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

Abstract

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.

Keywords: Crystallography; Enzymes; Ligands; Plant proteins; Salicylic acid; X-ray diffraction.