P cluster

Fig. 6. View of the nitrogenase MoFe protein P-cluster pair where ( ) represents Fe, (O) S, and (Q) C as modeled (153). The side chain of one of the...

The VFe protein also has the equivalent of P-cluster pairs which have similar properties to those found in the MoFe protein (159). No information is available on whether P-cluster pairs exist in the FeFe protein, but because of the relatively high sequence identity and the similar genetic basis of its biosynthesis, the occurrence seems highly likely. The catalytic role assigned to the P-cluster pair involves accepting electrons from the Fe protein for storage and future deUvery to the substrate via the FeMo-cofactor centers. As of this writing (ca early 1995), this role has yet to be proved. 

The MoFe proteins are all a2 2 tetramers of 220-240 kDa, the a and (3 subunits being encoded by the nifD and K genes, respectively. The proteins can be described as dimers of a(3 dimers. They contain two unique metallosulfur clusters the MoFeTSg homocitrate, FeMo-cofactors (FeMoco), and the FesSy, P clusters. Neither of these two types of cluster has been observed elsewhere in biology, nor have they been synthesized chemically. Each molecule of fully active MoFe protein contains two of each type of cluster 2-7). 

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.

Homocitrate is bound to the molybdenum atom by its 2-carboxy and 2-hydroxy groups and projects down from the molybdenum atom of the cofactor toward the P clusters. This end of FeMoco is surrounded by several water molecules (5, 7), which has led to the suggestion that homocitrate might be involved in proton donation to the active site for substrate reduction. In contrast, the cysteine-ligated end of FeMoco is virtually anhydrous. 

The MoFe proteins exhibit complex redox properties. Each tetra-meric a2/32 molecule of MoFe protein contains two P clusters and two FeMoco centers and, as normally isolated in the presence of sodium dithionite, the FeMoco centers are EPR-active, exhibiting an S = spin state with g values near 4.3 and 3.7 and 2.01 (Fig. 6). The P clusters are EPR silent and there is a wealth of evidence (39) using a variety of techniques that indicates that the iron atoms in these clusters are all reduced to the Fe state. 

During oxidation of the MoFe protein the P clusters are the first to be oxidized at about -340 mV. This redox potential was first measured (40) using Mossbauer spectroscopy and exhibited a Nemst curve consistent with a two-electron oxidation process. It is possibly low enough for this redox process to be involved in enzyme turnover (see Section V). No additional EPR signal was observed from this oxidized form at this time. However, later a weak signal near g = 12 was detected and was finally confirmed, using parallel mode EPR... 

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).

Removing two electrons from each P cluster renders each MoFe protein molecule oxidized by four electrons. Further oxidation leads to removal of electrons from the FeMoco centers. The potential of this oxidation is both species and pH dependent. At pH 7.9 the for Kpl is 180 mV, whereas for Cpl it is 0 mV and for Avl -95 mV (46). 

Yet further oxidation removes at least one more electron from each P cluster with an +90 mV to yield a protein oxidized by a total of at least eight electrons and with EPR signals from mixed spin states of S = I and S = I (42, 47). The combined integrations of these signals demonstrated that their intensity was equivalent to that of the FeMoco EPR signals in the same preparations. This provided the first evidence (47) that MoFe proteins contained equivalent numbers of FeMoco centers and P clusters and that P clusters contained 8 Fe atoms. Previously it had been considered that the P clusters were fully reduced Fe4S4 clusters and thus that there were two P clusters for every FeMoco center per molecule. 

The biosynthesis of the MoFe protein is extremely complex. Here we will first describe the biosynthesis of FeMoco, then that of the apo-MoFe protein, encoded by the nifD and nifK genes and containing the P clusters, and finally we will summarize what is known about the combination of FeMoco with the apo-MoFe protein to form active MoFe protein. 

The term apo-MoFe protein will be used here to denote the MoFe protein lacking FeMoco, although this protein is not devoid of prosthetic groups since it has bound P clusters. 

NifH and NifDK to GroEL. It is not clear from these data at which stage in the biosynthetic pathway just described GroEL might be involved in MoFe protein maturation, but it could be during P cluster insertion. 

Mossbauer spectroscopy of AvF clearly demonstrated the presence of P clusters (174). The EPR spectra of dithionite-reduced VFe proteins are complex, indicating the presence of several paramagnetic species. Avl exhibits broad EPR signals, with g values of 5.8 and 5.4 integrating to 0.9 spins per V atom, which have been assigned to transitions from the ground and first excited state of a spin S = system (175). EPR data for AcF are more complex, with g values at 5.6, 4.3, and 3.77 that appear to arise from a mixture of S = species (176). The signals were associated with a midpoint potential of... 

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. 

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