Rubredoxins, characterization

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-... 

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),... 

Although heme is absent in Clostridia, it was early recognized that anaerobic bacteria may contain substantial levels of iron (44). To date the best characterized iron compounds from this source are the iron-sulfur proteins termed ferredoxins and rubredoxins. Molecular structures of representatives of both types of protein have been worked out by Jensen and his colleagues by X-ray diffraction analysis (see below). 

Rubredoxins do not have acid-labile sulfur as do ferredoxins, with the iron characterized by a mercaptide coordination. They are small proteins composed of some 50 amino acids. Both oxidized and reduced forms are high spin. 

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... 

Chen L, Liu M-Y, LeGall J, et al. 1993b. Purification and characterization of an NADH-rubredoxin oxidoreductase involved in the utilization of oxygen by Desulfovibrio gigas. J Biochem 216 443-8. 

Moura I, Tavares P, Moura JJ, et al. 1990. Purification and characterization of desul-foferrodoxin. A novel protein from Desulfovibrio desulfuricans (ATCC 27774) and from Desulfovibrio vulgaris (strain Hildenborough) that contains a distorted rubredoxin center and a mononuclear ferrous center. J Biol Chem 265 21596-602. 

Proteins with dinuclear iron centres comprise some well studied representatives like ribonucleotide reductase (RNR), purple acid phosphatase (PAP), methane monooxygenase hydroxylase (MMOH), ruberythrin and hemerythrin. The latter is an oxygen carrier in some sea worms it has been first characterized within this group and has thus laid the foundation to this class of iron coordination motif. Ruberythrin is found in anaerobic sulfate-reducing bacteria. Its name implies that, in addition to a hemerythrin-related diiron site another iron is coordinated in a mononuclear fashion relating to rubredoxin which is an iron-... 

Iron Sulfur Compounds. Many molecular compounds (18—20) are known in which iron is tetrahedrally coordinated by a combination of thiolate and sulfide donors. Of the 10 or more structurally characterized classes of Fe—S compounds, the four shown in Figure 1 are known to occur in proteins. The mononuclear iron site REPLACE occurs in the one-iron bacterial electron-transfer protein rubredoxin. The [2Fe—2S] (10) and [4Fe—4S] (12) cubane structures are found in the 2-, 4-, and 8-iron ferredoxins, which are also electron-transfer proteins. The [3Fe—4S] voided cubane structure (11) has been found in some ferredoxins and in the inactive form of aconitase, the enzyme which catalyzes the stereospecific hydration—rehydration of citrate to isocitrate in the Krebs cycle. In addition, enzymes are known that contain either other types of iron sulfur clusters or iron sulfur clusters that include other metals. Examples include nitrogenase, which reduces N2 to NH3 at a MoFe S8 homocitrate cluster carbon monoxide dehydrogenase, which assembles acetyl-coenzyme A (acetyl-CoA) at a FeNiS site and hydrogenases, which catalyze the reversible reduction of protons to hydrogen gas. 

Tetrahedral iron sulfide species that can have two or more charge states are involved in many electron transfer proteins.737 The core structures that have been identified in proteins include the single iron centres of rubredoxin, and the two iron/two sulfide and four iron/ four sulfide centres of various ferredoxins. A wide range of model complexes have been prepared and characterized, and the results of this work, as well as that on the natural system, have been extensively reviewed.737-744... 

From the EPR spectrum, the iron cysteine content, and some preliminary characterization of tryptic and chymotryptic peptides of the M. aerogenes rubredoxin, Bachmayer et al. (218) proposed a simple model in which the iron atom plays a fundamental structural role by holding the molecule together (Fig. 12). The four cysteine residues are grouped in... 

The enzymatic system involved in hydroxylation reactions of long-chain alkanes had been previously studied by Coon and coworkers, who isolated an enzyme system from P. oleovorans that catalyzes co-hydroxylation of alkenes and fatty acids120, 106-nsl. This was resolved into three protein components rubredoxin (an iron-sulfur protein of molecular weight 19 000), an NADH-rubredoxin reductase (a flavoprotein of molecular weight 55 000) and an co-hydroxylase (characterized as being a non-heme iron protein, with one iron atom and one cysteine per polypeptide... 

Rubrerythrin has been isolated from D. desulfuricans ATCC 27774 and from D. vulgaris Hildenborough as a homodimer of 44kDa [65, 66]. The trivial name rubrerythrin results from the contraction of rubredoxin and hemerythrin. Rubrerythrin has a very unusual combination of prosthetic groups. Nigerythrin (niger = black), another protein found in D. vulgaris, exhibits some similarities with rubrey-thrin [65] but the former protein has not yet been structurally characterized. 

Iron-sulfur proteins occur in animal, plant, and bacterial cells. The proteins are characterized by the presence of 1-0, 2-2, 4rA, 6-6, or 8-8 atoms of iroursulfide. Only the structure of clostridial rubredoxin, a 1-0 protein, is knoum. It contains iron ligated to four sulfur atoms of cysteine residues of the polypeptide. With the exception of the ""high potential iron protein, all the proteins show unexpectedly low redox potentials and function in biological oxidationr-reduc-tion reactions. 

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