9YUT

Crystal structure of malonate-bound sulfoquinovose dioxygenase from Marinobacterium aestuarii

Summary for 9YUT

• Entry DOI: 10.2210/pdb9yut/pdb
• Descriptor: TauD/TfdA-like domain-containing protein, MALONIC ACID (3 entities in total)
• Functional Keywords: fe(ii)-dependent alpha-ketoglutarate dioxygenase, metal binding protein
• Biological source: Marinobacterium aestuarii
• Total number of polymer chains: 1
• Total formula weight: 36340.36

Authors

Lee, M. (deposition date: 2025-10-23, release date: 2026-07-22)

Primary citation

Lee, M.,Ho, H.N.N.,Maher, M.J.,Jameson, G.N.L.,Williams, S.J.
Structural and mechanistic basis of sulfolytic C-S bond cleavage by an Fe(ii)/ alpha-ketoglutarate-dependent sulfoquinovose dioxygenase.
Chem Sci, 17:8100-8107, 2026

PubMed 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 enzyme (SqoD) in multiple states with inert Mn in place of Fe (SQ-bound; Mn·αKG; Mn·αKG·SQ; Mn·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 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 O in the fully assembled Mn·αKG·SQ complex and thereby curbing uncoupled reactions. Pre-steady-state stopped-flow data support the canonical Fe(iv)[double bond, length as m-dash]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.

PubMed: 41777709
DOI: 10.1039/d5sc09188h

Experimental method

X-RAY DIFFRACTION (1.422 Å)