Rubredoxin Fe

Figure 20-5 (A) Stereo view of the D. gigas rubredoxin Fe(SCys)4 center viewed along the pseudo two-fold axis, with NH-S hydrogen bonds marked. The orientation is approximately the same as that of (B) for the Dx center. (B) Stereo view of the Fe SCys)4 center from desulforedoxin with NH-S hydrogen bonds marked. Water molecules, W27 and W28 are conserved in all metal-replaced Dx structures and are therefore considered structurally part of the desulforedoxin molecule. The water molecule W3010 is only observed for the Cd- and Hg-substituted Dx structures and makes a hydrogen bond to the Sy of Cys 29, the most exposed cysteine ligand. Figures prepared with TURBO-FRODO [84].

Figure 9 Structures of the (a) rubredoxin Fe(Cys)4 site (PDB IBRF) (b) Zri2Cd(Cys)9 metallothionein site (PDB 4MT2) (c) Zn(His)2(Cys)2 zinc finger site (PDB lAlH).

Lu TT, Chiou SJ et al (2006) Mononitrosyl tris(thiolate) iron complex [Fe(NO) (SPh)3] and dinitrosyl irrai ctnnplex [(EtS)2Fe(NO)2] formation pathway of dinitrosyl iron complexes (DNICs) frmn nibosylatirai of biomimetic rubredoxin [Fe(SR)4] (R = Ph, Et). Inorg Chem 45 8799-8806... 

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)...

The simplest NHIP is rubredoxin, in which the single iron atom is coordinated (Fig. 25.9a) to 4 S atoms belonging to cysteine residues in the protein chain. It differs from the other Fe-S proteins in having no labile sulfur (i.e. inorganic sulfur which can be liberated as H2S by treatment with mineral acid sulfur atoms of this type are not part of the protein, but form bridges between Fe atoms.)... 

Figure 25.9 Some non-haem iron proteins (a) rubredoxin in which the single Fe is coordinated, almost tetra-hedrally, to 4 cysteine-sulfurs, (b) plant ferredoxin, [Fe2S2(S-Cys)4], (c) [Fe4S4(S-Cys)4] cube of bacterial ferredoxins. (This is in fact distorted, the Fe4 and S4 making up the two interpenetrating tetrahedra, of which the latter is larger than the former).

Different metals are readily incorporated into rubredoxin-type centers after reconstitution of apoprotein with appropriate metal salts (5). Rd and Dx derivatives containing Ni and Co have been analyzed by UV-vis, NMR, EPR, electrochemistry, and MCD (13, 19-22). Fe replacement has been used for Mossbauer studies and an indium de-... 

In 1996, the 3D-structure of D. vulgaris Rr was published by de-Mare and collaborators 48), and all the studies earlier published were proved to be correct. The protein is described as a tetramer of two-domain subunits (Fig. 4). Each subunit contains a domain characterized by a four-helix bundle surrounding a diiron-oxo site and a C-terminal rubredoxin-like Fe(RS)4 domain (see Fig. 2). In this last do-... 

The Fe hyperfine tensor components were determined by Mossbauer spectroscopy in the case of the rubredoxin from Clostridium... 

In recent years, several model complexes have been synthesized and studied to understand the properties of these complexes, for example, the influence of S- or N-ligands or NO-releasing abilities [119]. It is not always easy to determine the electronic character of the NO-ligands in nitrosyliron complexes thus, forms of NO [120], neutral NO, or NO [121] have been postulated depending on each complex. Similarly, it is difficult to determine the oxidation state of Fe therefore, these complexes are categorized in the Enemark-Feltham notation [122], where the number of rf-electrons of Fe is indicated. In studies on the nitrosylation pathway of thiolate complexes, Liaw et al. could show that the nitrosylation of complexes [Fe(SR)4] (R = Ph, Et) led to the formation of air- and light-sensitive mono-nitrosyl complexes [Fe(NO)(SR)3] in which tetrathiolate iron(+3) complexes were reduced to Fe(+2) under formation of (SR)2. Further nitrosylation by NO yields the dinitrosyl complexes [(SR)2Fe(NO)2], while nitrosylation by NO forms the neutral complex [Fe(NO)2(SR)2] and subsequently Roussin s red ester [Fe2(p-SR)2(NO)4] under reductive elimination forming (SR)2. Thus, nitrosylation of biomimetic oxidized- and reduced-form rubredoxin was mimicked [121]. Lip-pard et al. showed that dinuclear Fe-clusters are susceptible to disassembly in the presence of NO [123]. 

Iron-sulfur (Fe-S) proteins function as electron-transfer proteins in many living cells. They are involved in photosynthesis, cell respiration, as well as in nitrogen fixation. Most Fe-S proteins have single-iron (rubredoxins), or two-, three-, or four-iron (ferredoxins), or even seven/eight-iron (nitrogenases) centers. 

For example, Fig. 9.40 shows the NIS spectra of the oxidized and reduced FeS4 centers of a rubredoxin mutant from Pyrococcus abyssi obtained at 25 K together with DFT simulations using different models for the Fe-S center [103]. The spectrum from the oxidized protein Fe S4 (S = 5/2) reveals broad bands around 15-25 meV (121-202 cm ) and 42-48 meV (339-387 cm ) consistent with the results on rubredoxin from Pyrococcus furiosus [104]. 

These results confirm Resonance Raman studies of oxidized rubredoxin from Desulfovibrio gigas, which indicates that there are three bands (43.15, 45.01, and 46.62 meV 348, 363, and 376 cm ) in the region where asymmetric Fe° -S stretch modes are expected [108]. Resonance Raman data of the reduced rubredoxin... 

Fig. 9.40 NIS spectra of oxidized (filled circle) and reduced rubredoxin mutant Rm 2-4 (filled triangle) from Pyrococcus abyssi obtained at 25 K. The protein samples have been prepared with Fe concentrations of about 10 mM. Theoretically calculated NIS spectra based on DFT calculations (B3LYP/CEP-3IG) of 9, 21 and 49 atoms are shown below. The dotted lines represent calculated NIS spectra for the oxidized Fe S4 center and the dashed lines for the reduced Fe°S4 center. (Taken from [103])...

As illustrated in Fig. 9.40, progressively more complex models for the environment of Fe in oxidized or reduced rubredoxin produce better simulations of the NIS pattern. A simple Fe(SCH3)4 model (21 atoms) predicts a division of the spectrum into Fe-S stretch and S-Fe-S/Fe-S-C bend regions, but at least a model with 49 atoms is needed to reproduce the splitting of the stretch region and to capture some of the features between 10 and 30 meV. These results confirm the delocalization of the dynamic properties of the redox-active Fe site far beyond the immediate Fe-S4 coordination sphere. 

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. 

Fe-S proteins contain four basic core structures, which have been characterized crystal-lographically both in model compounds (Rao and Holm, 2004) and in iron-sulfur proteins. These are (Figure 3.6), respectively, (A) rubredoxins found only in bacteria, in which the [Fe-S] cluster consists of a single Fe atom liganded to four Cys residues—the iron atom... 

The simplest of these proteins are rubredoxins, which are bacterial proteins having a characteristic red colour (from which their name is derived) containing an FeS4 assembly, consisting of an Fe(III) ion coordinated to four cysteine groups. The typical tetrahedral structure of this group is illustrated in Figure 17 for the rubredoxin isolated from Clostridium pasteurianum (FW 6100).35... 

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