Nitrogenase MoFe protein structure

Schmid B, Ribbe MW, Einsle O, et al. Structure of a Cofactor-Deficient Nitrogenase MoFe Protein. Science 2002 296 352-6. 

Bolin JT, Campobasso N, Muchmoee SW, Morgan TV and Moetenson LE (1993) The structure and environment of the metal clusters in the nitrogenase MoFe protein from Clostridium pasteurianum. In Stiefel El, Coucouvanis D and Newton WE, eds. Molybdenum enzymes, cofactors and model systems, pp. 186-195. American Chemical Society, Washington, D. C. 

Figure 12 35 GHz Fe and H CW ENDOR spectra of the hi-CO form of nitrogenase MoFe protein with varying types of Fe-enrichment. The H signals are included as intensity standards since the natural abundance samples contain observable amounts of Fe. The spectra were recorded at gobs = 2.06 (gi). Cartoons on the left indicate the specific sample, wherein the FeMo-cofactor is indicated by the diamond shape (in green), and the P-cluster is indicated by the two cubes (in red). These shapes roughly represent the clusters actual structures. Fe-enriched sites are indicated as colored blocks. The abbreviations used are as follows M(56)P(56) is natural abundance FeMo-cofactor and P-cluster M(56)P(57) is natural abundance FeMo-cofactor and enriched P-cluster M(57)P(56) is enriched FeMo-cofactor and natural abundance P-cluster M(57)P(57) is enriched FeMo-cofactor and P-cluster (i.e., globally enriched MoFe protein). (Adapted from Figure 1 in Christie, Lee, Cameron, Hales, Orme-Johnson and Hoffman. Reprinted with permission, 1996 American Chemical Society)...

A famous example is the structure of Nitrogenase MoFe-Protein, a protein that contains a Fe7MoS9 cluster. The inside of this cluster is about 4 A wide with six iron atoms closest to the centre, and older crystal stmctures had been determined at resolutions of about 2 A. Termination of the Fourier summation at that resolution creates an artefactual miiumum in the electron density of about —0.2 electrons about 2 A away from each iron atom. These spurious minima from all heavy atoms in the... 

Fig. 5. The structure of the P cluster prosthetic group of A vinelandii nitrogenase MoFe protein in its dye-oxidized (left) and normal dithionite-reduced (right) states. The coordinating amino acid residues (a-Cys-62, a-Cys-88, a-Cys-154, 8-Cys-70, )3-Cys-95, j8-Cys-153, and /S-Ser-188) are provided by both the a- and 8-subunits. The Fe atoms are the larger darker spheres and the S atoms are the medium-colored and medium-size spheres (38 PDB code 3MIN and 2MIN). See the text for how the two structures are proposed to interconvert during catalysis.

In late 1992 the first crystal structures of the Fe and MoFe proteins of Mo nitrogenase frora Azotobacter vinelandii were published (1-3). 

However, when the X-ray crystal structure of the MoFe protein was examined, it was clear that homocitrate could not directly hydrogen bond to the histidine, since the carboxylate group and imidazole are stacked parallel to each other in the crystal. Nevertheless, as noted in the previous section, studies on model complexes have suggested that homocitrate can become monodentate during nitrogenase turnover, with the molybdenum carboxylate bond breaking to open up a vacant site at molybdenum suitable for binding N2. 

To successfully describe the structure and function of nitrogenase, it is important to understand the behavior of the metal-sulfur clusters that are a vital part of this complex enzyme. Metal-sulfur clusters are many, varied, and usually involved in redox processes carried out by the protein in which they constitute prosthetic centers. They may be characterized by the number of iron ions in the prosthetic center that is, rubredoxin (Rd) contains one Fe ion, ferredoxins (Fd) contain two or four Fe ions, and aconitase contains three Fe ions.7 In reference 18, Lippard and Berg present a more detailed description of iron-sulfur clusters only the [Fe4S4] cluster typical of that found in nitrogenase s Fe-protein is discussed in some detail here. The P-cluster and M center of MoFe-protein, which are more complex metal-sulfur complexes, are discussed in Sections 6.5.2. and 6.5.3. 

Concurrently with the X-ray crystallographic studies, extended X-ray absorption fine structure (EXAFS) studies confirmed many of the bond distances proposed for nitrogenase s FeMoco cluster. The EXAFS data of reference 25 indicate short Fe-Fe distances of 2.61, 2.58, and 2.54 A for M+, M (resting state), and M forms, respectively. The authors believe that the short M center bond lengths indicate Fe-Fe bonds in this cluster. In another study using dithionite-reduced MoFe-protein Fe-S, Fe-Fe, Fe-Mo distances of 2.32, 2.64, and 2.73 A, respectively, were found in the 1 to 3 A region and Fe-Fe, Fe-S and Fe-Fe distances of 3.8, 4.3, and 4.7 A, respectively, were found in the 3 to 5 A region.30... 

Fe4(p3-S)3(p2-S)3, a 10-atom cluster present in the nitrogenase M center. Fragment condensation was used by the authors of reference 37 to synthesize [MoFe6S6(CO)i6 2 from the fragments Fe2S2(CO)612 and [Mo(CO)4I3] . None of the clusters mentioned so far mimic either the total structure or any function of those present in MoFe-protein. 

Mayer, S.M., Lawson, D.M., Gormal, C.A., Roe, S.M. and Smith B.E. (1999) New insights into structure-function relationships in nitrogenase A 1.6 A resolution X-ray crystallographic study of Klebsiella pneumoniae MoFe-protein, J. Mol Biol., 292, 871-891. 

The conversion of dinitrogen to ammonia is one of the important processes of chemistry. Whereas the technical ammonia synthesis requires high temperature and pressure (1), this reaction proceeds at room temperature and ambient pressure in nature, mediated by the enzyme nitrogenase (2). There is evidence that N2 is bound and reduced at the iron-molybdenum cofactor (FeMoco), a unique Fe/Mo/S cluster present in the MoFe protein of nitrogenase. Although detailed structural information on nitrogenase has been available for some time (3), the mechanism of N2 reduction by this enzyme is still unclear at the molecular level. Nevertheless, it is possible to bind and reduce dinitrogen at simple mono- and binuclear transition-metal systems which allow to obtain mechanistic information on elemental steps involved... 

Chiu, H-J, Peters, J. W., Lanzillota, W N., Ryle, M. J., Seefeldt, L. C., Howard, J.B., and Rees, D. C. (2001) MgATP-bound and nucleotide-free structure of a nitrogenase protein complex between the 127 D-Fe-protein and the MoFe-protein, Biochemistry 40, 641-650. 

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