FeMoco structure

In the related V clusters a similar core structure is seen but with shorter Fe4S3 bond distances. The ten atom Fe4( 43-S)3( 4-S)3 core is contained in the FeMoco structure, Figure 3, with the same bond connectivity and similar spatial arrangement and, as such, probably provides the best starting point for development of higher nuclearity clusters related to the nitrogenase cofactors. 

Pioneering studies with semi-empirical methods were carried out shortly after the discovery of the FeMoco structure via X-ray diffraction experiments (21,22). These extended-Hiickel calculations have been carried out for structurally fixed models of FeMoco (23,24) and of FeMoco, FeVco, and FeFeco (25), in which the three amino acid ligands have been replaced by hydride ligands. The main results of these studies are deduced based on the assumption that the character of the frontier orbitals, i.e., their composition in terms of atomic orbitals,... 

The three diazene isomers are all stabilized significantly upon coordination to Fe by the direct coordination energy as well as by hydrogen bonding. They should all be taken into account as possible stable intermediates in the FeMoco mechanism. Different open FeMoco structures could favor different isomers while traras-diazene needs a larger Fe-Fe distance than cis-diazene, cis-diazene, and especially NNH2 will become important if FeMoco opens only little. 

The FeMoco structure has be flexible enough to provide a free space for dinitrogen to come into in the cofactor cavity, transformating and then coming out from the cofactor. 

The dearth of concrete molecular data has not discouraged mechanistic debate. The protein-derived FeMoco structure in particular has inspired speculation that dinitrogen is activated while bound as a bridging ligand to multiple iron centers (Figure conjecture is drawn primarily from two... 

We felt it worthwhile to provide some level of theoretical overview given the number of DFT studies that have appeared recently and here limit the discussion to theoretical studies that have included an interstitial light atom in consideration of the FeMoco structure. Three of the most recent and comprehensive... 

Figure 3 shows the three-dimensional structure of the MoFe protein from Klebsiella pneumoniae, Kpl, obtained at 1.65-A resolution (7). The overall structure of the polypeptides is frilly consistent with that reported earlier for Avl (3). The a and /8 subunits exhibit similar polypeptide folds with three domains of parallel /3 sheet/a helical type. At the interface between the three domains in the a subunit is a wide shallow cleft with the FeMoco at the bottom of the cleft about 10 A from the solvent. FeMoco is enclosed within the a subunit. The P cluster, however, is buried within the protein at the interface between the a and /8 subunits, being bound by cysteine residues from each subunit. A pseudo-twofold rotation axis passes between the two halves of the P cluster and relates the a and (3 subunits. Each af3 pair of subunits contains one FeMoco and one P cluster and thus appears... 

Fig. 3. The tetrameric structure of the MoFe protein (Kpl) from Klebsiella pneumoniae (7). The two FeMoco clusters and the P clusters are depicted by space-filling models and the polypeptides by ribbons diagrams (MOLSCRIPT (196)). The FeMoco clusters are bound only to the a subunits, whereas the P clusters span the interface of the a and j8 subunits.

FeMoco can be extracted from the MoFe protein into A(-methylfor-mamide (NMF) solution 32) and has been analyzed extensively using a wide range of spectroscopic techniques both bound to the protein and in solution after extraction from it (33). The extracted FeMoco can be combined with the MoFe protein polypeptides, isolated from strains unable to synthesize the cofactor, to generate active protein. The structure of the FeMoco is now agreed 4, 5, 7) as MoFeTSg homocitrate as in Fig. 4. FeMoco is bound to the a subunit through residues Cys 275, to the terminal tetrahedral iron atom, and His 442 to the molybdenum atom (residue numbers refer to A. vinelandii). A number of other residues in its environment are hydrogen bonded to FeMoco and are essential to its activity (see Section V,E,2). The metal... 

Fig. 4. Structure of the iron molybdenum cofactor, FeMoco (after Chan, Kim, and Rees, (4) Bolin et al. (5) and Mayer et al. (7)). The FeMoco is ligated, within the a subunits of the a2j82 tetrameric structure, by residues Hisa442 and Cysa275 (Avl residue numbers).

From the crystal structure of the complex (Fig. 10) it appears that only minimal conformational changes occur within the MoFe protein on complexation, although it is hard to be dogmatic about these when at 3 A resolution. Nevertheless, ENDOR 116) studies on the FeMoco center demonstrated that at least one class of protons in the vicinity of the FeMoco center is altered in the complex relative to the free protein. 

The iron K-edge EXAFS measurements on AVI " 182) and the extracted FeVaco from AcF 183) show Fe-S and Fe-Fe interactions at 2.32 and 2.64 A, with a longer Fe-Fe distance of 3.7 A very similar again to the EXAFS data on FeMoco. These data emphasize the structural similarities between the cofactor centers of the MoFe and VFe proteins. 

A preparation of the third nitrogenase from A. vinelandii, isolated from a molybdenum-tolerant strain but lacking the structural genes for the molybdenum and vanadium nitrogenases, was discovered to contain FeMoco 194). The 8 subunit encoded by anfG was identified in this preparation, which contained 24 Fe atoms and 1 Mo atom per mol. EPR spectroscopy and extraction of the cofactor identified it as FeMoco. The hybrid enzyme could reduce N2 to ammonia and reduced acetylene to ethylene and ethane. The rate of formation of ethane was nonlinear and the ethane ethylene ratio was strongly dependent on the ratio of nitrogenase components. 

The elucidation of the crystal structures of two high-spin EPR proteins has shown that the proposals for novel Fe-S clusters are not without substance. Two, rather than one novel Fe-S cluster, were shown to be present in nitrogenase, the key enzyme in the biotic fixation of molecular nitrogen 4, 5). Thus the FeMoco-cofactor comprises two metal clusters of composition [4Fe-3S] and [lMo-3Fe-3S] bridged by three inorganic sulfur atoms, and this is some 14 A distant from the P-cluster, which is essentially two [4Fe-4S] cubane moieties sharing a corner. The elucidation of the crystal structure of the Fepr protein (6) provides the second example of a high-spin EPR protein that contains yet another unprecedented Fe-S cluster. 

Figure 2.10 Schematic structures of (a) sulfite reductase of Escherichia coli in which a 4Fe-4S cluster is linked via a cysteine to the iron in a sirohaem (b) P cluster of nitrogenase (c) FeMoCo cluster of nitrogenase (d) the binuclear site in Desulforibrio gigas hydrogenase.

Concurrently with the X-ray crystallographic studies, extended X-ray absorption fine structure (EXAFS) studies confirmed many of the bond distances proposed for nitrogenase s FeMoco cluster. The EXAFS data of reference 25 indicate short Fe-Fe distances of 2.61, 2.58, and 2.54 A for M+, M (resting state), and M forms, respectively. The authors believe that the short M center bond lengths indicate Fe-Fe bonds in this cluster. In another study using dithionite-reduced MoFe-protein Fe-S, Fe-Fe, Fe-Mo distances of 2.32, 2.64, and 2.73 A, respectively, were found in the 1 to 3 A region and Fe-Fe, Fe-S and Fe-Fe distances of 3.8, 4.3, and 4.7 A, respectively, were found in the 3 to 5 A region.30... 

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