A short protein description with the molecular wheight, isoforms, etc...
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CHEMICAL STRUCTURE AND IMAGES
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- Primary structure
- Secondary structure
- Tertiary structure
- Quaternary structure
Protein Aminoacids Percentage
The Protein Aminoacids Percentage gives useful information on the local environment and the metabolic status of the cell (starvation, lack of essential AA, hypoxia)
Protein Aminoacids Percentage (Width 700 px)
SYNTHESIS AND TURNOVER
- Cell signaling and Ligand transport
- Structural proteins
Superoxide dismutases (SODs EC 220.127.116.11) are enzymes that are found ubiquitously in oxygen-metabolising organisms. The substrate of superoxide dismutases (SODs) is the superoxide radical anion (O2-) which is generated by the transfer of one electron to molecular oxygen. It is responsible both for direct damage of biological macromolecules (such as proteins and DNA for example) and for generating other reactive oxygen species. SODs keep the concentration of superoxide radicals in low limits and therefore play an important role in the defence against oxidative stress. The chemical reaction that SODs very efficiently catalyse is the dismutation of two molecules of O2- to yield one molecules of molecular oxygen and one molecule of peroxide: 2 O2- + 2 H+ → O2 + H2O2.
SODs are generally classified according to the metal species which acts as redox-active centre to catalyse the above dismutation reaction. Until recently, three different metal species have been found: copper- and zinc-containing SOD (Cu,ZnSOD), with copper as the catalytic active metal, manganese-containing SOD (MnSOD), and iron-containing SOD (FeSOD). More recently a new superoxide dismutase containing nickel (NiSOD) was purified from a variety of Streptomyces species, aerobic soil-dwelling bacteria. NiSOD was suggested to represent a novel class of superoxide dismutases on its own since no amino acid sequence homology is found to enzymes of the two already existing classes, i.e. the Cu,ZnSOD class and the MnSOD/FeSOD class.
NiSOD was characterized biochemically as well as spectroscopically . The enzyme was crystallized to allow the determination of NiSOD’s molecular structure by X-ray crystallography (Figure 1).
Figure 1: Crystals of NiSOD in three different forms.
(A) Plate-like crystals of dimensions 0.2 × 0.2 × 0.05 mm3
(B) Rod and needle-shaped crystals with diameters of 0.1 and 0.03 mm, respectively.
The experimental procedure to solve the NiSOD structure involved the Multiple-wavelength Anomalous Dispersion (MAD) method.
The structure of NiSOD reveals a homohexameric architecture of four-helix-bundle subunits (Figure 2). Each of the subunits hosts an active site in a loop comprised of the N-terminal eight residues.
Figure 2: The NiSOD structure. (A) The solvent accessible surface of NiSOD viewed along the hexamer’s threefold symmetry axis. The outer surface (black mesh) is sliced to allow the view to the inner space (in orange) and the protein backbone trace (each subunit coloured differently, Ni ions: salmon spheres). Arrows indicate three twofold symmetry axes and the entrance to channels which render the inner space accessible to solvent molecules. (B) Ribbon representation of a NiSOD subunit. The N-terminal loop hosting the Ni ion protrudes from the body of the four-helix bundle. Residues involved in aromatic stacking are shown in ball-and-stick representation. © Residues linking the active site loop (here of subunit A in yellow) to neighbouring chains by polar interactions. The importance of these residues for the stability of the active site loop has been confirmed by mutagenesis studies.The NiSOD structure is distinct from those of Cu,ZnSODs and of MnSOD or FeSOD (the latter two showing high structural similarity) regarding oligomeric state, subunit structure and active site.
The overall dismutation reaction can formally be divided into two steps in which the metal centre is first reduced (in the case of NiSOD from Ni(III) to Ni(II)) and subsequently re-oxidised. Thus, the enzyme’s active site can exist in two states corresponding to the two formal oxidation states of the metal ion. NiSOD proved to be sensitive to X-ray induced reduction of its metal centre in the course of diffraction data collection. As a consequence, the structure of the resting enzyme state had to be inferred from data obtained after minimal exposure to X-rays. At the same time, sensitivity to absorbed X-ray doses allowed the utilization of X-ray induced reduction as a means of visualization of intermediate states between the resting and fully reduced state. The latter state was also produced by soaking of NiSOD crystals in a solution containing the reducing agent thiosulfate.
In the resting enzyme, the Ni(III) is five-coordinated in a square-pyramidal geometry by the amino-group and imidazole Nδ nitrogen of His-1, the amide nitrogen and thiolate sulphur of Cys-2 and the thiolate sulphur of Cys-6 (Figure 3). The fully reduced enzyme state shows square-planar geometry of the Ni(II)-ligands and the loss of the axial ligand His-1 Nδ is observed upon reduction. An intermediate state of His-1 imidazole rotation around the Cβ-Cγ bond was captured after application of an X-ray dose in-between those used in data collections for the resting and fully reduced enzyme state. The Nδ atom is found at hydrogen-bonding distance to the carbonyl oxygen of Val-8 after its ligation to the Ni-ion is broken (Figure 3).
Figure 3: Electron density maps of the Ni ion environment. (A-C) Structures captured at successively increasing X-ray doses. (A) The fifth ligand His-1 Nδ (2.5 Å distant to Ni here) is revealed at low X-ray exposure (map resolution 2.2 Å). (B) After longer exposure of the same crystal as in A, the imidazolate ligation is disrupted. (C) Electron density map at 1.6 Å resolution obtained from a different crystal as in A and B, applying a maximum total X-ray dose. The ligands show a distorted cis square-planar geometry equalling the thiosulfate-reduced NiSOD in panel E. (D) Superposition of models from A in green, B in magenta and C in grey illustrates the His-1 imidazole rotation upon which Nδ reaches a distance of about 2.9 Å to Val-8 O, thereby maintaining the hydrogen-bond triangle of His-1 Nε to Glu-17 Oε and Arg-47 Nη of the adjacent
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