Nitrogenase Reductase
Created by Waroot Nimjareansuk
Nitrogenase reductase is an enzyme that catalyzes the reduction of dinitrogen to ammonia in the bacterial species Azotobacter vinelandii. This reduction pathway is a main constituent of nitrogen fixation, providing the building blocks for biological molecules, such as amino acids, proteins, and nucleic acids. Biologically, nitrogenase exists as two identical MoFe-proteins linked to two Fe-proteins each one on opposite sides of the protein. The secondary structure of nitrogenase is dominated by alpha helices and beta sheets, although there are many random coils present. The Fe-protein is a homodimer of two identical subunits consisting of a 4Fe-4S cluster at the dimer interface (1). Each monomer of the Fe-protein is characterized by an alpha/beta type polypeptide fold, consisting of an eight-stranded beta sheet flanked by alpha helices (2). The core of each monomer contains seven parallel beta strands. The Adenosine-5'-Diphosphate Tetrafluoroaluminate complex (in yellow), an analogue of Adenosine-5'-Triphosphate, binds within the nucleotide-free Fe-protein conformation(pdb id=2afh), which induces a conformational change, binding the Fe-protein to the MoFe-protein (pdb id=1n2c) (8). Nucleotide binding causes the sidechains of residues Asp-129,Val-130,Val-131,and Cys-132 of both Fe-protein monomers rearrange connecting the nucleotide binding region to the P-cluster of the FeMo-protein by moving the 4Fe-4S cluster closer to the P-cluster. There are many residues present at this binding pocket, specifically the glycine-rich phosphate binding loop surrounded by an alpha helix and a beta sheet (3), and the coordination of Ser-16 and Asp-39 with the magnesium ion. The hydrolysis of the Adenosine-5'-Diphosphate Tetrafluoroaluminate complex is coupled to electron transfer in which the electrons flow from the 4Fe-4S cluster at the dimer interface to the P-cluster (1). The electron transfer from the P-cluster to FeMo-cofactor is facilitated by His-195 donating a hydrogen bond to one of the FeMo-cofactor sulfurs (3).The MoFe-protein is a heterotetramer consisting of two copies of each the FeMo-cofactor and the P-cluster. The secondary structure of the MoFe-protein consists of three domains of the type alpha/beta with random coils in each subunit (3). The FeMo-cofactor and the P-cluster are both coordinated by a four-stranded, parallel beta sheet surrounded on either side by alpha helices (3). The FeMo-cofactor is the active site of enzyme catalysis and lies within the alpha monomer of the FeMo-protein. However, the mechanism of the enzymatic reduction of dinitrogen has not been solved at the active site and is still under debate among biochemistry researchers. The FeMo-cofactor is coordinated by the covalent bonds of Cys-275 and an Fe on one end, and His-442 and Mo on the opposing end (4). A histidine triad of His-442,His-274,and His-451 coordinate the FeMo-cofactor into the MoFe-protein binding site (5). The negatively charged homocitrate is attracted to the positively charged histidine residues, thus stabilizing the transition of the cofactor into the binding site (5). The MoFe-proteins of Nitrogenase reductase (in white) from Azotobacter Vinelandii and the light-independent Protochlorophyllide reductase (in purple) from Rhodobacter capsulatus(pdb id=3aes) are shown to be structurally conserved by the Dali Structural Alignment test (6). The structural arrangement of the NB-cluster and Pchlide in Protochlorophyllide compared to the P-cluster and FeMo-cofactor, respectively, are nearly identical in spatial arrangement (7).The Fe-protein of Nitrogenase reductase from Azotobacter Vinelandii and the light-independent Protochlorophyllide reductase from Rhodobacter sphaeroides (pdb id=3fwy) are also structurally conserved (10).The NB-cluster and the L-protein of protochlorophyllide were structurally characterized separately. Protochlorophyllide has an analogous reduction pathway in which electron transfer is coupled to ATP hydrolysis in order to the C17=C18 bond of protochlorophyllide to chlorophyllide A, the precursor of chlorophyll A (7). The conserved and comparable tertiary structures allow both nitrogenase and protochlorophyllide to perform mettaloenzyme reduction of multibond molecules.