[Fe]-Hydrogenase II isolated from C. pasteurianum contains 14 Fe which are distributed among the so-called H cluster (the catalytic center) and two [4Fe-4S] clusters. Insights gained from Mössbauer studies of M-[4Fe-4S]2+ cluster assemblies (M is a paramagnetic center) in sulfite reductase and carbon monoxide dehydrogenase have suggested that the H cluster contains a [4Fe-4S]2+ cluster covalently linked to a smaller Fe-containing cluster. Recent X-ray studies of two [Fe]-hydrogenases, combined with the results of FTIR studies, have revealed that the H cluster contains a novel binuclear Fe cluster, [2Fe]H, that is linked by a cysteinyl sulfur to a [4Fe-4S] cluster; [2Fe]H was found to have CO, CN-, and thiolate ligands. The analysis of the Mössbauer spectra of Hydrogenase II in the oxidized, reduced, and the CO-inhibited states has enabled us to assign the 57Fe magnetic hyperfine tensors observed by ENDOR and Mössbauer spectroscopy to the two subclusters. Thus, AI = +25.3 MHz and AII = −28.4 MHz of Hox-CO can be assigned to the two delocalized pairs of [4Fe − 4S . In our coupling model these A-values result for j ≈ 100 cm-1 where j describes the exchange interaction between [4Fe − 4S and [2Fe]H. The 18 MHz A-value of Hox obtained by ENDOR must result from one Fe site of [2Fe]H, while the 7.5 MHz ENDOR A-value seems to be associated with [4Fe-4S]H. Analysis of the Mössbauer spectra of Hred shows that the 4Fe cluster is in the 2+ state and that [2Fe]H contains presumably two low-spin FeII sites with ΔE Q ≈ 0.85 mm/s and δ ≈ 0.08 mm/s. The observation that the [4Fe-4S] cluster is in the 2+ state in Hox, Hox-CO, and Hred suggests that the [2Fe]H subcluster is in the mixed-valent FeIIIFeII state in Hox and Hox-CO. Given the environment of strong-field ligands in [2Fe]H, the FeIII site must have low-spin configuration. While such an assignment is compatible with the EPR g-values, low-spin FeIII sites with g ≈ 2 commonly exhibit very anisotropic 57Fe A-tensors (due to spin-dipolar interactions) and thus the isotropic A-values of Hox and Hox-CO observed by ENDOR are difficult to explain. This point is discussed in some detail.

The transcription factor FNR (fumarate nitrate reduction) requires the presence of an iron-sulfur (Fe-S) cluster for its function as a global transcription regulator in Escherichia coli when oxygen becomes scarce. The ability to adapt to changes in oxygen concentrations in the environment is common to many organisms. In the facultative anaerobe, Escherichia coli, the transcription factor FNR ( fumarate nitrate reduction) regulates a network of genes that facilitates adaptation to oxygen deprivation by providing alternative pathways for energy generation (1). Recent data suggest that FNR contains a [4Fe-4S] cluster (2-4) and that this cluster apparently mediates the sensitivity of this transcription factor to oxygen, thus limiting FNR activity to anaerobic conditions. The stoichiometry of iron and labile sulfide relative to the number of cysteine ligands of anaerobically purified FNR is most compatible with the presence of a [4Fe-4S] cluster (3). Iron and sulfide analyses and CD spectra of FNR preparations derived from reconstitution of a cluster into apoprotein also supports this cluster assignment (4). The presence of the Fe-S cluster in the anaerobically purified form of FNR is correlated with an increase in dimerization and specific DNA binding (3), compared with the aerobically purified form that lacks an Fe-S cluster (2, 5, 6). Furthermore, the Fe-S cluster is disrupted by oxygen, and this is correlated with the conversion of FNR into an inactive monomeric protein (3). The loss of this cluster as well as the loss of specific DNA binding upon exposure of FNR to oxygen suggested that the [4Fe-4S] cluster, through its intrinsic instability, serves as an oxygen sensor.This paper reports observations on the path of disassembly of the [4Fe-4S] cluster of FNR in vitro. Little is known about the cluster disassembly mechanism of proteins in the absence of chelators, detergents, chemical oxidants, and other nonphysiological agents. The rapid destruction of the Fe-S cluster of FNR, simply upon exposure of a purified protein solution to air, offers an opportunity to obtain information on the progress and mode of the disassembly of the [4Fe-4S] cluster of this protein. We have used chemical analysis for iron and sulfide as well as electronic, EPR, and Mössbauer spectroscopies to monitor the disassembly process. We report here the unexpected observation that the [4Fe-4S] cluster of FNR is converted in less than 5 min to a [2Fe-2S] cluster in about 60% yield as judged from Mössbauer spectra and this conversion results in a reduction in DNA-binding ability. The [4Fe-4S] 2ϩ cluster can be regenerated from the [2Fe-2S] cluster or its components by reduction with dithionite.

The benzoate 1,2-dioxygenase system (BZDOS) from Pseudomonas putida mt-2 catalyzes the NADH-dependent oxidation of benzoate to 1-carboxy-1,2-cis-dihydroxycyclohexa-3,5-diene. Both the oxygenase (BZDO) and reductase (BZDR) components of BZDOS have been purified and characterized kinetically and by optical, EPR, and Mössbauer spectroscopies. BZDO has an (alpha beta)(3) subunit structure in which each alpha subunit contains a Rieske [2Fe-2S] cluster and a mononuclear iron site. Two different purification protocols were developed for BZDO allowing the mononuclear iron to be stabilized in either the Fe(III) or the Fe(II) state for spectroscopic characterization. Using single turnover reactions, it is shown that fully reduced BZDO alone is capable of yielding the cis-diol product in high yield at rates that exceed the BZDOS turnover number. At the conclusion of turnover, quantification of each oxidation state of the metal sites by EPR and Mössbauer spectroscopies shows that the Rieske cluster and mononuclear iron are each oxidized in amounts equal to the product yield, suggesting that the two electrons required for catalysis derive from the two metal centers. These results are in agreement with our previous study of naphthalene 1,2-dioxygenase [Wolfe, M. D., Parales, J. V., Gibson, D. T., and Lipscomb, J. D. (2001) J. Biol. Chem. 276, 1945-1953], which belongs to a different Rieske dioxygenase subclass, suggesting that it is a universal characteristic of Rieske dioxygenases that oxygen activation and substrate oxidation are catalyzed by the oxygenase component alone. The EPR spectrum of the Fe(III) center after a single turnover is distinct from either of those of substrate-free or substrate-bound enzyme. The complex with this spectrum is not formed by addition of cis-diol product to the resting Fe(III) form of the enzyme but is observed when the Fe(II) form is oxidized in the presence of product. Together, these results suggest that product exchange occurs only when the mononuclear iron is reduced. Stopped-flow and rapid scan analyses monitoring the oxidation of the Rieske cluster during the single turnover reaction show that it occurs in three phases that are kinetically competent for catalysis. The rate of each phase was found to be dependent on the type of substrate present, suggesting that the substrate influences the rate of electron transfer between the metal clusters. The participation of substrate in the oxygen activation reaction suggests a new aspect of the mechanism of this process by the Rieske dioxygenase class.