FIGURE 6.

The binding of a C4-CoA adduct and oxalate in the active site of ObcA. a, a magnified view for oxalate (yellow), C4-CoA adduct (green), and Co²⁺ (black spheres) is shown; the asterisk indicates the carbon atom in a tetrahedral configuration. In the left panel, the final model is overlaid with an F_o − F_c map (2.3 σ), showing the possible connection between the oxalate region and the C4-CoA adduct. However, after refinement, the density between the adduct and oxalate is clearly distinguished, which is shown in the right panel with a 2F_o − F_c map (1.7 σ). b, two different orientations with an F_o − F_c map (2.3 σ) are shown to indicate that the carbon atom joined to the sulfhydryl group of the adduct is in a tetrahedral configuration. c, a magnified view is displayed for the relative positioning of the ligands, including oxaloacetate (yellow), as well as oxalate and the C4-CoA adduct, both in green. The relative positions were determined by superposing the two complexes. The C3 of oxaloacetate is ∼2.6 Å away from the tetrahedral carbon in the C4-CoA adduct, implying that the enolate form of oxaloactate undergoes a direct nucleophilic attack on the thioester carbonyl carbon of acetyl-CoA. d, a schematic representation is shown for the interactions in the active site of the ObcA complexed with the C4-CoA adduct and oxalate. Dashed lines indicate possible hydrogen bonds within an interatomic distance of 3.5 Å among the metal-coordinating shell, ligand, and the nearby residues. Interaction distances between Lys⁴⁸⁹ and the phosphate and between Arg²⁷⁹ and the adduct are 3.8 and 3.6 Å, respectively. Many residues are within close enough distance to allow for hydrophobic interactions. Note that only a few interactions are identified in the vicinity of the adenosine 3′,5′-diphosphate moiety.