Rubredoxin

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Background

Rubredoxin is a nonheme iron protein, which was discovered in the anaerobe Clostridium pasteurianum and isolated from ferredoxin. These proteins are found in membrane-bound enzymes in conjunction with b-type cytochromes in mitochondria and chloroplasts, as well as in soluble bacterial dioxygenases. Membrane-bound rubredoxins are found exclusively in photosystem II containing organisms and are actually different from the soluble rubredoxins that are typically found in bacteria or archaea. Evidence has shown that thylakoid-associated rubredoxin that is encoded by the RBD1 gene is required for photosystem II in Chlamydomonas.

Function

It does not have a certain known function yet, however, this protein acts as electron carriers in biochemical processes, carbon fixation, fatty acid beta-oxidation using acyl-CoA dehydrogenase, and lipid homeostasis. The central iron atom changes between the +2 and +3 oxidation states and in both oxidation states, the metal remains in high spin, which helps minimize structural changes. The reduction potential of a rubredoxin is normally in the range +50 mV to -50 mV. This means it is likely that rubredoxin is involved in the function of the chloroplast. Rubredoxin also plays an important role in the reduction of superoxide in anaerobic bacteria. A critical role for this protein is in plant response. It is involved in plant tolerance and resistance to abiotic stresses specifically for Pyrococcus furiosus and Desulfovibrio vulgaris. The expression patterns of rubredoxins in glycophyte and halophytic plants under salt stress revealed that rubredoxin is one of the important stress response proteins. Further research could identify other rubredoxin proteins to improve the plant tolerance and resistance to these abiotic stresses. Rubredoxin does this by acting as an electron transfer donor to superoxide reductase reaction systems. A rubredoxin-like protein called Arabidopsis thaliana was encoded by ENH1. This was localized to the chloroplast and it increased the sensitivity to oxidative stress. Puccinellia tenuiflora, another rubredoxin-like protein, could increase the salt tolerance by reducing the accumulation of ROS. Another function of rubredoxin that has been previously found is it aids in oxygen tolerance. It does this by reacting with reactive oxygen species directly or by helping maintain the appropriate redox state of iron containing active sites found in enzymes. Some rubredoxins, specifically from the aerobe Pseudomonas oleovorans, participate in fatty acid ω-hydroxylation. For example, hydroxylation at the end of the hydrocarbon chain farthest from the carboxylic acid. Like the Fe2S2 proteins putidaredoxin and adrenodoxin, the rubredoxin provides electrons to the hydroxylase, which acts as a monooxygenase forming the w-alcohol product and water. In a reaction catalyzed by rubredoxin reductase, rubredoxin is reduced by NADH to the ferrous state and reoxidized by the w-hydroxylase to the ferric form during the catalytic cycle.

Mechanism

The protein mechanism of rubredoxin is carried out by a reversible Fe3+/Fe2+ redox coupling by the reduction of Fe3+ to Fe2+ and a gating mechanism caused by the conformational changes of Leucine 41. Leucine 41 is a nonpolar side chain that allows transient penetration of water molecules. This increases the polarity of the redox site environment and also provides protons. During this, the four iron-sulfur bond lengths increase while amide NH hydrogen bonding to the S(Cys) shortens in length. The presence of hydrogen bonds between neighboring amino acid backbones and sulfur atoms of the FeS4 unit has given a possible explanation for the low rupture force of the iron-sulfur bonds in rubredoxin by decreasing the covalent character of the iron-sulfur bonds.

Structure

This protein contains about 50-60 amino acids on a single polypeptide chain and is a simple form of iron-sulfide. It also has a low isoelectric point of 2.93. Most rubredoxins have a single iron atom that can exist in the ferrous or ferric state and it is bonded to four sulfur atoms in a tetrahedral shape. It has four cysteine residues which are responsible for the metal-binding in a tetrahedral coordination sphere. The sequence Cys-x-y-Cys is a common one for iron-sulfur proteins because it allows both cysteine residues to bind to the same metal site. Rubredoxin proteins have malleable metal sites associated with flexible polypeptide chains. Numerous novel folds are revealed in the iron-sulfur protein by the rapid growth of structural databases. It was predictable that polypeptide chains can fold in many different ways to position Cys residues appropriately for the binding of [2Fe–2S] or [4Fe–4S] active sites. For the accommodation of [4Fe–4S] clusters alone, over 30 distinct protein folds have now been structurally characterized. A specific pattern including the sequence C–x3–C–x2–C– binds a [4Fe–4S] cluster with three Cys residues and one open iron site. Rubredoxin can sometimes replace ferredoxin as an electron carrier, however, ferredoxin and rubredoxin are different spectrally and chemically. Rubredoxin lacks the amino acids alanine and serine when it is the most prevalent for ferredoxin in Clostridium pasteurianum. Ferredoxin lacks methionine and tryptophan while it is present in rubredoxin. Rubredoxin has been found to be mainly expressed in leaves and weakly expressed in tissues. All clostridial ferredoxins examined to date contain either zero or one basic residue. Rubredoxin, however, contains four residues of Lysine. Rubredoxin has fluorescence properties of a typical tryptophan-containing protein.

Structural highlights

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