MoFe Protein Research Articles

Conformations generated during turnover of the Azotobacter vinelandii nitrogenase MoFe protein and their relationship to physiological function

Various S=3/2 EPR signals elicited from wild-type and variant Azotobacter vinelandii nitrogenase MoFe proteins appear to reflect different conformations assumed by the FeMo-cofactor with different protonation states. To determine whether these presumed changes in protonation and conformation reflect catalytic capacity, the responses (particularly to changes in electron flux) of the αH195Q, αH195N, and αQ191K variant MoFe proteins (where His at position 195 in the α subunit is replaced by Gln/Asn or Gln at position α-191 by Lys), which have strikingly different substrate-reduction properties, were studied by stopped-flow or rapid-freeze techniques. Rapid-freeze EPR at low electron flux (at 3-fold molar excess of wild-type Fe protein) elicited two transient FeMo-cofactor-based EPR signals within 1s of initiating turnover under N2 with the αH195Q and αH195N variants, but not with the αQ191K variant. No EPR signals attributable to P cluster oxidation were observed for any of the variants under these conditions. Furthermore, during turnover at low electron flux with the wild-type, αH195Q or αH195N MoFe protein, the longer-time 430-nm absorbance increase, which likely reflects P cluster oxidation, was also not observed (by stopped-flow spectrophotometry); it did, however, occur for all three MoFe proteins under higher electron flux. No 430-nm absorbance increase occurred with the αQ191K variant, not even at higher electron flux. This putative lack of involvement of the P cluster in electron transfer at low electron flux was confirmed by rapid-freeze 57Fe Mössbauer spectroscopy, which clearly showed FeMo-factor reduction without P cluster oxidation. Because the wild-type, αH195Q and αH195N MoFe proteins can bind N2, but αQ195K cannot, these results suggest that P cluster oxidation occurs only under high electron flux as required for N2 reduction.

Analysis of active sites for N2 and H+ reduction on FeMo-cofactor of nitrogenase

Dinitrogen (N2) and proton (H+), which act as physiological substrates of nitrogenase, are reduced on FeMo-co of the MoFe protein. However, researchers have different opinions about their exact reduction sites. Nitrogenases were purified from the wild type (WT) and five mutants of Azotobacter vinelandii (Av), including Qα191K, Hα195Q, nifV−, Qα191K/nifV− Hα195Q/nifV−; and the activities of these enzymes for N2 and H+ reduction were analyzed. Our results suggest that the Fe2 and Fe6, atoms closed to the central sulfur atom (S2B) within FeMo-co, are sites for N2 binding and reduction and the Mo atom of FeMo-co is the site for H+ reduction. Combining these data with further bioinformatical analysis, we propose that two parallel electron channels may exist between the [8Fe7S] cluster and FeMo-co.

P-cluster maturation on nitrogenase MoFe protein.

Biosynthesis of nitrogenase P-cluster has attracted considerable attention because it is biologically important and chemically unprecedented. Previous studies suggest that P-cluster is formed from a precursor consisting of paired [4Fe-4S]-like clusters and that P-cluster is assembled stepwise on MoFe protein, i.e., one cluster is assembled before the other. Here, we specifically tackle the assembly of the second P-cluster by combined biochemical and spectroscopic approaches. By using a P-cluster maturation assay that is based on purified components, we show that the maturation of the second P-cluster requires the concerted action of NifZ, Fe protein, and MgATP and that the action of NifZ is required before that of Fe protein/MgATP, suggesting that NifZ may act as a chaperone that facilitates the subsequent action of Fe protein/MgATP. Furthermore, we provide spectroscopic evidence that the [4Fe-4S] cluster-like fragments can be converted to P-clusters, thereby firmly establishing the physiological relevance of the previously identified P-cluster precursor.

Conformational Differences between Azotobacter vinelandii Nitrogenase MoFe Proteins As Studied by Small-Angle X-ray Scattering

The nitrogenase MoFe protein is a heterotetramer containing two unique high-nuclearity metalloclusters, FeMoco and the P-cluster. FeMoco is assembled outside the MoFe protein, whereas the P-cluster is assembled directly on the MoFe protein polypeptides. MoFe proteins isolated from different genetic backgrounds have been analyzed using biochemical and spectroscopic techniques in attempting to elucidate the pathway of P-cluster biosynthesis. The DeltanifH MoFe protein is less stable than other MoFe proteins and has been shown by extended X-ray absorption fine structure studies to contain a variant P-cluster that most likely exists as two separate [Fe4S4]-like clusters instead of the subunit-bridging [Fe8S7] cluster found in the wild-type and DeltanifB forms of the MoFe protein [Corbett, M. C., et al. (2004) J. Biol. Chem. 279, 28276-28282]. Here, a combination of small-angle X-ray scattering and Fe chelation studies is used to show that there is a correlation between the state of the P-cluster and the conformation of the MoFe protein. The DeltanifH MoFe protein is found to be larger than the wild-type or DeltanifB MoFe proteins, an increase in size that can be modeled well by an opening of the subunit interface consistent with P-cluster fragmentation and solvent exposure. Importantly, this opening would allow for the insertion of P-cluster precursors into a region of the MoFe protein that is buried in the wild-type conformation. Thus, DeltanifH MoFe protein could represent an early intermediate in MoFe protein biosynthesis where the P-cluster precursors have been inserted, but P-cluster condensation and tetramer stabilization have yet to occur.

Alkyne substrate interaction within the nitrogenase MoFe protein

Nitrogenase catalyzes the biological reduction of N2 to ammonia (nitrogen fixation), as well as the two-electron reduction of the non-physiological alkyne substrate acetylene (HC≡CH). A complex metallo-organic species called FeMo-cofactor provides the site of substrate reduction within the MoFe protein, but exactly where and how substrates interact with FeMo-cofactor remains unknown. Recent results have shown that the MoFe protein α-70Val residue, whose side chain approaches one Fe–S face of FeMo-cofactor, plays a significant role in defining substrate access to the active site. For example, substitution of α-70Val by alanine results in an increased capacity for the reduction of the larger alkyne propyne (HC≡C–CH3), whereas, substitution by isoleucine at this position nearly eliminates the capacity for the reduction of acetylene. These and complementary spectroscopic studies led us to propose that binding of short chain alkynes occurs with side-on binding to Fe atom 6 within FeMo-cofactor. In the present work, the α-70Val residue was substituted by glycine and this MoFe protein variant shows an increased capacity for reduction of the terminal alkyne, 1-butyne (HC≡C–CH2–CH3). This protein shows no detectable reduction of the internal alkyne 2-butyne (H3C–C≡C–CH3). In contrast, substitution of the nearby α-191Gln residue by alanine, in combination with the α-70Ala substitution, does result in significant reduction of 2-butyne, with the exclusive product being 2-cis-butene. These results indicate that the reduction of alkynes by nitrogenases involves side-on binding of the alkyne to Fe6 within FeMo-cofactor, and that a terminal acidic proton is not required for reduction. The successful design of amino acid substitutions that permit the targeted accommodation of an alkyne that otherwise is not a nitrogenase substrate provides evidence to support the current model for alkyne interaction within the nitrogenase MoFe protein.

Diazene (HNNH) Is a Substrate for Nitrogenase: Insights into the Pathway of N2 Reduction

Nitrogenase catalyzes the sequential addition of six electrons and six protons to a N2 that is bound to the active site metal cluster FeMo-cofactor, yielding two ammonia molecules. The nature of the intermediates bound to FeMo-cofactor along this reduction pathway remains unknown, although it has been suggested that there are intermediates at the level of reduction of diazene (HN=NH, also called diimide) and hydrazine (H2N-NH2). Through in situ generation of diazene during nitrogenase turnover, we show that diazene is a substrate for the wild-type nitrogenase and is reduced to NH3. Diazene reduction, like N2 reduction, is inhibited by H2. This contrasts with the absence of H2 inhibition when nitrogenase reduces hydrazine. These results support the existence of an intermediate early in the N2 reduction pathway at the level of reduction of diazene. Freeze-quenching a MoFe protein variant with alpha-195His substituted by Gln and alpha-70Val substituted by Ala during steady-state turnover with diazene resulted in conversion of the S = 3/2 resting state FeMo-cofactor to a novel S = 1/2 state with g1 = 2.09, g2 = 2.01, and g3 approximately 1.98. 15N- and 1H-ENDOR establish that this state consists of a diazene-derived [-NHx] moiety bound to FeMo-cofactor. This moiety is indistinguishable from the hydrazine-derived [-NHx] moiety bound to FeMo-cofactor when the same MoFe protein is trapped during turnover with hydrazine. These observations suggest that diazene joins the normal N2-reduction pathway, and that the diazene- and hydrazine-trapped turnover states represent the same intermediate in the normal reduction of N2 by nitrogenase. Implications of these findings for the mechanism of N2 reduction by nitrogenase are discussed.

Molecular insights into nitrogenase FeMoco insertion – The role of His 274 and His 451 of MoFe protein α subunit

The final step of FeMo cofactor (FeMoco) assembly involves the insertion of FeMoco into its binding site in the molybdenum–iron (MoFe) protein of nitrogenase. Here we examine the role of His α274 and His α451 of Azotobacter vinelandii MoFe protein in this process. Our results from combined metal, activity, EPR, stability and insertion analyses show that mutations of His α274 and/or His α451, two of the histidines that belong to a so-called His triad, to small uncharged Ala specifically reduce the accumulation of FeMoco in MoFe protein. This observation indicates that the enrichment of histidines at the His triad is important for FeMoco insertion and that the His triad potentially serves as an intermediate docking point for FeMoco through transitory ligand coordination and/or electrostatic interaction.

The NifX Protein is Involved in the Final Stages of FeMo-cofactor Transport to the MoFe Protein

The nitrogenase enzyme catalyzes the reduction of dinitrogen to ammonia and is composed of the Fe and MoFe proteins. The iron molybdenum cofactor (FeMo-co) of the MoFe protein is the site of active substrate reduction. The NifX protein has also been suggested to have a role in the FeMo-co synthesis, although its exact role is still open to investigation. We attempted to understand the role of NifX by determining the specific interactions it may have with other Nif proteins involved in FeMo-co synthesis, such as NifD, NifK, NifN, NifDK and NifH. Using the BacterioMatch Two-Hybrid System, a translationally fused construct of NifX with the N-terminal α-RNAP of the pTRG target vector was made and its interaction was tested with the NifDK fusion protein, translationally fused to the λCI of the pBT vector. The strength of the interaction, as determined by measuring the β-galactosidase activity, demonstrated that direct protein-protein interaction exists between NifDK and NifX proteins; the extent of interaction between NifK and NifX proteins was much higher than between NifD and NifX, when individually tested; also, reduced interaction was found between NifH and NifX.

Connecting nitrogenase intermediates with the kinetic scheme for N 2 reduction by a relaxation protocol and identification of the N 2 binding state

A major obstacle to understanding the reduction of N2 to NH3 by nitrogenase has been the impossibility of synchronizing electron delivery to the MoFe protein for generation of specific enzymatic intermediates. When an intermediate is trapped without synchronous electron delivery, the number of electrons, n, it has accumulated is unknown. Consequently, the intermediate is untethered from kinetic schemes for reduction, which are indexed by n. We show that a trapped intermediate itself provides a "synchronously prepared" initial state, and its relaxation to the resting state at 253 K, conditions that prevent electron delivery to MoFe protein, can be analyzed to reveal n and the nature of the relaxation reactions. The approach is applied to the "H+/H- intermediate" (A) that appears during turnover both in the presence and absence of N2 substrate. A exhibits an S = 1/2 EPR signal from the active-site iron-molybdenum cofactor (FeMo-co) to which are bound at least two hydrides/protons. A undergoes two-step relaxation to the resting state (C): A --> B --> C, where B has an S = 3/2 FeMo-co. Both steps show large solvent kinetic isotope effects: KIE approximately 3-4 (85% D2O). In the context of the Lowe-Thorneley kinetic scheme for N2 reduction, these results provide powerful evidence that H2 is formed in both relaxation steps, that A is the catalytically central state that is activated for N2 binding by the accumulation of n = 4 electrons, and that B has accumulated n = 2 electrons.

Molecular insights into nitrogenase FeMo cofactor insertion: the role of His 362 of the MoFe protein α subunit in FeMo cofactor incorporation

The assembly of the complex iron-molybdenum cofactor (FeMoco) of nitrogenase molybdenum-iron (MoFe) protein has served as one of the central topics in the field of bioinorganic chemistry for decades. Here we examine the role of a MoFe protein residue (His alpha362) in FeMoco insertion, the final step of FeMoco biosynthesis where FeMoco is incorporated into its binding site in the MoFe protein. Our data from combined metal, activity and electron paramagnetic resonance analyses show that mutations of His alpha362 to small uncharged Ala or negatively charged Asp result in significantly reduced FeMoco accumulation in MoFe protein, indicating that His alpha362 plays a key role in the process of FeMoco insertion. Given the strategic location of His alpha362 at the entry point of the FeMoco insertion funnel, this residue may serve as one of the initial docking points for FeMoco insertion through transient ligand coordination and/or electrostatic interaction.

Intrinsic Dinitrogen Activation at Bare Metal Atoms

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Purification of a NifEN Protein Complex That Contains Bound Molybdenum and a FeMo-Co Precursor from an Azotobacter vinelandii ΔnifHDK Strain

The NifEN protein complex serves as a molecular scaffold where some of the steps for the assembly of the iron-molybdenum cofactor (FeMo-co) of nitrogenase take place. A His-tagged version of the NifEN complex has been previously purified and shown to carry two identical [4Fe-4S] clusters of unknown function and a [Fe-S]-containing FeMo-co precursor. We have improved the purification of the his-NifEN protein from a DeltanifHDK strain of Azotobacter vinelandii and have found that the amounts of iron and molybdenum within NifEN were significantly higher than those reported previously. In an in vitro FeMo-co synthesis system with purified components, the NifEN protein served as a source of both molybdenum and a [Fe-S]-containing FeMo-co precursor, showing significant FeMo-co synthesis activity in the absence of externally added molybdate. Thus, the NifEN scaffold protein, purified from DeltanifHDK background, contained the Nif-Bco-derived Fe-S cluster and molybdenum, although these FeMo-co constituents were present at different levels within the protein complex.

Variable-Temperature, Variable-Field Magnetic Circular Dichroism Spectroscopic Study of the Metal Clusters in the ΔnifB and ΔnifH MoFe Proteins of Nitrogenase from Azotobacter vinelandii

Deletion of nifB results in the formation of a variant nitrogenase MoFe protein (DeltanifB MoFe protein) that appears to contain two normal [8Fe-7S] P clusters. This protein can be reactivated to form the holo MoFe protein upon addition of isolated FeMo cofactor. In contrast, deletion of nifH results in a variant protein (DeltanifH MoFe protein) that appears to contain FeS clusters different from the normal P cluster, presumably representing precursors of the normal P cluster. The DeltanifH MoFe protein is not reconstituted to the holo MoFe protein with isolated FeMo cofactor. The EPR and EXAFS spectroscopic properties of FeS clusters in the DeltanifH MoFe protein clearly differ from those of the normal P cluster found in the DeltanifB MoFe protein and suggest the presence of [4Fe-4S]-like clusters. To further characterize the metal cluster structures in the DeltanifH MoFe protein, a variable-temperature, variable-field magnetic circular dichroism (VTVH-MCD) spectroscopic study has been undertaken on both the DeltanifB MoFe protein and the DeltanifH MoFe protein in both the dithionite-reduced and oxidized states. This study clearly shows that each half of the dithionite-reduced DeltanifH MoFe protein contains a [4Fe-4S]+ cluster paired with a diamagnetic [4Fe-4S]-like cluster. Upon oxidation, the VTVH-MCD spectrum of the DeltanifH MoFe protein reveals a paramagnetic, albeit EPR-silent system, suggesting an integer spin state. These results suggest that the DeltanifH MoFe protein contains a pair of neighboring, unusual [4Fe-4S]-like clusters, which are paramagnetic in their oxidized state.

A methyldiazene (HNNCH 3 )-derived species bound to the nitrogenase active-site FeMo cofactor: Implications for mechanism

Methyldiazene (HN=N-CH3) isotopomers labeled with 15N at the terminal or internal nitrogens or with 13C or 2H were used as substrates for the nitrogenase alpha-195Gln-substituted MoFe protein. Freeze quenching under turnover traps an S = (1/2) state that has been characterized by EPR and 1H-, 15N-, and 13C-electron nuclear double resonance spectroscopies. These studies disclosed the following: (i) a methyldiazene-derived species is bound to the active-site FeMo cofactor; (ii) this species binds through an [-NHx] fragment whose N derives from the methyldiazene terminal N; and (iii) the internal N from methyldiazene probably does not bind to FeMo cofactor. These results constrain possible mechanisms for reduction of methyldiazene. In the Chatt-Schrock mechanism for N2 reduction, H atoms sequentially add to the distal N before N-N bond cleavage (d-mechanism). In a d-mechanism for methyldiazene reduction, a bound [-NHx] fragment only occurs after reduction by three electrons, which leads to N-N bond cleavage and the release of the first NH3. Thus, the appearance of bound [-NHx] is compatible with the d-mechanism only if it represents a late stage in the reduction process. In contrast are mechanisms where H atoms add alternately to distal and proximal nitrogens before N-N cleavage (a-mechanism) and release of the first NH3 after reduction by five electrons. An [-NHx] fragment would be bound at every stage of methyldiazene reduction in an a-mechanism. Although current information does not rule out the d-mechanism, the a-mechanism is more attractive because proton delivery to substrate has been specifically compromised in alpha-195Gln-substituted MoFe protein.

How many metals does it take to fix N 2 ? A mechanistic overview of biological nitrogen fixation

During the process of biological nitrogen fixation, the enzyme nitrogenase catalyzes the ATP-dependent reduction of dinitrogen to ammonia. Nitrogenase consists of two component metalloproteins, the iron (Fe) protein and the molybdenum-iron (MoFe) protein; the Fe protein mediates the coupling of ATP hydrolysis to interprotein electron transfer, whereas the active site of the MoFe protein contains the polynuclear FeMo cofactor, a species composed of seven iron atoms, one molybdenum atom, nine sulfur atoms, an interstitial light atom, and one homocitrate molecule. This Perspective provides an overview of biological nitrogen fixation and introduces three contributions to this special feature that address central aspects of the mechanism and assembly of nitrogenase.

FeMo cofactor maturation on NifEN.

FeMo cofactor (FeMoco) biosynthesis is one of the most complicated processes in metalloprotein biochemistry. Here we show that Mo and homocitrate are incorporated into the Fe/S core of the FeMoco precursor while it is bound to NifEN and that the resulting fully complemented, FeMoco-like cluster is transformed into a mature FeMoco upon transfer from NifEN to MoFe protein through direct protein-protein interaction. Our findings not only clarify the process of FeMoco maturation, but also provide useful insights into the other facets of nitrogenase chemistry.

Molecular Insights into Nitrogenase FeMoco Insertion: TRP-444 OF MoFe PROTEIN α-SUBUNIT LOCKS FeMoco IN ITS BINDING SITE

Biosynthesis of the FeMo cofactor (FeMoco) of nitrogenase MoFe protein is arguably one of the most complex processes in metalloprotein biochemistry. Here we investigate the role of a MoFe protein residue (Trp-alpha444) in the final step of FeMoco assembly, which involves the insertion of FeMoco into its binding site. Mutations of this aromatic residue to small uncharged ones result in significantly decreased levels of FeMoco insertion/retention and drastically reduced activities of MoFe proteins, suggesting that Trp-alpha444 may lock the FeMoco tightly in its binding site through the sterically restricting effect of its bulky, aromatic side chain. Additionally, these mutations cause partial conversion of the P-cluster to a more open conformation, indicating a potential connection between FeMoco insertion and P-cluster assembly. Our results provide some of the initial molecular insights into the FeMoco insertion process and, moreover, have useful implications for the overall scheme of nitrogenase assembly.

Intrinsic Dinitrogen Activation at Bare Metal Atoms

There is ongoing interest in metal complexes which bind dinitrogen and facilitate either its reduction or oxidation under mild conditions. In nature, the enzyme nitrogenase catalyzes this process, and dinitrogen fixation occurs under mild and ambient conditions at a metal-sulfur cluster in the center of the MoFe protein, but the mechanism of this process remains largely unknown. In the last few years, new important discoveries have been made in this field. In this review are discussed recent findings on the interaction of N(2) with metal atoms and metal-atom dimers from all groups of the periodic table as provided by gas-phase as well as matrix-isolation experiments. Intrinsic dinitrogen activation at such bare metal atoms is then related to corresponding processes at complexes, clusters, and surfaces.

Characterization of a nitrogenase CrFe protein from a mutant UW3 of Azotobacter vinelandii grown on a Cr-containing medium

Through the anoxic chromatography on the columns of DEAE-52, Q-Sepharose and Sephacryl S-200, a CrFe protein preparation was obtained from UW3, a mutant of Azotobacter vinelandii, which grew well on the Cr-containing medium. Compared with MoFe protein (OP Av1) from wild-type strain OP, ∼50% protein in the preparation had similar subunits composition and had immune reaction with antibody of OP Av1. The preparation had ∼40% of C2H2-, H+-and N2 (expressed by the difference in H+-reduction activity between under Ar and under N2)-reduction activity of OP Av1 and similar electron pairs to those of OP Av1. And metal analysis showed that the preparation contained Fe, Cr and Mo. The circular dichroism (CD) spectrum in the preparation at ∼450 nm was similar to that of OP Av1, while the relative intensities of three EPR signals appearing at the same g values (g≈4.3, 3.7 and 2.0) were different. The EPR-based calculated results showed that (1) the ratios of Mo to Cr and of Fe to (Cr+Mo) of the CrFe protein preparation were 0.41 and 15, respectively, indicating that in the preparation, a ratio of Cr-containing protein to MoFe protein was about 2.5; (2) the ratios of activity to Fe and to Cr of the preparation were close to the ratios of activity to Fe and to Mo of OP Av1, respectively; (3) the ratios of the EPR signal intensities at the above three g values to Cr of CrFe protein were about ∼83%, 0% and ∼40% of those to Mo of OP Av1, respectively. The results indicate further that CrFe protein might be a new nitrogenase component I protein with a similar function and structure including metallocluster to those of MoFe protein instead of simple replacement of Mo by Mn in the cofactor.

The Correlation of Redox Potential, HOMO Energy, and Oxidation State in Metal Sulfide Clusters and Its Application to Determine the Redox Level of the FeMo-co Active-Site Cluster of Nitrogenase

This paper describes a procedure that permits the total charge state (i.e., oxidation state) of a complex molecule to be obtained from its redox potential data by comparison with good data (both charge state and redox potential) for reference compounds that are chemically similar. The link between the reference data and the unknown compound is made by the calculated energies of the Fermi level or highest occupied molecular orbital (HOMO). The HOMO energies are calculated by unrestricted density functional methods (DMol) for the reference compounds in their known charge states, and a graphical correlation of HOMO energy and redox potential for oxidation (corresponding to loss of an electron from the HOMO) is constructed. The measured redox potential of the unknown is then applied to the correlation to yield the HOMO energy of the unknown, against which the calculated HOMO energies for various charge states of the unknown are assessed. This method is generally applicable. Using 26 reference data, the method is used here to determine the resting redox state, [NFe6MoS9]0, of the core of the FeMo cofactor (FeMo-co, bound to the MoFe protein) which is the active site of nitrogen-fixing enzymes. The analysis also shows that if the atom at the center of FeMo-co is C rather than N, then FeMo-co must be protonated in its resting state, but if FeMo-co is N-centered, it would not be protonated in the resting state.