Crystal structure of the metal-bound superoxide dismutase from pyrobaculum aerophilum and comparison with the metal-free form

Superoxide dismutase provides a safeguard against reactive oxygen species by converting toxic superoxide to oxygen and hydrogen peroxide. Biological function of a superoxide dismutase mandates the presence of a metal ion. Previously the crystal structure of the metal-free form of superoxide dismutase from a hyperthermophile Pyrobaculum aerophilum (PaSOD) was reported. PaSOD, when expressed as the metal-free form in a bacterial system, is known to incorporate a metal ion by thermal activation. In this study, the crystal structure of PaSOD in its metal-bound form has been determined at 1.85 Å resolution in the space group P3₂21. The structure exhibits a canonical Mn-or-Fe superoxide dismutase fold with one tetramer in the asymmetric unit. Active site geometry is consistent with those of previously known Mn-or-Fe superoxide dismutase orthologs. Structure comparison of the metal-bound form with the previously determined metal-free form revealed almost identical conformations in overall fold other than the presence of a metal ion in the active site for the metal-bound form. However, subtle changes were observed in the conformations of active site residues and loop residues positioned at the entry to the active site. Such results imply that the structure of PaSOD appears to be rigid against metal incorporation overall with locally confined conformational changes to facilitate the incorporation process.