nifD

nifD is the gene encoding the alpha subunit of the molybdenum-iron nitrogenase dinitrogenase, a key component of biological nitrogen fixation. In nitrogen-fixing organisms, the Mo-dependent nitrogenase consists of two components: the electron-donating Fe protein (NifH) and the dinitrogenase MoFe protein, which is a heterotetramer composed of two NifD (alpha) and two NifK (beta) subunits. The catalytic site for nitrogen reduction, FeMo-co, is located at the interface of NifD and NifK and is accompanied by the P-cluster, both essential for electron transfer and substrate reduction.

NifD proteins are typically around 60 kilodaltons in size, corresponding to roughly 450–550 amino acids depending on the organism. The MoFe protein contains two catalytic centers that coordinate the FeMo-cofactor and facilitate the reduction of N2 to NH3. Key conserved residues, including cysteines and histidines, participate in cofactor binding and electron transfer, though exact residues vary among species. The enzyme requires electrons from NifH and energy from ATP hydrolysis to drive the multi-electron reduction of N2, releasing byproducts such as H2 in the process.

Genetically, nifD is usually located within nif gene clusters alongside nifH and nifK (the nifHDK operon) and is regulated by nitrogen availability and oxygen sensitivity. Regulation commonly involves the transcriptional activator NifA and other regulatory networks that respond to nitrogen limitation and cellular redox state. NifD homologs exist in alternative nitrogenases (such as those using vanadium or iron-only cofactors), though nifD itself denotes the Mo-containing dinitrogenase alpha subunit.

Distribution and significance: nifD is widespread among diazotrophic bacteria and archaea and is central to biological nitrogen fixation. It has been the subject of extensive structural and functional studies and remains a focus for efforts to engineer nitrogen fixation in non-diazotrophs.