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Nitrogenase
PDB Entry: 1n2c
Structural Highlights
The structure of nitrogenase consists of metal clusters centered throughout the protein. Three of these clusters are the , , and (MoFe-cluster). At either end of the protein, there are also two copies of the Fe protein dimer, which is also the site of the ATP binding site (also known as the ) At these sites are ADP molecules which form a stable complex with the Fe protein. The MoFe protein, the central components of the protein, is where most of the nitrogenase’s function is carried out. This protein requires a constant state of electrons which is supplied by the Fe protein which uses the hydrolysis of ATP to pump these electrons into the MoFe protein. Thus, it is helpful for the Fe protein to be coupled with ADP/ATP at the ends of the protein. Important amino acids within these complexes include primarily cysteines (acting as nonpolar, more inner structural subunits) and histidines (acting as polar, outer structural subunits), as these make up the structural units of the clusters, but also the Homocitrate molecule within the M-cluster.
Function
Usable nitrogen is essential for all organisms, as it is widely used throughout their bodies. Nitrogen makes up parts of amino and nucleic acids, which therein synthesize DNA, RNA, and all proteins. All of these molecules are necessary for proper bodily function, yet usable nitrogen, in the form of Nitrates (NO3-) or Ammonia (NH3, is difficult to obtain. Most of the nitrogen surrounding organisms is in the form of atmospheric nitrogen (N2), which does not break down easily due to its triple bonded nature. Nitrogenase solves this problem by catalyzing the formation of NH3 from this unusable N2, as shown in the following process.
N2 + 8H+ + 16MgATP + 8e- → 2NH3 + H2 + 16MgADP + 16Pi
Nitrogenase’s many chains are split up into three functional clusters: Fe4S4, P, and M, as discussed before. The ADP complexes on the end shuttle electrons into the enzyme by accepting ATP and hydrolyzing it. the directly transports the electrons (one at a time) to the P-cluster. This has several oxidation states so it takes those electrons and moves them into the main part of the machine, the . The M-cluster uses these electrons to cleave N2 and add Hydrogen from the surrounding environment, synthesizing Ammonia. Homocitrate molecule also stabilizes M-cluster.
Relevance
Nitrogenase can be applied mainly in agriculture. Given that it creates Ammonia, once again, an essential form of Nitrogen for plants. Crop plants can be genetically modified to express nitrogenase, boosting their overall survivability and yield potential. Alternatively, as Nitrogenase releases a lot of H2, making it a somewhat viable source for hydrogen fuel cells and more renewable energy (given the abundance of atmospheric nitrogen).
Reference
Goodsell, David. “Nitrogenase.” PDB-101: Nitrogenase, Protein Data Bank, Feb. 2002, pdb101.rcsb.org/motm/26. Seefeldt, L. C., Hoffman, B. M., & Dean, D. R. (2009). Mechanism of Mo-Dependent Nitrogenase. Annual Review of Biochemistry, 78, 701. http://doi.org/10.1146/annurev.biochem.78.070907.103812
