The enzyme complex that catalyses the reduction of atmospheric N2 to ammonium (nitrogen fixation) is called nitrogenase and is encoded by the nif operon. Nitrogenase is composed of two proteins called component I, the MoFe-protein and component II, the Fe-protein. The Mo-Fe protein (~200 kDa) is composed of two sets of heterodimers. The heterodimers are composed of - and -subunits encoded by the nifD and the nifK genes. This multisubunit structure organises into FeS clusters (P clusters) and contains the MoFe cofactor which is probably the substrate binding site for nitrogen reduction. Several alternative nitrogenases have been found in diazotrophs. These often have a second and/or a third copy of the nif operon that encodes for component I proteins containing V or Fe as a cofactor instead of Mo.
The Fe-protein (~60 kDa) is encoded by the nifH gene and is composed of a pair of identical subunits. The Fe protein has high conservation among species which makes it an attractive target for molecular studies in the environment. The Fe-protein reduces the MoFe-protein through a series of single electron transfers that each require docking and undocking of the two proteins and hydrolysis of ATP.