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 Fe͞S 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. (9), which is located at the ␣␤-interface and ligated to six protein residues; and the [Mo-7Fe-9S-X-homocitrate] (the identity of X is unknown but is considered to be C, O, or N; ref. 10) FeMo cofactor (FeMoco), which is situated within the ␣-subunit and bound to only two protein residues and an exogenous homocitrate ligand. Both P-cluster and FeMoco are composed of smaller substructures: the P-cluster comprises two subclusters that share a 6 -sulfide (9) and FeMoco consists of [Mo-3Fe-3S] and [4Fe-3S] subcubanes that are bridged by three 2 -sulfides and share a central 6 -light atom (10). These metal clusters are essential for nitrogenase reaction, a process that involves ATP-dependent electron transfer from the [4Fe-

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The iron-molybdenum cofactor (FeMoco) of the nitrogenase MoFe protein is a highly complex metallocluster that provides the catalytically essential site for biological nitrogen fixation. FeMoco is assembled outside the MoFe protein in a stepwise process requiring several components, including NifB-co, an iron-and sulfurcontaining FeMoco precursor, and NifEN, an intermediary assembly protein on which NifB-co is presumably converted to FeMoco. Through the comparison of Azotobacter vinelandii strains expressing the NifEN protein in the presence or absence of the nifB gene, the structure of a NifEN-bound FeMoco precursor has been analyzed by x-ray absorption spectroscopy. The results provide physical evidence to support a mechanism for FeMoco biosynthesis. The NifEN-bound precursor is found to be a molybdenum-free analog of FeMoco and not one of the more commonly suggested cluster types based on a standard [4Fe-4S] architecture. A facile scheme by which FeMoco and alternative, non-molybdenum-containing nitrogenase cofactors are constructed from this common precursor is presented that has important implications for the biosynthesis and biomimetic chemical synthesis of FeMoco.biosynthesis ͉ extended x-ray absorption fine structure ͉ nitrogenase ͉ x-ray absorption spectroscopy

Nitrogenase is a multicomponent metalloenzyme that catalyzes the conversion of atmospheric dinitrogen to ammonia. For decades, it has been generally believed that the [8Fe-7S] P-cluster of nitrogenase component 1 is indispensable for nitrogenase activity. In this study, we identified two catalytically active P-cluster variants by activity assays, metal analysis, and EPR spectroscopic studies. Further, we showed that both P-cluster variants resemble [4Fe-4S]-like centers based on x-ray absorption spectroscopic experiments. We believe that our findings challenge the dogma that the standard P-cluster is the only cluster species capable of supporting substrate reduction at the FeMo cofactor and provide important insights into the general mechanism of nitrogenase catalysis and assembly.MoFe protein ͉ VFe protein N itrogenase catalyzes one of the most remarkable chemical transformations in biological systems, the reduction of atmospheric dinitrogen to a bioavailable form, ammonia. Three classes of nitrogenase systems, namely, the Mo-, V-, and Fe-only nitrogenases, have been identified (for recent reviews see refs. 1-11). f Although encoded by different structural genes, all three nitrogenases are comprised of two essential component metalloproteins, component 1 (MoFe, VFe, or FeFe protein) and component 2 (Fe protein). g The homodimeric Fe protein of the Mo-nitrogenase has one [4Fe-4S] cluster bridged between the two subunits, whereas the ␣ 2 ␤ 2 -tetrameric MoFe protein contains two unique metal clusters per ␣␤-subunit: the [8Fe-7S] P-cluster (14), which is located at the ␣␤-interface, and the [Mo-7Fe-9S-X-homocitrate] h FeMo cofactor (FeMoco), which is situated within the ␣-subunit. ATP-dependent electron transfer is believed to proceed from the [4Fe-4S] cluster of the Fe protein to the P-cluster of the MoFe protein and finally to FeMoco where substrate reduction takes place. The Fe protein of the V-nitrogenase shares a high degree of homology with the Fe protein of the Mo-nitrogenase and, apart from the presence of an additional ␥-subunit, the VFe protein is also believed to be highly homologous to the MoFe protein with respect not only to the structural genes encoding the ␣-and ␤-subunits, but also to the redox centers contained within the protein, designated the P-cluster and the FeV cofactor (FeVco), respectively, in this case (4, 10, 16). The structurally homologous heterometal centers, i.e., FeMoco and FeVco, are also categorically termed cofactors.It is generally believed that the structural integrity of the P-cluster is indispensable for nitrogenase reactivity. However, the exact mechanism by which the P-cluster carries out its function in substrate reduction and, in particular, the oxidation states and structural conformations of the P-cluster involved in this process, remain largely a puzzle (17). Two types of cofactordeficient MoFe or VFe protein variants, generated by nifH or nifB deletion, i respectively, have been used to study the features of P-clusters without the interference of the cofactor centers...

Nitrogenase, the enzyme system responsible for biological nitrogen fixation, is believed to utilize two unique metalloclusters in catalysis. There is considerable interest in understanding how these metalloclusters are assembled in vivo. It has been presumed that immature iron-molybdenum cofactor-deficient nitrogenase MoFe proteins contain the P-cluster, although no biosynthetic pathway for the assembly of this complex cluster has been identified as yet. Through the comparison by iron K-edge x-ray absorption edge and extended fine structure analyses of cofactor-deficient MoFe proteins resulting from nifH and nifB deletion strains of Biological nitrogen fixation, the essential conversion of atmospheric nitrogen to ammonia, is catalyzed by the nitrogenase enzyme system. Nitrogenase consists of two components, the iron (Fe) protein 1 and molybdenum-iron (MoFe) protein (reviewed in Refs. 1-5).2 Substrate reduction occurs within the MoFe protein, an ␣ 2 ␤ 2 heterotetramer that contains two unique metalloclusters, the iron-molybdenum cofactor (FeMoco) and the P-cluster. The Fe protein, which is the obligate electron donor to the MoFe protein, is a homodimer containing two nucleotide binding sites (one per subunit) and a single [Fe 4 S 4 ] cluster at the dimer interface. Nitrogenase catalysis consists of a series of Fe protein-MoFe protein complex formation and dissociation reactions in which electrons are sequentially transferred from the [Fe 4 S 4 ] cluster in the Fe protein through the P-cluster in the MoFe protein to the ultimate site of substrate reduction (FeMoco) concomitant with ATP hydrolysis by the Fe protein.There is substantial interest in elucidating the mechanism by which the metalloclusters of the MoFe protein are formed in vivo because of their importance in nitrogen fixation and because they are biologically and chemically unprecedented. FeMoco is a heterometallic double cubane consisting of one [Fe 4 S 3 ] and one [MoFe 3 S 3 ] partial cubane that are bridged by three sulfides and share a 6 -central atom of which the identity is unknown but is considered to be carbon, oxygen, or nitrogen (see Fig. 1) (6). Situated entirely in the ␣-subunit, FeMoco is attached to the protein by only two ligands, a cysteine at the terminal iron and a histidine at the opposite molybdenum, which is also coordinated by bidentate homocitrate. The Pcluster, with a topology similar to that of FeMoco, consists of a symmetric double cubane in which two [4Fe-3S] partial cubanes share a central 6 -sulfur atom (see Fig. 1). It is situated at the ␣␤ dimeric interface and is connected to the protein through six cysteine ligands, two terminal and one bridging cysteine from each subunit. The P-cluster can be reversibly oxidized from this native all-ferrous state, designated P N with indigodisulfonate (IDS) to yield a two-electron oxidized state, designated P 2ϩ or P OX . Following redox-dependent conformational change, the [Fe 4 S 4 ] cube associated with the ␣-subunit is largely unchanged, whereas the [Fe 4 S 4 ] cube associated with...

X-ray damage to protein crystals is often assessed on the basis of the degradation of diffraction intensity, yet this measure is not sensitive to the rapid changes that occur at photosensitive groups such as the active sites of metalloproteins. Here, X-ray absorption spectroscopy is used to study the X-ray dose-dependent photoreduction of crystals of the [Fe(2)S(2)]-containing metalloprotein putidaredoxin. A dramatic decrease in the rate of photoreduction is observed in crystals cryocooled with liquid helium at 40 K compared with those cooled with liquid nitrogen at 110 K. Whereas structural changes consistent with cluster reduction occur in the active site of the crystal measured at 110 K, no such changes occur in the crystal measured at 40 K, even after an eightfold increase in dose. When the structural results from extended X-ray absorption fine-structure measurements are compared with those obtained by crystallography on this and similar proteins, it is apparent that X-ray-induced photoreduction has had an impact on the crystallographic data and subsequent structure solutions. These results strongly indicate the importance of using liquid-helium-based cooling for metalloprotein crystallography in order to avoid the subtle yet important changes that can take place at the metalloprotein active sites when liquid-nitrogen-based cooling is used. The study also illustrates the need for direct measurement of the redox states of the metals, through X-ray absorption spectroscopy, simultaneously with the crystallographic measurements.

and Stanford Synchrotron Radiation Laboratory, SLAC, Stanford, CA 94309 μ-η 2 :η 2 -peroxodicopper(II) (P) and bis(μ-oxo)dicopper(III) (O) complexes are valence isomers that differ by the degree of O 2 reduction and the presence of an O−O bond. 1,2 These isomers can exist in a measurable equilibrium with a small activation energy. 3-6 This facile isomerization is significant to the processes of making and breaking an O-O bond, which are key steps in photosynthesis, respiration, and the catalytic cycle of tyrosinase, a binuclear copper enzyme that ortho-hydroxylates phenols. The characterized P species of oxygenated tyrosinase is accepted as the active oxidant in the oxygen atom transfer reaction, but a transient O-type species in which the O-O bond is cleaved prior to oxygen insertion cannot be overlooked. 7 Understanding these steps in detail is important to the design of synthetic catalysts that use O 2 as a terminal oxidant.A systematic study of the influence of the Lewis basicity of various anions, i.e. their coordinating ability, on the P/O equilibrium was undertaken as a model of substrate binding to the P core in tyrosinase. 5,6 P/O mixtures were prepared with the ligand N,N exhibits rapid, reversible interconversion between equilibrium positions upon temperature change. 9 A Van't Hoff analysis yields ΔH° = −4.3(2) kJ mol −1 and ΔS° = −24(2) J K −1 mol −1 for this P ⇔ O equilibrium in THF: O is favored enthalpically and P is favored entropically, as previously determined for other systems. 4,5More strongly coordinating counteranions bias the P:O equilibrium position towards P, from ∼10:90 with SbF 6 − to ∼100:0 with CH 3 SO 3 − (Figure 1a). The P:O ratio follows anion basicity regardless of size: e.g. CH 3 SO 3 − is slightly smaller than CF 3 SO 3 − , yet the more compact O isomer is not observed with CH 3 SO 3 − . Such a basicity effect is counter-intuitive, as more electron donation to the Cu 2 O 2 core is anticipated to stabilize the higher oxidation state of the copper centers and hence favor the O isomer. 10Titration experiments with competing anions highlight the importance of anion basicity and reveal the existence of specific anion/dication interactions. Addition of a more coordinating anion Y − (CF 3 SO 3 − , TsO − , CH 3 SO 3 − , CF 3 CO 2 − , PhCO 2 − ) to a preformed P/O solution with a "weaker" anion X − (SbF 6 − , CF 3 SO 3 − ) results in a rapid, isosbestic isomerization in the direction O → P. Spectroscopically pure P species are obtained by addition of 1.0 equivalent of TsO − , CH 3 SO 3 − , CF 3 CO 2 − or PhCO 2 − per binuclear complex (Figure 1b) (Figure 2a). 1 The scattering atom at 2.26 Å is required for a good fit and is ascribed to a CH 3 SO 3 − oxygen atom, 15 consistent with the titration experiments. Coordination of CH 3 SO 3 − would place the sulfur atom within 3.3-3.8 Å of the copper centers, which corresponds to the poorly fitted region in the 4-component model. A 5-component EXAFS fit with a Cu···S interaction at a refined distance of 3.47 Å 16 provides a better match to...

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.