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enzyme nitrogenase is found in certain bacteria and blue-green algae, which
can reduce N2 to NH3 (nitrogen fixation). Some of these bacteria
are free-living while others are symbiotic (in the anaerobic environment
of roots of legume plants). This bacterial reaction is the key step in
the nitrogen cycle, which maintains a balance between two reservoirs of the
nitrogen compounds: the Earths atmosphere and the biosphere. The plants cannot
extract nitrogen directly from the atmosphere. N2 must be fixed
by these bacteria (as NH3) or converted by lightning to NOx and then
NO3- in the reaction with water. The fixed nitrogen is lost through leaching of
the soil, harvesting of crops and the action of the denitrifying bacteria.
The overall net reaction that occurs at this enzyme can be presented with the following equation:
Note that in addition to the dinitrogen reduction, the reduction of protons to dihydrogen also takes place so nitrogenase is also a hydrogenase.
In order to "pump" the eight electrons required for reduction of the substrate (dinitrogen), ATP is hydrolysed to ADP with the stoichiometry of two ATP for each electron (16 equivalents of ATP per 1 equivalent of N2).
Nitrogenase actually consists of two proteins that work in tandem: the iron (Fe) protein (currently shown in the left frame as wireframe model) and the molybdenum-iron (MoFe) protein.  During the catalytic reduction of dinitrogen, the electrons are transferred from the Fe-protein to the MoFe-protein.
The Iron Protein
The Fe-protein accepts the electrons from a flavedoxin or a ferredoxin and transfers them further to the MoFe-protein. This electron transfer is enabled by (probably) simultaneous hydrolysis of ATP to ADP. The protein has a molecular weight of 60 kDaltons and 578 amino acid residues.
This is followed by the dissociation of the protein, preventing the back-electron-transfer
reaction. This dissociation likely represents the rate-limiting step in the reduction of N2. MgATP hydrolysis occurs only when the dimer complex is formed.
Therefore, the non-productive electron loss is prevented and the mechanism only
allows the unidirectional flow of the electrons to the FeMo-protein.
2β2 tetramer. It consists of four subunits, two alpha
colored blue and two beta subunits colored red.
8S7 and the FeMo-cofactor cluster (sometimes referred to as an M-cluster or simply FeMoCo), Fe7MoS9N. While the FeMo-cofactor is located in the alpha subunit, the P-cluster sits at the interface between the alpha and beta subunits. Both are buried in the protein to prevent access of H2O, which would be converted to H2 by these very reducing metal centres.
If you would like to learn more about the nitrogenase and its model compounds see the following:
Much could be learned from the synthetic models for nitrogenase's cluster and cofactors (their function, mechanism of dinitrogen reduction, possible applications as industrial catalysts etc). However, the design and preparation of such compounds presents a major challenge for synthetic chemists. The most notable examples, described below, come from Holm's research group.
A Model For the P Cluster
Holm's model complex: The structure in the left frame presents a model cluster of the reduced form of the P cluster - [(Tp)2 Mo2Fe6S9(SH)2]3-  [Tp = hydrido(trispyrazolyl)borate]. The bridging pattern is Mo2Fe6( µ2-S)2( µ3-S)6( µ6-S). The structure can be described as one consisting of two MoFe3( µ3-S)3 cuboidal clusters linked by two µ2-S atoms from HS- ligands (simulating µ2-SCYS bridges) and one µ6-S atom (simulating S1 atom in the cluster). Each iron atom has distorted tetrahedral FeS4 geometry. The experimental results suggest the following oxidation states: Mo(III)2Fe(II)5Fe(III). The complex shows three oxidation steps in the cyclic voltamogram.
A Model For the MoFe Cofactor
3S4(SEt)3(Cl4cat)(CN)]3-, (Cl4cat = C6Cl4O2) . It has a mixed Mo-Fe cuboidal core which resembles one part of the MoFe cofactor. The molybdenum atom has an octahedral geometry with Cl4cat2- ligand replacing homocitrate. The interesting part of the structure is the presence of a cyano (CN-) ligand on molybdenum atom. Since dinitrogen molecule and CN- anion are isoelectronic, this complex suggests that N2 substrate might be coordinated to the Mo atom of the MoFe cofactor during the reduction.
A Theoretical Model
2-MoFe cofactor complex . In order to make the calculations easier, the system is usually simplified. So in the case of the MoFe cofactor, an imidazole ring and glycolate have been used to replace the histidine and homocitrate ligands and an SH group instead of the cysteine terminal ligand. Of the three N2 binding modes (end-on bonding to the iron atom, bridging between two Fe atoms or end-on bonding to the Mo atom), the one with dinitrogen end-on bonded to an Fe atom (left) was shown to be the most probable structure. The calculations also indicate that the central N atom adds to the cluster flexibility by offering a variable number of bonds to the Fe atoms (these calculations were done before it was established that the central atom is actually a carbon). These calculations have also provided a plausible reaction mechanism.
 Picture taken from Whitten, Davis & Larry Peck "General Chemistry", 6th edition, Saunders College Publishing (2000), pg. 959.
 Nitrogenases in which molybdenum is replaced with vanadium are also known (VFe protein).
 Zhang, Y. and Holm, R.H. (2003) J. Am. Chem. Soc. 125(13) 3910. See also Zhang, Y. et al. (2002) J. Am. Chem. Soc. 124(48) 14292.
 Palermo, R.E. et al. (1984) J. Am. Chem. Soc. 106(9) 2600. See also Huang, J.S. et al. (1997) J. Am. Chem. Soc. 119(37) 8662.Note that the compounds in these articles have been prepared before the existence of the central N atom in the MoFe cofactor was established.
 Schimpl, J. et al. (2003) J. Am. Chem. Soc. 125(51) 15772.