Structural and mechanistic basis of sulfolytic C–S bond cleavage by an Fe(ii)/α-ketoglutarate-dependent sulfoquinovose dioxygenase

Abstract

Sulfoquinovose dioxygenase (SqoD) enables bacterial carbon assimilation from the abundant sulfosugar sulfoquinovose (SQ) by Fe(II)/α-ketoglutarate (αKG)-dependent C–S bond cleavage. Here we report crystal structures of the Marinobacterium aestuarii enzyme (MaSqoD) in multiple states with inert Mn²⁺ in place of Fe²⁺ (SQ-bound; Mn²⁺·αKG; Mn²⁺·αKG·SQ; Mn²⁺·succinate), together with steady-state and pre-steady-state kinetics that link the structures with kinetically-inferred intermediates. The X-ray crystal structures show a canonical 2-His-1-carboxylate core metal center with SQ recognition via a mainly neutral network (Gln120, Trp253, backbone carbonyl of Ala185, and backbone amides of Ala89/Met118). Substrate binding triggers a hexacoordinate octahedral-to-pentacoordinate change at the metal center, unveiling a vacant site for O₂ in the fully assembled Mn²⁺·αKG·SQ complex and thereby curbing uncoupled reactions. Pre-steady-state stopped-flow data support the canonical Fe(IV)O chemistry of the dioxygenase and reveal an additional intermediate consistent with an enzyme-bound α-hydroxysulfonate or 6-dehydroglucose species. Together, these findings define the structural and mechanistic basis of sulfolytic SQ catabolism and illuminate the functional repertoire of Fe(II)/αKG-dependent dioxygenases in organosulfur carbon assimilation.