Ferredoxins EXAFS

Figure 8.39 Fourier transformed Fe extended X-ray absorption fine structure (EXAFS) and retransformation, after applying a 0.9-3.5 A filter window, of (a) a rubredoxin, (b) a plant ferredoxin and (c) a bacterial ferredoxin, whose structures are also shown. (Reproduced, with permission, Ifom Teo, B. K. and Joy, D. C. (Eds), EXAFS Spectroscopy, p. 15, Plenum, New York, 1981)...

It seems likely that the active site for dinitrogen binding involves the molybdenum atom. It has been established by EXAFS that the coordination sphere consists of several sulfur atoms at distances of about 235 pm. An Mo=0 double bond, so common in complexes of Mo(IV) and Mo(Vl), is not present. There are other heavy atoms, perhaps iron, nearby (—270 pm). The ultimate source of reductive capacity is pyruvate, and the electrons are transferred via ferredoxin (see page 911) to nitro-... 

Azotobactor vinelandii ferredoxin I has two Fe/S clusters, [4Fe-4S] and a [3Fe-xS], with redox potentials at —0.42 and +0.32 V versus NHE, respectively (36). The existence of a normal Fe4S42+ core and a [3Fe-3S](S-cys)s(oxo) core has been considered. In the ferredoxin I the unique sequence Cys-Val-Glu-Val-Cys has been suggested as a tridentate ligand for the [3Fe-3S] cluster (37). Recently, the structure has been crystallographically (38) corrected, and the iron-sulfur centers are now believed to consist of Fe4S42+ and [3Fe-4S] clusters, as proposed by EXAFS (39). One possibility is that the above-mentioned [3Fe jcS] structure is formed during isolation by oxidative removal of an Fe ion from the [4Fe-4S] cluster (40). 

FDH = Formate dehydrogenase CAR = Carboxyhc acid reductase FMDH = Formylmethanofuran dehydrogenase MFR = Methanofuran AOR = Aldehyde ferredoxin oxi-doreductase MPT = Molybdopterin Fdox = Oxidized ferredoxin Fdred = Reduced ferredoxin FOR = Formaldehyde ferredoxin oxidoreductase EXAFS = X-ray absorption edge fine structure kDa = Kilodaltons EPR = Electron paramagnetic resonance. 

A situation similar to that outlined above for rubredoxin occurred for the 7Fe-7S ferredoxin of A. vinelandii. Thus spectroscopic studies, including iron K-edge EXAFS data for this and related systems (63, 64), caused crystallographers to reconsider and correct the structural details for the [3Fe-4Sl center (65). 

GTP = 5 -guanosine triphosphate AE = Activating enzyme BAN = Backbone amide nitrogen BioB = Biotin synthase CD = Circular dichroism cyt = Cytochrome DFT = Density functional theory DMSO = Dimethylsulfoxide Dx = Desulforedoxin ENDOR = Electron-nuclear double resonance EPR = Electron paramagnetic resonance ESEEM = Electron-spin echo envelop modulation ETF = Electron transferring flavoprotein EXAFS = Extended x-ray absorption fine structure FAD = Flavin adenine dinucleotide Fd = Ferredoxin FMN = Flavin mononucleotide FNR = Fumarate-nitrate reduction FTIR =... 

The smaller protein has a molecular mass of 60000-70000 daltons. Extended X-ray absorption fine structure (EXAFS) studies show that it includes a single Fe4S4 cubane cluster (P-cluster) similar to that in ferredoxins, which are important for various electron transport chains in living organisms. The smaller protein in the nitrogenase system is a strongly reductive reductase that is obviously responsible for the transfer of electrons to the larger protein. 

The anion of [NEt4]3[Fe3S4(SPh)4] consists of two tetrahedral FeS4 units linked by a central Fe atom also in tetrahedral sites the two outer Fe atoms are each coordinated by two thiolate groups (structure 47). The Fe -Fe separation is 2.714 A, i.e. similar to that deduced from EXAFS experiments for D. gigas ferredoxin II. Despite this, the structures of the three-iron cores in the natural and synthetic systems are considered to be quite different as judged by their different ESR spectra (g 2.01 in the oxidized form of the protein, g x 4.2 in [Fe3S4(SEt)4l ") and other properties. 

Fig. 4. Iron EXAFS Fourier isolates (solid line) and the fits to the data (dotted line), Fourier transforms, and the Fe-S structures found in (a) IFe Fe-S protein rubredoxin, (b) 2Fe-2S plant ferredoxin, and (c) 4Fe-4S bacterial ferredoxin. In (a) the EXAFS spectrum from the IFe protein rubredoxin shows a single damped sine wave indicating the presence of one major Fe-S distance. This is reflected in the Fourier transform which shows only one major peak. The peak at 1.5 A is due to residual background and/or Fourier truncation. In (b) and (c) and EXAFS spectra show a beat pattern indicating the presence of Fe-S and Fe-Fe distances. The Fourier transforms shows two peaks that are due to backscattering from S and Fe atoms, respectively. [Adapted from B.-K. Teo and R. G. Shulman, in Iron-Sulfur Proteins (T. G. Spiro, ed.), p. 343. Wiley, New York, 1982.]...

Fe-S distance of 2.05 A. The crystal structure has since been refined, and the results have been found to be consistent with the EXAFS results. In contrast to the EXAFS spectrum from rubredoxin, the EXAFS spectra of the 2Fe-2S soluble plant ferredoxin and the 4Fe-4S bacterial ferredoxin (see Fig. 4B,C) exhibit a beat pattern indicating the presence... 

The major difficulty with assigning a cluster identity for Fx is that the Fa and Fb clusters, which constitute 8 out of the 12 iron atoms in the Photosystem I core complex, contribute most of the backscattering to the EXAFS spectrum. This problem can be circumvented by using the newly isolated Photosystem I core protein incorporating the components P700, Aq, (Ai by inference) and Fx, but devoid of Fa and Fb. In this preparation, the X-ray K-edge spectrum was found to be similar to that of four-coordinate [4Fe-4S] clusters and unlike six-coordinate iron complexes that are present in heat-denatured Photosystem I or oxidatively denatured ferredoxin. This indicates that the 4 iron atoms in the Photosystem I core protein are most certainly in the form of an intact iron-sulfur complex. The k-space spectrum of Fx (Fig. 1) can be simulated by assuming... 

---