonstrating how protein conformational changes expose the Fe2–Fe6 edge for larger or alternative ligands.^[25] These variants highlight the cofactor's dynamic nature, where sulfido ligands can relocate to accommodate binding without permanent structural disruption.^[7]

Catalytic Mechanism

The catalytic mechanism of FeMoco in nitrogenase involves the stepwise transfer of eight electrons and eight protons to dinitrogen (N₂), ultimately yielding two molecules of ammonia (NH₃) and one molecule of dihydrogen (H₂), in a process that obligatorily hydrolyzes 16 ATP molecules.^[36] The nitrogenase enzyme complex consists of the Fe protein (NifH), which acts as the obligate electron donor, and the MoFe protein containing the P-cluster and FeMoco as the site of N₂ reduction. Each cycle of Fe protein docking to the MoFe protein delivers one electron to the P-cluster concomitant with the hydrolysis of two ATP molecules, requiring eight such docking events to provide the necessary reducing equivalents for N₂ reduction.^[36] The overall reaction is thus represented as N₂ + 8 e⁻ + 8 H⁺ + 16 ATP → 2 NH₃ + H₂ + 16 ADP + 16 Pᵢ. Electron transfer proceeds from the [4Fe-4S] cluster of the Fe protein to the P-cluster ([8Fe-7S]) in the MoFe protein during transient complex formation, after which the P-cluster relays electrons one at a time to FeMoco, the catalytically active site.^[37] This sequential reduction accumulates electrons and protons on FeMoco in discrete states denoted E₀ through E₈ in the Lowe-Thorneley kinetic scheme, with recent studies using selenium incorporation to trap and analyze early intermediates (E₀ to E₃), revealing details of initial electron accumulation and cluster rearrangements.^[38] N₂ binding typically occurring at or near the E₄ state to initiate substrate reduction.^[36] The P-cluster undergoes redox state changes (e.g., from Pᴼ to P⁺ to Pᴺ), facilitating efficient electron tunneling to FeMoco while preventing back-transfer, and its structural rearrangements upon reduction help gate the process to match the timing of ATP hydrolysis.^[37] A pivotal intermediate in the mechanism is the E₄ state, where four electrons and four protons have been delivered to FeMoco, often characterized by the formation of two bridging hydride ligands ([Fe–H–Fe]) between specific iron atoms (e.g., Fe₂/Fe₆ and Fe₃/Fe₇), which bridge a central cavity and prime the cluster for N₂ binding by exposing coordination sites.^[39] Upon N₂ binding at this state, further electron-proton delivery reduces the substrate through key intermediates such as diazene (N₂H₂), which represents a two-electron reduced form of N₂, and potentially hydrazine (N₂H₄) as a four-electron intermediate, leading to sequential release of the two NH₃ molecules and obligatory H₂ evolution from the E₄ hydrides or later steps.^[36] The mechanism ensures that H₂ production is coupled to N₂ reduction, accounting for the extra two electrons beyond the six required for 2 NH₃, and computational studies support a pathway where proton-coupled electron transfers progressively weaken the N≡N triple bond.^[40] FeMoco's ability to reduce alternative substrates underscores the mechanism's versatility; for instance, acetylene (C₂H₂) is reduced to ethylene (C₂H₄) with a two-electron, two-proton transfer, bypassing deeper reduction steps and serving as a diagnostic probe for nitrogenase activity.^[41] Additionally, in the absence of N₂, excess electrons reduce protons directly to H₂, highlighting the enzyme's default hydrogenase activity and the role of FeMoco in multi-electron redox chemistry.^[36]

Isolation and Synthesis

Extraction Methods

The initial laboratory isolation of native FeMoco from the molybdenum-iron (MoFe) protein of nitrogenase was developed in the 1970s, primarily using solvent extraction techniques on preparations from Azotobacter vinelandii. In the pioneering method reported by Shah and Brill, the MoFe protein was denatured with citric acid and phosphate buffer under anaerobic conditions, followed by extraction of the cofactor into N-methylformamide (NMF), which solubilized approximately 90% of the intact clusters based on molybdenum recovery and activity metrics.^[42] This approach yielded a dark brown solution containing the cofactor, with the Fe/Mo/S ratio determined to be roughly 8:1:6 through metal and sulfide analysis.^[42] Purification of the extracted FeMoco involves initial centrifugation at 8000 × g to separate the soluble cofactor from denatured protein precipitates, followed by gel filtration chromatography on Sephadex G-100 columns equilibrated with NMF or related solvents to remove contaminants and concentrate the cluster.^[43] The integrity and functionality of the isolated FeMoco are confirmed through reconstitution assays, where the extract restores nitrogenase activity in apo-MoFe protein from FeMoco-deficient mutants like A. vinelandii UW45, as measured by acetylene reduction to ethylene with specific activities up to 425 nmol C₂H₄/min/nmol Mo.^[42] Key challenges in these extraction protocols include the cofactor's high instability, with rapid degradation in aqueous media (losing up to 40% activity within hours) and extreme sensitivity to oxygen, which inactivates it within minutes under aerobic exposure, resulting in consistently low overall yields.^[42] To address these issues, variants have employed chaotropic solvents like N-methylformamide (NMF), which coordinates directly to the cluster and enhances stability without requiring additional ligands.^[43]

Synthetic Models

Efforts to synthesize models of the iron-molybdenum cofactor (FeMoco) began in the 1980s with the development of cubane-type [MoFe₃S₄] clusters, which aimed to replicate the core metal-sulfur framework proposed for the enzyme's active site based on early spectroscopic data.^[44] These single-cubane units, synthesized via self-assembly methods involving molybdenum and iron precursors with sulfide ligands, provided initial insights into the electronic properties and redox behavior of Mo-Fe-S assemblies but were limited by their smaller size—containing only four metal atoms compared to FeMoco's eight—and inability to bind or reduce N₂, highlighting the need for more complex architectures.^[44]^[45] Significant advances occurred by 2025 with the synthesis of larger cluster mimics that more closely approximate FeMoco's overall topology, particularly a trigonal prismatic [Fe₆C] core encapsulated within a MoFeS shell, formulated as [MoFe₇S₉C].^[8] Reported by Xu et al., this model was achieved through a cluster-coupling strategy that assembles an unsaturated [Fe₆C] unit with Mo and sulfide components, resulting in a structure featuring a μ₆-carbide ligand central to the iron prism, akin to the interstitial carbon in native FeMoco.^[8] An analogous [Fe₆N] variant was also prepared, demonstrating partial N₂ activation upon coordination, where spectroscopic studies revealed weakening of the N≡N bond, though full reduction to ammonia was not observed.^[8] These models offer critical benchmarks for understanding FeMoco's geometric constraints and ligand effects on substrate binding. Smaller bi- and trinuclear FeMoS complexes have been developed to probe specific edge sites of FeMoco implicated in catalysis, focusing on the Fe-Mo connectivity at the cluster periphery.^[46] Laurans et al. synthesized such complexes using tridentate sulfur donors to bridge Fe and Mo centers, mimicking partial motifs where N₂ might bind to iron atoms adjacent to molybdenum.^[46] These models exhibit stoichiometric reactivity with nitrogenous substrates, such as hydrazine disproportionation, and provide electronic structure data via Mössbauer and EPR spectroscopy, supporting the hypothesis that edge Fe sites facilitate initial N₂ coordination without requiring the full cluster.^[46]^[26] Despite these progresses, synthetic FeMoco models face persistent challenges in replicating the enzyme's full 8-electron reduction of N₂ to 2 NH₃, as most exhibit only partial activation or require external reductants without catalytic turnover.^[8] The incorporation of the interstitial carbide remains technically demanding due to its high coordination and the cluster's instability during assembly, limiting reactivity to stoichiometric levels.^[8] Additionally, these models aid in elucidating FeMoco biosynthesis by simulating intermediates, such as the Fe₈S₉C cluster formed during nitrogenase assembly, thereby informing the roles of scaffold proteins like NifB in carbide insertion.^[47]^[2]

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Radical SAM Enzymes and Metallocofactor Assembly: A Structural ...
Nov 20, 2021 · NifB is arguably the key enzyme in FeMo-co assembly as it catalyzes the fusion of two [Fe4S4] clusters and the insertion of carbide and ...Introduction · Nitrogenase · The Radical SAM Carbide... · Perspective and Future...
[14]
In vitro synthesis of the iron–molybdenum cofactor of nitrogenase ...
Nov 6, 2007 · FeMo-co is composed of 7Fe, 9S, Mo, R-homocitrate, and one unidentified light atom. Here we demonstrate the complete in vitro synthesis of FeMo- ...Missing: empirical formula
[15]
Metal trafficking for nitrogen fixation: NifQ donates molybdenum to ...
Aug 19, 2008 · NifQ served as direct source of molybdenum for FeMo-co biosynthesis in vitro. The role of NifQ appears to be in substituting sulfur by oxygen ...
[16]
Heterologous synthesis of a simplified nitrogenase analog ... - Science
May 2, 2025 · Science Advances. 2 May 2025. Vol 11, Issue 18. DOI: 10.1126/sciadv.adw6785 · PREVIOUS ARTICLE. Inhalable myofibroblast targeting nanoparticles ...
[17]
https://www.pnas.org/doi/10.1073/pnas.0803576105
[18]
Revisiting the Mössbauer Isomer Shifts of the FeMoco Cluster of ...
Jan 10, 2017 · ... oxidation states of FeMoco have been controversial. With the ... Fe(II)–Fe(III) pairs. We also note that localized Fe(II) and Fe(III) ...
[19]
The discovery of Mo(III) in FeMoco: reuniting enzyme and model ...
Dec 31, 2014 · Mo–Fe–S compounds with [MoFe3S4]n cores have been prepared with oxidation states of n = 5+, 4+, 3+, 2+ and 1+, either as single or double cubane ...
[20]
The role of X-ray spectroscopy in understanding the geometric and ...
We note, however, that the Mo(IV) oxidation state assignment has recently been reassigned as Mo(III) (vide infra), thus requiring a greater complement of ...
[21]
Nitrogenase FeMoco investigated by spatially resolved anomalous ...
Mar 14, 2016 · The [Mo:7Fe:9S:C] iron-molybdenum cofactor (FeMoco) of nitrogenase is the largest known metal cluster and catalyses the 6-electron reduction ...Missing: formula | Show results with:formula
[22]
Postbiosynthetic modification of a precursor to the nitrogenase iron ...
Mar 8, 2021 · ... carbide-containing precursor to FeMoco, the L-cluster. We further ... The stability of the [Fe6C] core is notable in the context of ...
[23]
An Fe 6 C Core in All Nitrogenase Cofactors - Wiley Online Library
Aug 17, 2022 · Earlier spectroscopic and structural studies have shown that the cofactors of molybdenum and vanadium nitrogenases contain a central μ6-carbide.
[24]
Analysis of the Geometric and Electronic Structure of Spin-Coupled ...
Feb 15, 2022 · The iron–molybdenum cofactor of the Mo nitrogenase enzyme (FeMoco) features 8 metal ions in Fe(II) and Fe(III) oxidation states, 41 unpaired ...
[25]
The Spectroscopy of Nitrogenases | Chemical Reviews
Apr 2, 2020 · In this review, we summarize how different spectroscopic approaches have shed light on various aspects of these enzymes.
[26]
Understanding the Electronic Structure Basis for N2 Binding to ...
Mar 29, 2023 · The FeMo cofactor (FeMoco) of Mo nitrogenase is responsible for reducing dinitrogen to ammonia, but it requires the addition of 3–4 e–/H+ ...
[27]
https://doi.org/10.1021/acs.chemrev.9b00650
[28]
https://doi.org/10.1021/acs.inorgchem.6b02540
[29]
https://doi.org/10.1021/jacs.9b06988
[30]
Structural Characterization of CO-Inhibited Mo-Nitrogenase by ...
Oct 2, 2014 · All of our data and calculations are consistent with the notion that the N2ase FeMo-cofactor has a flexible cage with multiple binding sites.Figure 5 · Figure 6 · Discussion
[31]
Structural evidence for a dynamic metallocofactor during N ... - Science
Jun 19, 2020 · We report a 1.83-angstrom crystal structure of the nitrogenase molybdenum-iron (MoFe) protein captured under physiological N 2 turnover conditions.<|control11|><|separator|>
[32]
The E 3 state of FeMoco: one hydride, two hydrides or dihydrogen?
Jul 31, 2023 · In this work we systematically explore the energy surface of the E 3 redox state, comparing single hydride and two-hydride isomers with varying coordination ...Missing: variations | Show results with:variations
[33]
Binding Affinity of an Fe 2 (μ-H) 2 Core upon Reduction to a Mixed ...
The transient bridging hydrides on FeMoco may favor the formation of locally low or intermediate spin Fe ions, apt for N2 coordination and efficient nitrogenase ...
[34]
Cyanide and Methylisocyanide Binding to the Isolated Iron ...
Their binding increases the electronic relaxation time of the complex and increases the lifetime of the FeMo cofactor-p-CF3CeH4S− bond. Parallel molybdenum K ...Missing: FeMoco | Show results with:FeMoco
[35]
Mechanism of Nitrogen Fixation by Nitrogenase: The Next Stage
Jan 27, 2014 · This relaxation protocol thus revealed that the trapped intermediate is the E4 state, which has accumulated n = 4 electrons and protons.
[36]
Dissecting Electronic-Structural Transitions in the Nitrogenase MoFe ...
Mar 22, 2022 · The [8Fe-7S] P-cluster of nitrogenase MoFe protein mediates electron transfer from nitrogenase Fe protein during the catalytic production of ammonia.Supporting Information · Author Information · Acknowledgments · References
[37]
The Critical E4 State of Nitrogenase Catalysis - ACS Publications
Jul 2, 2018 · We report a crystal structure of carbon monoxide (CO)-inhibited nitrogenase molybdenum-iron (MoFe)-protein at 1.50 angstrom resoln., which ...<|control11|><|separator|>
[38]
Unification of reaction pathway and kinetic scheme for N 2 reduction ...
Nitrogenase catalyzes the reduction of N2 and protons to yield two NH3 and one H2. Substrate binding occurs at a complex organo-metallocluster called ...
[39]
Reduction of Substrates by Nitrogenases - PMC - PubMed Central
Both acetylene and cyanide were long ago reported as substrates for nitrogenase under turnover conditions, being reduced to ethylene (C2H4) and methane (CH4) ...
[40]
https://www.pnas.org/doi/10.1073/pnas.1202197109
[41]
Assignment of protonated R-homocitrate in extracted FeMo-cofactor ...
Oct 28, 2020 · Through long-term exploration, the structure of FeMo-co has been clarified as Mo*Fe7S9C(R-homocit*)(cys)(Hhis) (H4homocit = homocitric acid, ...
[42]
Self-assembly of molybdenum-iron-sulfur clusters as a synthetic ...
Self-assembly of molybdenum-iron-sulfur clusters as a synthetic approach to the molybdenum site in nitrogenase. Identification of the major products formed ...
[43]
Fluorine-19 chemical shifts as structural probes of metal-sulfur - PNAS
Aug 23, 1982 · cubane-type MoFe3S4 clusters withS = 3/a ground states, it was concluded that the essential FeMo-co cluster structure remains intact and a ...
[44]
Bioinspired bi- or trinuclear FeMoS model complexes for the partial ...
Sulfur-rich {FeMo} complexes of low nuclearity ({Fe2Mo}, {FeMo}) can be considered as simple truncated models of the cofactor of Mo‑nitrogenase.
[45]
Insight into the FeMoco of nitrogenase from synthetic iron complexes ...
The Fe-S bond lengths are all the same within ± 0.03 Å, suggesting that none of them are protonated. The FeMoco is mixed-valent in the resting state with both ...