P clusters, structure

Fe4 and Fe5 (both Fe2+ in Pox). P-cluster structural models are reprinted from reference 24 in Figure 6.7 (see also Figure 6.6). 

An abundance of synthetic targets in iron-sulfur cluster remains, especially in unexplored areas such as pentanuclear clusters. Whether known clusters represent all energetically feasible topologies under ordinary conditions for nuclearities m = 4, 6, and 8, remains an open issue. Given that the nitrogenase P-cluster structure (5) (Figure 1) was not correctly predicted and is unprecedented, it is reasonable to assume that not all iron-sulfur cluster products of biosynthesis have been discovered. 

Parks E K, Welller B H, Bechthold P S, Hoffman W F, NIeman G C, Pobo L G and Riley S J 1988 Chemical probes of metal cluster structure reactions of Iron clusters with hydrogen, ammonia and water J. Chem. Rhys. 88 1622... 

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.

Fig. 5. Structure of the P clusters, (a) Reduced FesSy as proposed by Bolin et al. (5) and confirmed by Peters et al. (6) and Mayer et al. (7). (b) Oxidized FesSy as described by Peters et al. (6) and Mayer et al. (7).

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. 

Downs GM, Willett P. Clustering of chemical structure databases for compound selection. In van de Waterbeemd H, editor, Advanced computer-assisted techniques in drug discovery. Weinheim VCH Verlag, 1994. p. 111-30. 

Soler, J.M., Beltran, M.R., Michaelian, K., Garzon, I.L.. Ordejon, P., Sanchez-Portal, D. and Artacho, E. (2000) Metallic bonding and cluster structure. Physical Review B - Condensed Matter, 61, 5771-5780. 

Martin, J. M. L., El-Yazal, J., Francis, J.-P, 1995b, Structure and Vibrational Spectra of Carbon Clusters Cn (n = 2-10, 12, 14, 16, 18) Using Density Functional Theory Including Exact Exchange Contributions , Chem. Phys. Lett., 242, 570. 

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.

Figure 8 Structures of P-cluster. (a) Reduced form (PN-cluster) and (b) Oxidized form ( Pox-cluster )...

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. 

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