Binding of benzoic acid and anions within the cupin domains of the vicilin protein canavalin from jack bean (Canavalia ensiformis): Crystal structures

X-ray intensities extending to 1.4 Å resolution were collected on the P63 hexagonal crystal form of canavalin, and extended to 1.9 Å for the orthorhombic C2221 crystals. Structure determination of a new crystal form of canavalin having space group P212121 is reported as well. Both the N and C terminal cupin domains contained identifiable ligands. For hexagonal crystals, in the cavity of the C terminal cupin, a molecule of benzoic acid was found, bound through carboxyl oxygens to Histidine 297, asparagine 284 and Arginine 376. The benzene ring was immersed in a cluster of at least 8 hydrophobic amino acid side chains. The N terminal cupin contained a molecule of citrate. Benzoic acid was also found to be present in the C terminal cupins of in the C2221 and P212121 crystal forms. In rhombohedral crystals, the C terminal cupin domain appeared to be occupied by a phosphate ion, but this was ambiguous. In cubic crystals, both domains were vacant. The N terminal cupin domains of canavalin in the P212121 and rhombohedral crystals were also vacant, but the N terminal cupin domain of the C2221 crystals contained a ligand whose identity is uncertain, but which has been modeled as HEPES buffer. A possible physiological role for the ligands and their complexes with canavalin is considered. Benzoic acid, an important plant metabolite, is shown as it is bound in a cupin domain of a vicilin protein, canavalin, from Canavalia ensiformis. The binding suggests that vicilin proteins may serve additional biochemical roles other than as storage proteins. [Display omitted] •Cupin domains of vicilin proteins bind metabolic intermediates.•Benzoic acid, an important metabolite was found to bind in the carboxy terminal cupin domain of canavalin.•Structure of a new crystal form of canavalin was determined crystallographically.•Resolution was significantly extended, to 1.4 Å in one case, on other crystal forms.•Vicilin proteins from plants may play other biochemical roles other than serving as storage proteins.