MoFe-Protein Structure

Structure of the MoFe Protein. Extensive spectroscopic studies of the MoEe proteia, the appHcation of cluster extmsion techniques (84,151), x-ray anomalous scattering, and x-ray diffraction (10,135—137,152) have shown that the MoEe proteia contains two types of prosthetic groups, ie, protein-bound metal clusters, each of which contains about 50% of the Ee and content. Sixteen of the 30 Ee atoms and 14—16 of the 32—34... 

In late 1992 the first crystal structures of the Fe and MoFe proteins of Mo nitrogenase frora Azotobacter vinelandii were published (1-3). 

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... 

Studies (113) on Fe protein with an Asp39Asn mutation in the nucleotide binding site indicate that the conformational change observed in the crystal structure of the complex is dependent on electron treuis-fer from the Fe protein to the MoFe protein. 

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. 

However, when the X-ray crystal structure of the MoFe protein was examined, it was clear that homocitrate could not directly hydrogen bond to the histidine, since the carboxylate group and imidazole are stacked parallel to each other in the crystal. Nevertheless, as noted in the previous section, studies on model complexes have suggested that homocitrate can become monodentate during nitrogenase turnover, with the molybdenum carboxylate bond breaking to open up a vacant site at molybdenum suitable for binding N2. 

The solutions of the structures of the Fe protein, the MoFe proteins, and the putative transition-state complex of these two proteins with ADP and A1F represent major advances in our understanding of ni-trogenase, but still many questions remain. 

For further details about the progress in the syntheses of the structural models of the clusters in MoFe protein, please see the other recent reviews,33 together with those dealing with the reactions of metal-sulfur clusters relating to the nitrogen-fixation chemistry.34... 

To successfully describe the structure and function of nitrogenase, it is important to understand the behavior of the metal-sulfur clusters that are a vital part of this complex enzyme. Metal-sulfur clusters are many, varied, and usually involved in redox processes carried out by the protein in which they constitute prosthetic centers. They may be characterized by the number of iron ions in the prosthetic center that is, rubredoxin (Rd) contains one Fe ion, ferredoxins (Fd) contain two or four Fe ions, and aconitase contains three Fe ions.7 In reference 18, Lippard and Berg present a more detailed description of iron-sulfur clusters only the [Fe4S4] cluster typical of that found in nitrogenase s Fe-protein is discussed in some detail here. The P-cluster and M center of MoFe-protein, which are more complex metal-sulfur complexes, are discussed in Sections 6.5.2. and 6.5.3. 

It is now believed that the MoFe-protein s P-cluster contains a [4Fe-3S] cuboid joined to a [4Fe-4S] cuboid, although, as discussed below, it was first reported crystallographically as two [4Fe-4S] clusters.8 Uncertainty existed for sometime as to exact nature of bridging disulfide or sulfide ligand joining the two Fe S clusters but it is now known that the P-cluster does NOT contain a disulfide bond. This is important because the all-ferrous structure [4Fe-4S]° proposed from Mossbauer studies then becomes more possible for the P-cluster s [4Fe-4S] cube. In 1993 Bolin et al.1 proposed a six-coordinate S for the P-cluster s center as in Figure la,b of Thorneley s article.8 This is now believed to be the correct conformation. A central six-coordinate S makes this cluster much harder to synthesize in the laboratory, and this feat has not been accomplished as of the date of this text s publication. Whatever its oxidation state or structure, the P-cluster mediates electron transfer from Fe-protein to the M center of MoFe-protein, and it must be reduced at some point to allow transfer of its electron(s). 

The P-cluster, located at the interface of MoFe-protein s a- and (3-subunits, is believed to function as the electron transfer mediator between Fe-protein and the N2 reduction site at the M center. The P-cluster is contained within a hydrophobic environment and located approximately 10 A below the MoFe-protein surface. Three cysteine side chains from each subunit bind to iron ions in the P-cluster. The cluster is now known to exist in Pox and PN forms in active enzyme, both with stoichiometry FegS7. The PN form, with its octahedrally coordinated central sulfur, has the structure shown in Figure 6.6. As can be seen in Table 6.3, the PN form contains all ferrous irons, corresponding to the P (5 = 0) state, whereas the Pox form corresponds to the P2+ (5=3 or 4) form. 

The 1.6-A resolution X-ray crystal structure of Klebsiella pneumoniae MoFe-protein, called Kpl, was solved in 1999 using the coordinates of the 2.2-A Avl... 

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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