The concentration of cellular nitrogenase proteins in Azotobacter vinelandii whole cells as determined by activity measurements and electron paramagnetic resonance spectroscopy.

The concentration of MoFe protein (Av1) in Azotobacter vinelandii whole-cell crude extract was measured by electron paramagnetic resonance spectroscopy at g = 3.7 resonance. The Av1 concentration was also measured from the activity of crude extract to which increasing amounts of purified Av1 and Av2 were added. The Av2 concentration was determined by fitting activity measurements of crude extract and crude extract to which purified Av2 was added. The Av1 concentration was found to be 26-28 microM and that for Av2 was 42-45 microM in whole cells, with a Av2/Av1 ratio of 1.6. In vitro activity measurements carried out as a function of Av1 concentration at Av2/Av1 ratios of 1 and 4 showed a dilution effect below 0.08 microM, a factor of 2 below that observed for nitrogenase reactivity for Klebsiella pneumoniae. No deviations from linearity were observed up to 26 microM for the Av1-Av2 interaction. The flavoprotein (AvFlp) was shown to enhance nitrogenase reactivity at low Av2/Av1 ratios, a result attributed to decreasing the Km for Av2-Av1 interaction. Direct reduction of bound Av2 is possibly the source of this kinetic enhancement. The kinetic results are considered in terms of the Thorneley and Lowe scheme.

The in-vivo identification of the MoFe protein (FeMo cofactor) of nitrogenase in Klebsiella pneumoniae and of the Mo-storage protein in Azotobacter vinelandii via the nuclear quadrupole interaction of 99Mo(beta-)99Tc.

The expression of the MoFe protein of nitrogenase in Klebsiella pneumoniae was identified in vivo via the nuclear quadrupole interaction (NQI) of 99Mo(beta-)99Tc using perturbed angular correlations of gamma-rays. The NQI parameters were: omega approx. 360 Mrad/s and eta approx. 1. In addition, the NQI of the 'Mo-storage protein' in Azotobacter vinelandii cells which had been grown in the presence of NH4+ (13 mM), i.e. under conditions of strict repression of nitrogenase synthesis, was determined: omega approx. 190 Mrad/s, eta approx. 0.25. Under these conditions, the characteristic signal of the MoFe protein (FeMo cofactor) was absent.

Analysis of Azotobacter vinelandii strains containing defined deletions in the nifD and nifK genes.

Strains of Azotobacter vinelandii which contain defined deletions within the nifD and nifK genes which encode, respectively, the alpha and beta subunits of the MoFe protein of nitrogenase were analyzed. When synthesized without its partner, the beta subunit accumulated as a soluble beta 4 tetramer. In contrast, when the alpha subunit was present without its partner, it accumulated primarily as an insoluble aggregate. The solubility of this protein was increased by the presence of a form of the beta subunit which contained a large internal deletion, such that the alpha subunit could participate in the assembly of small amounts of an alpha 2 beta 2 holoprotein. When synthesized alone, the beta subunit was remarkably stable, even when the protein contained a large internal deletion. The alpha subunit, however, was much more rapidly degraded than the beta subunit, both when it was synthesized alone in its native background and when it was synthesized with its beta subunit partner in a foreign background. Antibodies raised against purified alpha 2 beta 2 MoFe protein recognized epitopes only on the nondenatured beta subunit and not on the nondenatured alpha subunit. Our findings that all epitopes for the alpha2beta2 tetramer appeared to be on the beta subunit, that the beta subunit assembled into beta4 tetramers, and that the alpha subunit alone was very insoluble, combined with the previous finding that the Fe protein binds to the beta subunit (A. H. Willing, M. M. Georgiadis, D. C. Rees, and J. B. Howard, J. Biol. Chem. 264:8499-8503, 1989) all suggest that the beta subunit has a more surface location than the alpha subunit in the alpha2beta2 tetramer.

Mössbauer spectroscopy applied to the oxidized and semi-reduced states of the iron-molybdenum cofactor of nitrogenase.

Mössbauer parameters at 125K for both the oxidized and semi-reduced states of FeMoco isolated from the MoFe protein of Azotobacter vinelandii nitrogenase of delta/Fe = 0.32 and 0.37 mm/s and delta Eq = 0.84 and 0.71 mm/s, respectively, are reported. FeMoco(ox) fits the Debye model perfectly from 4.2-125K and has a S = 0 ground state. FeMoco(ox) apparently contains 10-20% FeMoco(s-r) and vice versa, possibly as a result of the spontaneous oxidation phenomenon. Quantitation of the spectra indicates a Fe:Mo ratio of 5 +/- 1:1 and the similar quadrupole splittings and isomer shifts suggest a similar environment for all iron atoms.

Iron K-edge X-ray absorption spectroscopy of the iron-molybdenum cofactor of nitrogenase from Klebsiella pneumoniae.

Iron K-edge X-ray absorption data for the iron-molybdenum cofactor ('FeMoco') from Klebsiella pneumoniae reported here provide the first evidence for long-range structural order in the cofactor [Fe...Fe(Mo) = 0.368 nm in addition to Fe...S = 0.22 nm and Fe...Fe(Mo) = 0.27 nm] and, in contrast with previously published data [Antonio, Teo, Orme-Johnson, Nelson, Groh, Lindahl, Kauzlarich & Averill (1982) J. Am. Chem. Soc. 104, 4703-4705], indicate that most of the iron centres are not co-ordinated to light (oxygen, nitrogen) atoms. This demonstrates that presently available chemical models for FeMoco are inadequate.

A quantitative approach to sequence comparisons of nitrogenase MoFe protein alpha- and beta-subunits including the newly sequenced nifK gene from Klebsiella pneumoniae.

The nucleotide sequence was determined for part of the Klebsiella pneumoniae nif gene cluster containing the 3' end of the nifD gene and the entire length of the nifK gene (encoding the alpha- and beta-subunits of the nitrogenase MoFe protein respectively), as well as the putative start of the nifY gene, a gene of as yet unknown function. A broad-based comparison of a number of MoFe protein alpha-subunits, beta-subunits and alpha-versus beta-subunits was carried out by the use of a computer program that simultaneously aligns three protein sequences according to the mutation data matrix of Dayhoff. A new kind of quantitative statistical measure of the similarity between the aligned sequences was obtained by calculating and plotting standardized similarity scores for overlapping segments along the aligned proteins. This calculation determines if a test sequence is similar to the consensus sequence of two other proteins that are known to be related to each other. The different beta-subunits compared were found to be significantly similar along most of their sequence, with the exception of two relatively short regions centred around residues 225 and 300, which contain insertions/deletions. The overall pattern of similarity between different alpha-subunits exhibits resemblance to the overall pattern of similarity between different beta-subunits, including regions of low similarity centred around residues 225 and 340. Comparison of alpha-subunits with beta-subunits showed that a region of significant similarity between the two types of subunits was located approximately between residues 120 and 180 in both subunits, but other parts of the proteins were only marginally similar. These results provide insights into likely tertiary structural features of the MoFe protein subunits.

Nucleotide sequence of the Klebsiella pneumoniae nifD gene and predicted amino acid sequence of the alpha-subunit of nitrogenase MoFe protein.

The nucleotide sequence of the Klebsiella pneumoniae nifD gene is presented and together with the accompanying paper [Holland, Zilberstein, Zamir & Sussman (1987) Biochem. J. 247, 277-285] completes the sequence of the nifHDK genes encoding the nitrogenase polypeptides. The K. pneumoniae nifD gene encodes the 483-amino acid-residue nitrogenase alpha-subunit polypeptide of Mr 54156. The alpha-subunit has five strongly conserved cysteine residues at positions 63, 89, 155, 184 and 275, some occurring in a region showing both primary sequence and potential structural homology to the K. pneumoniae nitrogenase beta-subunit. A comparison with six other alpha-subunit amino acid sequences has been made, which indicates a number of potentially important domains within alpha-subunits.

Studies on nitrate reductase of Clostridium perfringens. IV. Identification of metals, molybdenum cofactor, and iron-sulfur cluster.

Nitrate reductase of Clostridium perfringens was purified by an improved method using immuno-affinity chromatography. The purified preparation contained Mo, Fe, and acid-labile sulfide; the Mo content was 1 mol per mol and the Fe 3.7 mol per mol of the enzyme. The inactive enzyme obtained from cells grown in the presence of tungstate did not hold Mo but contained 1 mol of W. The content of Fe was not increased. The presence of molybdenum cofactor in the nitrate reductase was indicated by the formation of molybdopterin form A in the oxidation of the enzyme by iodine and by the complementation of NADPH-nitrate reductase with the heart-treated enzyme in the extract of Neurospora crassa nit-1. The Clostridium nitrate reductase had an absorption maximum at 279 nm and shoulders at 320, 380, 430, and 520 nm. This enzyme seems to contain an iron sulfur cluster since the reduced enzyme showed decreased absorption in visible region. The CD spectrum of the enzyme has a positive peak at 425 nm and negative ones at 310, 360, and 595 nm. It was compared with the CD spectrum of ferredoxin (2Fe-2S or 4Fe-4S cluster) and the nitrate reductase of Plectonema boryanum.

The importance of quantitative Mössbauer spectroscopy of MoFe-protein from Azotobacter vinelandii.

The Mössbauer spectra of MoFe-protein of Azotobacter vinelandii, as isolated under dithionite and taken at temperatures from 125 K to 175 K, are the sums of four resolved quadrupole doublets. Our results indicate that the currently accepted interpretation of these doublets can be questioned. Our data reduction method converts the Mössbauer transmission spectra to source lineshape deconvolved absorption spectra linear in iron. We used these absorption spectra to determine the stoichiometry of the Fe clusters in MoFe-protein and we obtained much better fits if we assumed that there are four iron atoms in the 'Fe2+, doublet, two iron atoms in the 'S' doublet, twelve iron atoms in the 'D' doublet and sixteen iron atoms in the 'M' doublet. Therefore we propose that the MoFe-cofactor contains one molybdenum and eight iron atoms ('M'). We also argue that none of the previous Mössbauer spectroscopic studies have been performed on the highest-activity preparation now obtainable, nor has there been any study to prove that the Mössbauer spectra are independent of activity. We consider that the Mössbauer spectroscopic studies of the MoFe-protein of nitrogenase are a re-opened and unsolved problem.

A Mössbauer spectroscopic investigation of the redox behaviour of the molybdenum-iron protein from Klebsiella pneumoniae nitrogenase. Mechanistic and structural implications.

The redox properties of the nitrogenase Mo-Fe protein from Klebsiella pneumoniae have been monitored by 57Fe Mössbauer spectroscopy between -460 and -160mV (relative to the normal hydrogen electrode). Two redox processes associated with the atoms of the protein were observed. One at -216mV (pH 8.7) was associated with the Fe-Mo cofactor centres in the protein and allowed identification of the Mössbauer parameters of the oxidized form of these centres. The other redox process at -340mV (pH 8.7) was associated with species M5 [Smith & Lang (1974) Biochem. J. 137, 169-180]. This latter redox process may be involved in enzyme turnover. The oxidized form of species M5 interacts magnetically with species M4. The structural implications of the data have been considered in relation to other published data. It is concluded that an unequivocal assignment of the M4 and M5 atoms to Fe-S cluster types is not yet possible.

Redox and spectroscopic properties of oxidized MoFe protein from Azotobacter vinelandii.

The MoFe protein from Azotobacter vinelandii undergoes a six-electron oxidation by various organic dye oxidants with full retention of initial activity. Reduction of the oxidized protein by S2O42- and by controlled potential electrolysis indicates the presence of two reduction regions at -290 and -480 mV, each requiring three electrons for complete reaction. Control of the oxidation conditions provides a means for preparing two distinct MoFe protein species selectively oxidized by three electrons. Selective reduction of the redox region at -290 mV causes development of the EPR signal associated with fully reduced MoFe protein while reduction at -480 mV produces a change in the visible spectrum but has no effect on the EPR signal intensity. Kinetic differences for reduction of the two redox regions indicate that the cofactor region undergoes a more rapid reaction with reductant than the other metal redox sites.

Nitrogenase XII. Mössbauer studies of the MoFe protein from Clostridium pasteurianum W5.

We have studied the molybdenum-protein (MoFe protein) from Clostridium pasteurianum with Mössbauer spectroscopy in the temperature range from 1.5 to 200 K in magnetic fields up to 55 kG. Except for some small differences in the hyperfine parameters the results for the C. pasteurianum protein are essentially the same as those published previously for the protein from Azotobacter vinelandii, i.e. (30 +/- 2) Fe atoms partition into two identical cofactor centers M (each center most likely containing six Fe atoms and one Mo atom), four P-clusters (each center containing four Fe atoms), and one iron environment labeled S (about two Fe atoms per holoenzyme). We have analyzed the spectra of the cofactor centers in three distinct oxidation states, Formula: (see test). The diamagnetic (electronic spin S = 0) state MOX is attained by oxidation of the native, EPR-active (S = 3/2) state MN. The reduced state MR is observed in steady state under nitrogen fixing conditions; high-field Mössbauer studies show that the cofactor centers are paramagnetic (integer electronic spin S greater than or equal to 1) in the state MR. We have evaluated the complex high-field spectra resulting from the P-clusters in the oxidized state POX. The analysis shows that one iron site is characterized by a positive hyperfine coupling constant A0 while the other three sites have A0 less than 0. A slightly modified set of parameters also fits the high-field data of the MoFe protein from A. vinelandii. Finally, we will present a discussion summarizing our principle results obtained to date for the proteins from A. vinelandii and C. pasteurianum.

Two forms of nitrogenase from the photosynthetic bacterium Rhodospirillum rubrum.

Acetylene reduction by nitrogenase from Rhodospirillum rubrum, unlike that by other nitrogenases, was recently found by other investigators to require an activation of the iron protein of nitrogenase by an activating system comprising a chromatophore membrane component, adenosine 5'-triphosphate (ATP), and divalent metal ions. In an extension of this work, we observed that the same activating system was also required for nitrogenase-linked H(2) evolution. However, we found that, depending on their nitrogen nutrition regime, R. rubrum cells produced two forms of nitrogenase that differed in their Fe protein components. Cells whose nitrogen supply was totally exhausted before harvest yielded predominantly a form of nitrogenase (A) whose enzymatic activity was not governed by the activating system, whereas cells supplied up to harvest time with N(2) or glutamate yielded predominantly a form of nitrogenase (R) whose enzymatic activity was regulated by the activating system. An unexpected finding was the rapid (less than 10 min in some cases) intracellular conversion of nitrogenase A to nitrogenase R brought about by the addition to nitrogen-starved cells of glutamine, asparagine, or, particularly, ammonia. This finding suggests that mechanisms other than de novo protein synthesis were involved in the conversion of nitrogenase A to the R form. The molecular weights of the Fe protein and Mo-Fe protein components from nitrogenases A and R were the same. However, nitrogenase A appeared to be larger in size, because it had more Fe protein units per Mo-Fe protein than did nitrogenase R. A distinguishing property of the Fe protein from nitrogenase R was its ATP requirement. When combined with the Mo-Fe protein (from either nitrogenase A or nitrogenase R), the R form of Fe protein required a lower ATP concentration but bound or utilized more ATP molecules during acetylene reduction than did the A form of Fe protein. No differences between the Fe proteins from the two forms of nitrogenase were found in the electron paramagnetic resonance spectrum, midpoint oxidation-reduction potential, or sensitivity to iron chelators.

The molecular weight of, and evidence for two types of subunits in, the molybdenum-iron protein of Azotobacter vinelandii nitrogenase.

The weight-average molecular weight of the Mo-Fe protein isolated from Azotobacter vinelandii has been determined by sedimentation-equilibrium techniques. In buffer, the value is 245000+/-5000; in 8M-urea, the value is 61000+/-1000. The protein was separated into two components by chromatography on CM-cellulose in 7M-urea, pH 4.5. These components have similar molecular weights but were shown to differ in charge, amino acid content and arginine-containing peptides. It is proposed that the tetramer has the subunit composition (nalpha2nbeta2).