Structural basis for the conformational protection of nitrogenase from O2

Abstract

The low reduction potentials required for the reduction of dinitrogen (N₂) render metal-based nitrogen-fixation catalysts vulnerable to irreversible damage by dioxygen (O₂)^1,2,3. Such O₂ sensitivity represents a major conundrum for the enzyme nitrogenase, as a large fraction of nitrogen-fixing organisms are either obligate aerobes or closely associated with O₂-respiring organisms to support the high energy demand of catalytic N₂ reduction⁴. To counter O₂ damage to nitrogenase, diazotrophs use O₂ scavengers, exploit compartmentalization or maintain high respiration rates to minimize intracellular O₂ concentrations^4,5,6,7,8. A last line of damage control is provided by the ‘conformational protection’ mechanism⁹, in which a [2Fe:2S] ferredoxin-family protein termed FeSII (ref. ¹⁰) is activated under O₂ stress to form an O₂-resistant complex with the nitrogenase component proteins^11,12. Despite previous insights, the molecular basis for the conformational O₂ protection of nitrogenase and the mechanism of FeSII activation are not understood. Here we report the structural characterization of the Azotobacter vinelandii FeSII–nitrogenase complex by cryo-electron microscopy. Our studies reveal a core complex consisting of two molybdenum–iron proteins (MoFePs), two iron proteins (FePs) and one FeSII homodimer, which polymerize into extended filaments. In this three-protein complex, FeSII mediates an extensive network of interactions with MoFeP and FeP to position their iron–sulphur clusters in catalytically inactive but O₂-protected states. The architecture of the FeSII–nitrogenase complex is confirmed by solution studies, which further indicate that the activation of FeSII involves an oxidation-induced conformational change.