Manipulating the coordination mumber of the ferric iron within the cambialistic superoxide dismutase of Propionibacterium shermanii by changing the pH‐value

Abstract

The structure of the Propionibacterium freudenreichii subspecies shermanii superoxide dismutase (SOD) was determined at various pH values. As a comparison, the structure of the fluoride coordinated SOD was solved. The SOD crystallizes at pH 6.1 in the space group C222 1 with two subunits, A and B, in the asymmetric unit. An increase of the pH value changes the cell parameters slightly but not the symmetry of the crystals. The overall structure of the SOD remains a compact tetrameter and is comparable to that at pH 6.1 no matter whether the pH increases or fluoride is added. At values above pH 7.4, an additional hydroxide ion can bind to the active center. Its position is similar to the binding site of the fluoride. The coordination number changes from five to six if the pH increases or fluoride is added. The binding behavior of the hydroxide ion is different for subunit A and B. Structures at different pH-values are comparable with models derived by spectroscopic methods. The influence of temperature on the binding properties of the hydroxide ion was investigated using analysis of an X-ray structure solved at pH 8.1 and 140 K. Compared to the structure at room temperature, the structural changes are observable but remain small. The consequences of hydroxide binding to the iron are discussed.

Novel mechanisms for superoxide-scavenging activity of human manganese superoxide dismutase determined by the K68 key acetylation site

“…The underlying mechanism may be that the lysine acetylation will diminish the positive charge, thereby decreasing the electrostatic repulsion between monomers, making the tetramer stable. According to Marius Schmidt et al, the four subunits of SOD2 in Propionibacterium shermanii are held together by H-bonds between residues of the two distorted helical turns, following one sheet and the equivalent area in the other monomer [38,47]. One H-bond also exists between Q122, located in the loop from H4 to B1, and D64, located in the H2 of the other monomer.…”

Sulfur K-Edge X-ray Absorption Spectroscopy and Density Functional Theory Calculations on Superoxide Reductase: Role of the Axial Thiolate in Reactivity

“…For calculating the SOD reaction, the co-ordinates from the X-tal structure of Fe-SOD from P. shermanii (pdbid: 1BSM) were used for the starting structure. 44 The α carbons of the histidine and the glutamate residues were frozen during optimization. All other geometric parameters were optimized.…”

Superoxide interaction with nickel and iron superoxide dismutases

“…1) has been a matter of debate: although the iron-oxygen distance in SOD crystal structures is distinctly longer than expected for an Fe-OH interaction, evidence has been presented that in solution the solvent ligand may cycle between hydroxo and aqua, depending on the iron oxidation state [8,21]. Table 1 also lists data for the Fe(III)SOD-superoxide models assuming a hydroxo rather than aqua ligand.…”

“…Geometries for NiSOD models were optimized without any constraints. The starting coordinates for FeSOD models were taken from the crystal structure of resting FeSOD (pdb code 1BSM [8]). Geometries for FeSOD models were optimized by freezing the coordinates of the heavy atoms within the protein-derived iron ligands, in order to avoid massive rearrangement of the imidazole and carboxylate ligands to relative orientations that would impose steric and electronic constraints not present and thus not directly relevant to the FeSOD active site; such rearrangement does not occur in the NiSOD models.…”