Rubredoxin

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)...

One example of a sequence determinant of redox potentials that has been identified in this manner is an Ala-to-Val mutation at residue 44, which causes a 50 mV decrease in redox potential (and vice versa) in the rubredoxins [68]. The mutation was identified because the sum of the backbone contributions to ( ) of residues 43 and 44 change by 40 mV due to an —0.5 A backbone shift away from the redox site. This example points out the importance of examining the backbone contributions. The corresponding site-specific mutants have confirmed both the redox potential shift [75] and the structural shift [75]. 

Eree energy curves for the self-exchange reaction between two rubredoxins (Rdi and Rd2) were generated from MD simulations [86,87]. 

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).

Fig. 5. Structure-based alignment of the sequences of the water-soluble Rieske fragment from bovine heart bci complex (ISF), the water-soluble Rieske fragment from spinach b f complex (RFS), and of the Rieske domain of naphthalene dioxygenase (NDO) and of the metal binding loops of rubredoxin (RXN) and transcriptional factor TFIIS (TFI). The numbering of the j3 strands is the same for the ISF and RFS. The metal binding ligands are highlighted the asterisks indicate those residues that are fully conserved between the three Rieske proteins.

The general topology of rubredoxins is also observed in the general zinc-ribbon motif in RNA polymerases or in transcription factors (59). The first published zinc-ribbon structure was that of the nucleic-acid binding domain of human transcriptional elongation factor TFIIS (PDB file ITFI) 40). These zinc binding domains and rubredoxins... 

In this review we will deal with iron-sulfur proteins where the iron atoms are coordinated only by cysteine ligands and bridging sulfurs, as well as rubredoxin (Rd hereafter), which is the initial building block in all subsequent discussions. 

Fig. 1. Iron-sulfur clusters basic building blocks. In most cases the iron is tetrahe-drally coordinated by sulfur from cysteinyl residues (and labile sulfur). Variability on coordination is allowed (see text). A, Rubredoxin type FeS4 (simplest cluster, no labile sulfur) B, plant-type ferredoxin [2Fe-2S] C, bacterial ferredoxin [3Fe-4S] D, bacterial ferredoxin and HiPIP [4Fe-4S] E, novel cluster [4Fe-2S, 20] ( hybrid cluster ).

While crystal structures of rubredoxins have been known since 1970 (for a full review on rubredoxins in the crystalline state, see Ref. (15)), only recently have both crystal and solution structures of Dx been reported (16, 17) (Fig. 3). The protein can be described as a 2-fold symmetric dimer, firmly hydrogen-bonded and folded as an incomplete /3-barrel with the two iron centers placed on opposite poles of the molecule, 16 A apart. Superimposition of Dx and Rd structures reveal that while some structural features are shared between these two proteins, significant differences in the metal environment and water structure exist. They can account for the spectroscopic differences described earlier. 

Mutants of Dx were constructed, introducing Gly and Pro-Val sequences between Cys 28 and Cys 29 residues, altering the spacing between the adjacent coordinating cysteines. The properties of the mutated proteins are altered and the center became more close to that in rubredoxin (18). 

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... 

No EPR spectra have yet been reported to our knowledge in the case of a protein containing a well-characterized reduced FeS4 center, although a spectrum has been observed in the case of a model complex (24 ). The lack of EPR signals in the case of proteins is apparently directly related to the D and E values, which are equal to D = +7.5 cm E D = 0.28 in the case of C. pasteurianum rubredoxin (15), and D = 6 cm E D = 0.19 in that of D. gigas desulforedoxin (18),... 

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