Rubredoxin

Rubredoxin Structure and Function

spinqualitylabelsall models Caption for this structure Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D This is a default text for your page Rubredoxin. Click above on edit this page to modify. Be careful with the < and > signs. You may include any references to papers as in: the use of JSmol in Proteopedia or to the article describing Jmol to the rescue. 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. The 2pac mutant of the unicellular green alga Chlamydomonas reinhardtii was isolated and found to have no photosystem II activity, however, other components of the photosynthetic electron transport chain, including photosystem I, were still functional. Photosystem II activity was fully restored by complementation with the RBD1 gene, which encodes rubredoxin. Phylogenetic evidence supports the hypothesis that this rubredoxin and its orthologs are unique to oxygenic phototrophs and distinct from rubredoxins in Archaea and bacteria (excluding cyanobacteria). Rubredoxin is stable in acid conditions at room temperature. It takes 10 hours of exposure to 1% sulfuric acid to produce denaturation characterized by complete loss of absorabncy at 490 nm. Nonheme iron proteins, probably containing inorganic sulfide, have been implicated as functional entities in electron transport in mitochondria from mammalian tissue. Rubredoxin is a distinct class of electron transfer proteins because of its striking feature of the lack of an inorganic sulfide. 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 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. A study was done to figure out how the protein environment influences the electron transfer properties of its redox site and what underlying structural features are responsible for the redox reaction. Based on the two 1.5 Å resolution structures, an electron would be transferred from an electron donor protein to an oxidized rubredoxin, which would result in a reduced rubredoxin. The reduced rubredoxin could be stabilized by the transient entry of water through the gate. Next, the stabilized reduced rubredoxin could diffuse to a partner electron-acceptor protein. If the acceptor protein-bound while the gate is closed and no water is present in a manner that makes it difficult for the gate to open, the reduced rubredoxin would be kept in the less stable state without the water. This would favor electron transfer to the acceptor protein, which could occur through the exposed Cys 42 Sγ. 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. Rubredoxin at 1.1 angstroms resolution has a structured weight of 6.11 kDa with an atom count of 543. It has one unique protein chain with a deposited residue count of 54. Rubredoxin shows absorption maxima at 490, 380, and 280 nm with molar extinction coefficients of 8.85 x 10^3, 10.8 x 10^3, and 21.3 x 10^3. The reduced form has maxima at 333, 311, and 275 nm with molar extinction coefficients of 6.3 x 10^3, 10.8 x 10^3, and 24.8 x 10^3 at these wavelengths. The Zn(Scys)4 unit is typically found in proteins and it assumes the structural, regulatory, or catalytic roles. The Zn(Scys)4 unit is found in rubredoxin around the iron as well. Rubredoxin has a nearly identical fold around the iron or zinc. This shows that the metal has a mainly structural role. At 1.6 angstroms, a neutron diffraction study has been carried out on a mutant rubredoxin from Pyrococcus furiosus. Three residues in this Pyrococcus furiosus mutation were changed (Trp3 → Tyr3, Ile23 → Val23, Leu32 → Ile32). There were also some changes that were found between the wild-type and mutant proteins in the Trp3/Tyr3 region. The N-H amide bonds of the protein backbone are important because they could contain information about the mechanism of unfolding of this small protein. The 1.6 A resolution of this neutron structure reveals some orders of the water structure such as the ordered and disordered O-D bonds. The total structure weight is 5.92 kDa with an atom count of 446. There is one unique protein chain and a deposited residue count of 51. Structural highlights This is a sample scene created with SAT to color by Group, and another to make a transparent representation of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

References

Almeida AV;Jacinto JP;Guerra JPL;Vieira BJC;Waerenborgh JC;Jones NC;Hoffmann SV;Pereira AS;Tavares P; (n.d.). Structural features and stability of apo- and holo-forms of a simple iron-sulfur protein. European biophysics journal : EBJ. Retrieved April 21, 2022, from https://pubmed.ncbi.nlm.nih.gov/34009405/

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