Rubredoxin: Difference between revisions

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 == 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. <ref>https://pubmed.ncbi.nlm.nih.gov/34009405/</ref> 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.
+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. <ref>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/</ref> 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.
 <scene name='90/909991/Rubredoxin_3/1'>Rubredoxin at 1.1</scene> 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.
 <scene name='90/909991/Rubredoxin_2/1'>At 1.6 angstroms</scene>, 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.