Rubredoxin 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)...

XAS data comprises both absorption edge structure and extended x-ray absorption fine structure (EXAFS). The application of XAS to systems of chemical interest has been well reviewed (4 5). Briefly, the structure superimposed on the x-ray absorption edge results from the excitation of core-electrons into high-lying vacant orbitals (, ] ) and into continuum states (8 9). The shape and intensity of the edge structure can frequently be used to determine information about the symmetry of the absorbing site. For example, the ls+3d transition in first-row transition metals is dipole forbidden in a centrosymmetric environment. In a non-centrosymmetric environment the admixture of 3d and 4p orbitals can give intensity to this transition. This has been observed, for example, in a study of the iron-sulfur protein rubredoxin, where the iron is tetrahedrally coordinated to four sulfur atoms (6). 

Blue copper proteins, 36 323, 377-378, see also Azurin Plastocyanin active site protonations, 36 396-398 charge, 36 398-401 classification, 36 378-379 comparison with rubredoxin, 36 404 coordinated amino acid spacing, 36 399 cucumber basic protein, 36 390 electron transfer routes, 36 403-404 electron transport, 36 378 EXAFS studies, 36 390-391 functional role, 36 382-383 occurrence, 36 379-382 properties, 36 380 pseudoazurin, 36 389-390 reduction potentials, 36 393-396 self-exchange rate constants, 36 401-403 UV-VIS spectra, 36 391-393 Blue species... 

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). 

ACP = acyl carrier protein ACPA D = ACPA desat-urase AlkB = octane 1-monooxygenase AOX = alternative oxidase DMQ hydroxylase = 5-demethoxyquinone hydroxylase EXAFS = extended X-ray absorption fine structure spectroscopy FMN = flavin mononucleotide FprA = flavoprotein A (flavo-diiron enzyme homologue) Hr = hemerythrin MCD = magnetic circular dichroism MME hydroxylase = Mg-protophorphyrin IX monomethyl ester hydroxylase MMO = methane monooxygenase MMOH = hydroxylase component of MMO NADH = reduced nicotinamide adenine dinucleotide PAPs = purple acid phosphatases PCET = proton-coupled electron transfer, PTOX = plastid terminal oxidase R2 = ribonucleotide reductase R2 subunit Rbr = rubrerythrin RFQ = rapid freeze-quench RNR = ribonucleotide reductase ROO = rubredoxin oxygen oxidoreductase XylM = xylene monooxygenase. 

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... 

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