Dinitrogen reduction by nitrogenase: if N2 isn't broken, it can't be fixed

Expression, Isolation, and Characterization of Vanadium Nitrogenase from Azotobacter vinelandii

Nitrogenases are the sole enzymes known to mediate biological nitrogen fixation, an essential process for sustaining life on earth. Among the three known variants, molybdenum nitrogenase is the best-studied to date. Recent work on the alternative vanadium nitrogenase provided important insights into the mechanism of nitrogen fixation since this enzyme differs from its molybdenum counterpart in some important aspects. Here, we present a protocol to obtain unmodified vanadium nitrogenase in high yield and purity from the paradigmatic diazotroph Azotobacter vinelandii, including procedures for cell cultivation, purification, and protein characterization.

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.

The Critical E4 State of Nitrogenase Catalysis

The reaction catalyzed by the nitrogenase enzyme involves breaking the stable triple bond of the dinitrogen molecule and is consequently considered among the most challenging reactions in biology. While many aspects regarding its atomic mechanism remain to be elucidated, a kinetic scheme established by David Lowe and Roger Thorneley has remained a gold standard for functional studies of the enzyme for more than 30 years. Recent three-dimensional structures of ligand-bound states of molybdenum- and vanadium-dependent nitrogenases have revealed the actual site of substrate binding on the large active site cofactors of this class of enzymes. The binding mode of an inhibitor and a reaction intermediate further substantiate a hypothesis by Seefeldt, Hoffman, and Dean that the activation of N₂ is made possible by a reductive elimination of H₂ that leaves the cofactor in a super-reduced state that can bind and reduce the inert N₂ molecule. Here we discuss the immediate implications of the structurally observed mode of binding of small molecules to the enzyme with respect to the early stages of the Thorneley-Lowe mechanism of nitrogenase. Four consecutive single-electron reductions give rise to two bridging hydrides at the cluster surface that can recombine to eliminate H₂ and enable the reduced cluster to bind its substrate in a bridging mode.

The structure of vanadium nitrogenase reveals an unusual bridging ligand

Nitrogenases catalyze the reduction of N₂ gas to ammonium at a complex heterometallic cofactor. Most commonly this is the FeMo cofactor (FeMoco), a [Mo:7Fe:9S:C] cluster whose exact reactivity and substrate binding mode remain unknown. Alternative nitrogenases replace molybdenum with either vanadium or iron and differ in reactivity, prominently in the ability of vanadium nitrogenase to reduce CO to hydrocarbons. Here we report the 1.35 Å structure of vanadium nitrogenase from Azotobacter vinelandii. The 240 kDa protein contains an additional α-helical subunit not present in molybdenum nitrogenase. The FeV cofactor (FeVco) is a [V:7Fe:8S:C] cluster with a homocitrate ligand to vanadium. Unexpectedly, it lacks one sulfide ion compared to FeMoco that is replaced by a bridging ligand, likely a μ-1,3-carbonate. The anion fits into a pocket within the protein that is obstructed in molybdenum nitrogenase, and its different chemical character helps to rationalize the altered chemical properties of this unique N₂- and CO-fixing enzyme.

FeMo cofactor of nitrogenase: a density functional study of states M(N), M(OX), M(R), and M(I)

The M(N) S = (3)/(2) resting state of the FeMo cofactor of nitrogenase has been proposed to have metal-ion valencies of either Mo(4+)6Fe(2+)Fe(3+) (derived from metal hyperfine interactions) or Mo(4+)4Fe(2+)3Fe(3+) (from Mössbauer isomer shifts). Spin-polarized broken-symmetry (BS) density functional theory (DFT) calculations have been undertaken to determine which oxidation level best represents the M(N) state and to provide a framework for understanding its energetics and spectroscopy. For the Mo(4+)6Fe(2+)Fe(3+) oxidation state, the spin coupling pattern for several spin state alignments compatible with S = (3)/(2) were generated and assessed by energy and geometric criteria. The most likely BS spin state is composed of a Mo3Fe cluster with spin S(a) = 2 antiferromagnetically coupled to a 4Fe' cluster with spin S(b) = (7)/(2). This state has a low DFT energy for the isolated FeMoco cluster and the lowest energy when the interaction with the protein and solvent environment is included. This spin state also displays calculated metal hyperfine and Mössbauer isomer shifts compatible with experiment, and optimized geometries that are in excellent agreement with the protein X-ray data. Our best model for the actual spin-coupled state within FeMoco alters this BS state by a slight canting of spins and is analogous in several respects to that found in the 8Fe P-cluster in the same protein. The spin-up and spin-down components of the LUMO contain atomic contributions from Mo(4+) and the homocitrate and from the central prismane Fe sites and muS(2) atoms, respectively. This qualitative picture of the accepting orbitals for M(N) is consistent with observations from Mössbauer spectra of the one-electron reduced states. Similar calculations for the Mo(4+)4Fe(2+)3Fe(3+) oxidation state yield results that are in poorer agreement with experiment. Using the Mo(4+)6Fe(2+)Fe(3+) oxidation level as the most plausible resting state, the geometric, electronic and energetic properties of the one-electron redox transition to the oxidized state, M(OX), catalytically observed M(R) and radiolytically reduced M(I) states have also been explored.

Catalytic Reduction of Hydrazine to Ammonia with MoFe(3)S(4)-Polycarboxylate Clusters. Possible Relevance Regarding the Function of the Molybdenum-Coordinated Homocitrate in Nitrogenase

The catalytic function of the previously synthesized and characterized [(L)MoFe(3)S(4)Cl(3)](2)(-)(,3)(-) clusters (L = tetrachlorocatecholate, citrate, citramalate, methyliminodiacetate, nitrilotriacetate, thiodiglycolate) and of the [MoFe(3)S(4)Cl(3)(thiolactate)](2)(4)(-) and [(MoFe(3)S(4)Cl(4))(2)(&mgr;-oxalate)](4)(-) clusters in the reduction of N(2)H(4) to NH(3) is reported. In the catalytic reduction, which is carried out at ambient temperature and pressure, cobaltocene and 2,6-lutidinium chloride are supplied externally as electron and proton sources, respectively. In experiments where the N(2)H(4) to the [(L)MoFe(3)S(4)Cl(3)](n)()(-) catalyst ratio is 100:1, and over a period of 30 min, the reduction proceeds to 92% completion for L = citrate, 66% completion for L = citramalate, and 34% completion for L = tetrachlorocatecholate. The [Fe(4)S(4)Cl(4)](2)(-) cluster is totally inactive and gives only background ammonia measurements. Inhibition studies with PEt(3) and CO as inhibitors show a dramatic decrease in the catalytic efficiency. These results are consistent with results obtained previously in our laboratory and strongly suggest that N(2)H(4) activation and reduction occur at the Mo site of the [(L)MoFe(3)S(4)Cl(3)](2)(-)(, 3)(-) clusters. A possible pathway for the N(2)H(4) reduction on a single metal site (Mo) and a possible role for the carboxylate ligand are proposed. The possibility that the Mo-bound polycarboxylate ligand acts as a proton delivery "shuttle" during hydrazine reduction is considered.

Dinitrogen Cleavage by a Three-Coordinate Molybdenum(III) Complex

Cleavage of the relatively inert dinitrogen (N(2)) molecule, with its extremely strong N identical withN triple bond, has represented a major challenge to the development of N(2) chemistry. This report describes the reductive cleavage of N(2) to two nitrido (N(3-)) ligands in its reaction with Mo(NRAr)(3), where R is C(CD(3))(2)CH(3) and Ar is 3,5-C(6)H(3)(CH(3))(2'), a synthetic three-coordinate molybdenum(III) complex of known structure. The formation of an intermediate complex was observed spectroscopically, and its conversion (with N identical withN bond cleavage) to the nitrido molybdenum(VI) product N identical withMo(NRAr)(3) followed first-order kinetics at 30 degrees C. It is proposed that the cleavage reaction proceeds by way of an intermediate complex in which N(2) bridges two molybdenum centers.