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Nitrogenase X: Mössbauer and EPR studies on reversibly oxidized MoFe protein from Azotobacter vinelandii OP. Nature of the iron centers.

Under anaerobic conditions the molybdenum-iron protein (MoFe protein) from Azotobacter vinelandii can be reversibly oxidized with thionine. Electron paramagnetic resonance studies reveal that the oxidation proceeds in two distinct phases: the MoFe protein can be oxidized by four electrons without loss of the EPR signal from the S = 3/2 cofactor centers. A second oxidation step, involving two electrons, leads to the disappearance of the cofactor EPR signal. In order to correlate the events during the thionine titration with redox reactions involving individual iron centers we have studied the MoFe proteins from A vinelandii and Clostridium pasteurianum with Mössbauer spectroscopy. Spectra were taken in the temperature range from 1.5 K to 200 K in applied magnetic fields of up to 54 kG. Analysis of the Mössbauer data allows us to draw three major conclusions: (1) the holoprotein contains 30 +/- 2 iron atoms. (2) Most probably, 12 iron atoms belong to two, apparently identical, iron clusters (labeled M) which we have shown previously to be structural components of the iron and molybdenum containing cofactor of nitrogenase. The M-centers can be stabilized in three distinct oxidation states, MOXe- in equilibrium MNe- in equilibrium MR. The diamagnetic (S = 0) state MOX is attained by oxidation of the native state MN with either thionine or oxygen. MR is observed under nitrogen fixing conditions. (3) The data strongly suggest that 16 iron atoms are associated with four iron centers which we propose to call P-clusters. Each P-cluster contains four spin-coupled iron atoms. In the native protein the P-clusters are in the diamagnetic state PN, yielding the Mössbauer signature which we have labeled previously 'components D and Fe2+'. Three irons of the D-type and one iron of the Fe2+-type appear to comprise a P-cluster. A one-electron oxidation yields the paramagnetic state POX. Although the state POX is characterized by half-integral electronic spin a peculiar combination of zero-field splitting parameters and spin relaxation renders this state EPR-silent. Spectroscopically, the P-clusters are novel structures; there is, however, evidence that they are closely related to familiar 4Fe-4S centers.

Azotobacter↗

Nitrogenase XI: Mössbauer studies on the cofactor centers of the MoFe protein from Azotobacter vinelandii OP.

We have studied the MoFe protein from Azotobacter vinelandii OP with Mössbauer spectroscopy in applied magnetic fields up to 50 kG. The results are as follows. (1) The Mössbauer spectra of the S = 3/2 centers, which reside on the cofactor of nitrogenase, have been decomposed into six subcomponents. This suggests that each center contains 5-7, most probably 6, Fe atoms, thus confirming our earlier conclusions which were based on the quantitation of EPR data and on the assumption that the MoFe protein contains (30 +/- 2) Fe atoms. (2) Analysis of the high-field data shows that three subsites are characterized by a positive magnetic hyperfine coupling constant, A0, while A0 is negative for the other three sites. This observation demonstrates that the S = 3/2 centers are spin-coupled structures. (3) The zero-field splitting parameter D = +(6 +/- 1.5) cm-1 obtained from the Mössbauer data is in good agreement with our earlier EPR results, D approximately +5.5 cm-1. (4) The resolution of the Mössbauer spectra of the MoFe protein can be dramatically increased by employing Fourier transform deconvolution techniques. This allows a clear demonstration of spectral component S.

Azotobacter↗

Short-term ammonium inhibition of nitrogen fixation in Azotobacter.

Addition of NH4Cl at low concentrations to Azotobacter chroococcum cells caused an immediate cessation of nitrogenase activity, which was recovered once the added NH+4 was exhausted from the medium. In the presence of inhibitors of ammonium assimilation, such as L-methionine-DL-sulfoximine, L-methionine sulfone or 6-diazo-5-oxo-L-norleucine, externally added NH+4 had no effect on nitrogenase activity and the newly-fixed nitrogen was excreted into the medium as NH+4. It is concluded that, in A. chroococcum, NH+4 must be assimilated to exert its short-term inhibitory effect on nitrogen fixation.

Ammonium Chloride↗

The lack of a solvent accessible hydroxide or water ligand to iron at the 3Fe center of Azotobacter vinelandii ferredoxin I.

The X-ray crystal structure of Azotobacter vinelandii ferredoxin I (FdI) describes a planar 3Fe-3S center in which one of the iron atoms is ligated to a solvent accessible oxo ligand, presumably from water or hydroxide (Ghosh et al., (1982) J. Mol. Biol. 158, 73-109). Efforts to displace the proposed oxo ligand with cyanide were unsuccessful, even in 80% dimethylsulfoxide. In addition, comparison of the electron spin echo envelopes for H2O- and D2O-equilibrated samples of FdI showed only a slight deuterium modulation, far less than would be expected were water to be bound as an iron ligand. These results do not support the presence of a solvent accessible oxo ligand to the 3Fe center as described in the X-ray crystal structure.

Azotobacter↗

Purification and spectroscopic characteristics in N-methylformamide of the Azotobacter vinelandii Fe-Mo cofactor.

The iron-molybdenum cofactor from Azotobacter vinelandii can be removed from significant amounts of extraneous iron and other contaminants using anaerobic gel filtration. Electronic absorption spectra of the so-purified FeMoco along with analysis of the so-called 'easily complexed' iron are suggestive that FeMoco occupies at least two different states in N-methylformamide solution. Batch-related differences in spectral characteristics of independently isolated FeMoco samples are demonstrated. Non-cofactor iron, found in unpurified FeMoco, may affect the interpretation of ligand binding and other experiments probing FeMoco structure and reactivity. Oxidized FeMoco is shown to be clearly discernable from the semi-reduced species by means of electronic spectroscopy, and this method now forms a convenient analytical tool for study of the chemistry and electronic structure of FeMoco.

Azotobacter↗

Structural studies of the extracellular polysaccharide elaborated by Azotobacter vinelandii strain 1484.

The structure of the extracellular polysaccharide from Azotobacter vinelandii strain 1484 has been investigated, specific degradations and n.m.r. spectroscopy being the main methods used. It is concluded that the polysaccharide is composed of tetrasaccharide repeating-units having the following structure, [sequence: see text] in which Sug is 3-deoxy-D-threo-hexulosonic acid. The polysaccharide also contains a non-stoichiometric amount of O-acetyl groups, distributed over at least two positions.

Azotobacter↗

Resonance Raman spectroscopy of Azotobacter vinelandii ferredoxin I. Vibrational features of the [3Fe-3S] cluster.

Low temperature resonance Raman spectra have been obtained for Clostridium pasteurianum and Bacillus stearothermophilus ferredoxins. Several heretofore undetected fundamental bands have been observed and these data have been used to discriminate the vibrational contribution of the [3Fe-3S] cluster to the spectrum of Azotobacter vinelandii ferredoxin I. The vibrational features of the [3Fe-3S] core distinguish it from other 3-iron clusters and imply structural differences among this class of iron-sulfur clusters.

Azotobacter↗

Selective oxidative destruction of iron-sulfur clusters. Ferricyanide oxidation of Azotobacter vinelandii ferredoxin I.

The destructive oxidation of aerobically isolated 7Fe Azotobacter vinelandii ferredoxin I [(7Fe)FdI] by Fe(CN)3-6 is examined using low-temperature magnetic circular dichroism (MCD) and EPR. The results demonstrate that oxidation of the [3Fe-3S] cluster occurs only after essentially complete destruction of the [4Fe-4S] cluster. It is therefore feasible by controlled Fe(CN)3-6 oxidation to obtain a partially metallated form of FdI, (3Fe)FdI, containing only a [3Fe-3S] cluster. The MCD and EPR data demonstrate that the [3Fe-3S] cluster in (3Fe)FdI is essentially identical in structure to that in the native protein.

Azotobacter↗

Mobile sequences in the pyruvate dehydrogenase complex, the E2 component, the catalytic domain and the 2-oxoglutarate dehydrogenase complex of Azotobacter vinelandii, as detected by 600 MHz 1H-NMR spectroscopy.

600 MHz 1H-NMR spectroscopy demonstrates that the pyruvate dehydrogenase complex of Azotobacter vinelandii contains regions of the polypeptide chain with intramolecular mobility. This mobility is located in the E2 component and can probably be ascribed to alanine-proline-rich regions that link the lipoyl subdomains to each other as well as to the E1 and E3 binding domain. In the catalytic domain of E2, which is thought to form a compact, rigid core, also conformational flexibility is observed. It is conceivable that the N-terminal region of the catalytic domain, which contains many alanine residues, is responsible for the observed mobility. In the low-field region of the 1H-NMR spectrum of E2 specific resonances are found, which can be ascribed to mobile phenylalanine, histidine and/or tyrosine residues which are located in the E1 and E3 binding domain that links the lipoyl domain to the catalytic domain. In the 1H-NMR spectrum of the intact complex, these resonances cannot be observed, indicating a decreased mobility of the E1 and E3 binding domain.

Acetyltransferases↗

Time-resolved fluorescence studies on mutants of the dihydrolipoyl transacetylase (E2) component of the pyruvate dehydrogenase complex from Azotobacter vinelandii.

Fluorescence anisotropy decays were measured for the wild-type dihydrolipoyl transacetylase (E2) component of pyruvate dehydrogenase complex from Azotobacter vinelandii and E. coli and for E2-mutants from A. vinelandii in which the alanine-proline-rich sequence between the binding domain and the catalytic domain is partially or completely deleted. In both E2-mutants the rotational mobility of the lipoyl domain and the overall activity after reconstitution of the complex are significantly decreased indicating the important role of the deleted sequence for the movement of the lipoyl domain and the transfer of substrates between the different active sites within the complex.

Acyltransferases↗

Does ferredoxin I (Azotobacter) represent a novel class of DNA-binding proteins that regulate gene expression in response to cellular iron(II)?

Azotobacter vinelandii (Av) and chroococcum (Ac) ferredoxin I contain [3Fe-4S]1 + 0 and [4Fe-4S]2+1+ clusters, when isolated aerobically, which undergo one-electron redox cycles at potentials of -460 +/- 10 mV (vs SHE) at pH 8.3 and -645 +/- 10 mV, respectively. The X-ray structure of Fd I (Av) reveals that the N-terminal half of the polypeptide folds as a sandwich of beta-strands which enclose the iron-sulphur clusters. The C-terminal sequence contains an amphiphilic alpha-helix of four turns which lies on the surface of the beta-barrel. Fd I (Av) controls expression of an unknown protein of Mr approximately 18,000. Fd I (Ac) will complex iron(II) avidly above pH approximately 8.0 only when the [3Fe-4S] cluster is reduced and provided that cellular nucleic acid is bound. Fd I (Ac) rigorously purified from nucleic acid does not undergo iron(II) uptake. These facts, together with recent evidence that the interconversion process [3Fe-4S]0 + Fe2+----[4Fe-4S]2+ in the iron-responsive element binding protein (IRE-BP) of eukaryotic cells is controlling protein expression at the level of mRNA [1991, Cell 64, 4771; 1991, Nucleic Acid Res. 19, 1739] leads to the following hypothesis. Fd I is a DNA-binding protein which interacts by single alpha-helix binding in the wide groove of DNA. The binding is regulated by iron(II) levels in the cell. The 7Fe form binds to DNA and represses gene expression. Only the DNA-bound form of the 7Fe Fd I will take up iron(II), not the form free in solution. Iron(II) becomes bound when the [3Fe-4S] cluster is reduced. The 8Fe Fd I thus generated no longer binds DNA and the gene is de-repressed. Sequence comparisons and the crystal structure suggests that the two central turns of the alpha-helix are important elements of the DNA-recognition process and that residues Gln69 and Glu73, which lie on the outer surface of the helix, hydrogen-bond with specific base pairs.

Amino Acid Sequence↗

Carboxyl-terminal processing may be essential for production of active NiFe hydrogenase in Azotobacter vinelandii.

The NiFe hydrogenase from Azotobacter vinelandii is a membrane-bound alpha beta heterodimer that can oxidize H2 to protons and electrons and thereby provide energy. Genes encoding the alpha and beta subunits, hoxG and hoxK respectively, followed by thirteen contiguous accessory genes potentially involved in H2 oxidation, have been previously sequenced. Mutations in some of these accessory genes give rise to inactive enzyme containing an alpha subunit with decreased electrophoretic mobility. Mass spectral analysis of the subunits demonstrated that the alpha subunit had a molecular weight 1,663 Da less than that predicted from hoxG. Since the N-terminal sequence of the purified alpha subunit matches the sequence predicted from hoxG we suggest this difference is due to removal of the C-terminus of the alpha subunit which may be an important step linked to metal insertion, localization, and formation of active hydrogenase.

Amino Acid Sequence↗

Antimycin inhibition of the cytochrome bd complex from Azotobacter vinelandii indicates the presence of a branched electron transfer pathway for the oxidation of ubiquinol.

Antimycin A and UHBDT inhibit the activity of the purified cytochrome bd complex from Azotobacter vinelandii. Inhibition of activity is non-competitive and antimycin A binding induces a shift to the red in the spectrum of a b-type haem. No inhibitory effects were seen with myxothiazol. Steady-state experiments indicate that the site of inhibition for antimycin A lies on the low-potential side of haem b558. In the presence of antimycin A at concentrations sufficient to inhibit respiration, some direct electron transfer from ubiquinol-1 to haem b595 and haem d still occurs. The results are consistent with a branched electron transfer pathway from ubiquinol to the oxygen reduction site.

Antimycin A↗

Purification and characterization of an iron superoxide dismutase from the nitrogen-fixing Azotobacter vinelandii.

Two electrophoretically distinct forms of superoxide dismutase (SOD; EC 1.15.1.1) which show different inhibition patterns to hydrogen peroxide have been identified in Azotobacter vinelandii. The SOD inhibited by hydrogen peroxide was purified to homogeneity, and turned out to be an iron superoxide dismutase. The enzyme is present in only one molecular form with an isoelectric point of 4.1, and it is composed of two identical subunits with an apparent molecular weight of 21,000 Da. Spectroscopic analyses indicated that this enzyme contains ferric iron (1.4-1.6 mol/mol protein) in the typical high-spin form present in other prokaryotic Fe-SODs. N-Terminal sequence alignments (up to the 49th residue) showed that A. vinelandii Fe-SOD has high similarity with other prokaryotic Fe-SODs.

Amino Acid Sequence↗

Formation and characterization of a transition state complex of Azotobacter vinelandii nitrogenase.

A stable complex is formed between the nitrogenase proteins of Azotobacter vinelandii, aluminium fluoride and MgADP. All nitrogenase activities are inhibited. The complex formation was found to be reversible. An incubation at 50 degrees C recovers nitrogenase activity. The complex has been characterized with respect to protein and nucleotide composition and redox state of the metal-sulfur clusters. Based on the inhibition by aluminium fluoride together with MgADP, it is proposed that a stable transition state complex with nitrogenase is isolated.

Adenosine Diphosphate↗

A sensor protein involved in induction of nitrate assimilation in Azotobacter chroococcum.

Nitrogen-fixing Azotobacter chroococcum cells, but not ammonium- or nitrate-grown cells, exhibited two polypeptide components of 22 and 35 kDa, respectively, that we termed P22 and P35. Bidimensional polyacrylamide gel electrophoresis analysis of preparations from N2-fixing cells that had been transferred to nitrate medium and then incubated for 2 h revealed that P22 had shifted to a more acidic part of the gel while P35 did not change its electrophoretic pattern. Using [32P]orthophosphoric acid it could be demonstrated that the shift in mobility of P22 was due to the phosphorylation of the polypeptide dependent on nitrate (nitrite). The A. chroococcum TR1 strain, which is unable to use nitrate as a nitrogen source and displays activities of nitrogenase, nitrate reductase and nitrite reductase, exhibited both polypeptides. In contrast, P22 and P35 were absent from A. chroococcum MCD1, a mutant strain that cannot assimilate nitrate and lacks the nitrate-reducing enzymatic system. The results suggest that P22 could act as a sensor protein for nitrate in A. chroococcum.

Azotobacter↗

Crystal structure of Azotobacter cytochrome c5 at 2.5 A resolution.

The crystal structure of cytochrome c5 from Azotobacter vinelandii has been solved and refined to an R value of 0.29 at 2.5 A resolution. The structure of the oxidized protein was solved using a monoclinic crystal form. The structure was solved by multiple isomorphous replacements, re-fit to a solvent-leveled multiple isomorphous replacement map, and refined by restrained least squares. The structure reveals monomers associated about the crystallographic 2-fold axis by hydrophobic contacts at the "exposed heme edge". The overall conformation for the monomer is similar to that of Pseudomonas aeruginosa cytochrome c551. However, relative to a common heme conformation, c5 and c551 differ by an average of 6.8 A over 82 alpha-carbon positions and the propionates of c5 are much more exposed to solvent. The shortest heme--heme contact at the "dimer" interface is 6.3 A (Fe to Fe 16.4 A). Alignment of c5 and c551 shows that the two cytochromes, in spite of sequence differences, have remarkably similar charge distributions. A disulfide stacks on a tyrosine between the N- and C-terminal helices.

Amino Acid Sequence↗

Refinement of the 7 Fe ferredoxin from Azotobacter vinelandii at 1.9 A resolution.

The recently redetermined structure of the 7 Fe ferredoxin from Azotobacter vinelandii has been refined against a new 1.9 A data set. The crystallographic R-factor is 0.215 for all 9586 observed reflections 8.0 to 1.9 A. The model contains 106 amino acid residues, two Fe-S clusters and 21 water molecules. The root-mean-square deviations from ideality of bonds and angles are 0.014 A and 3.3 degrees, respectively. The refinement confirms the presence of two free cysteines: the thiol of C11 is in association with the side-chain of K100; the thiol of C24 is 3.35 A from inorganic sulfur of the [4 Fe-4 S] cluster. The refinement confirms a [3 Fe-4 S] model for the 3 Fe cluster. The two Fe-S clusters have similar bond distances and angles. The structure of the protein for residues 1 to 57 superposes within 0.85 A on residues 1 to 53 of the 8 Fe ferredoxin structure for main-chain N, CA and C atoms, if residues 9, 10, 29 and 30 of 7 Fe ferredoxin are omitted. These residues are part of two loops in contact with residues of the extended C-terminal chain of 7 Fe ferredoxin.

Amino Acids↗