6V7G

Binding of Benzoic Acid and Anions Within the Cupin Domains of the Vicillin Protein Canavalin from Jack Bean (canavalia ensiformis): Crystal Structures

Replaces:  6CB4

Summary for 6V7G

• Entry DOI: 10.2210/pdb6v7g/pdb
• Descriptor: Canavalin, ACETATE ION, BENZOIC ACID, ... (5 entities in total)
• Functional Keywords: plant proteins, ligands, salicylic acid, enzymes, plant protein
• Biological source: Canavalia ensiformis (Jack bean)
• Total number of polymer chains: 1
• Total formula weight: 50804.76

Authors

McPherson, A. (deposition date: 2019-12-08, release date: 2020-02-19, Last modification date: 2023-11-15)

Primary citation

McPherson, A.
Binding of benzoic acid and anions within the cupin domains of the vicilin protein canavalin from jack bean (Canavalia ensiformis): Crystal structures.
Biochem.Biophys.Res.Commun., 524:268-271, 2020

PubMed Abstract: X-ray intensities extending to 1.4 Å resolution were collected on the P6 hexagonal crystal form of canavalin, and extended to 1.9 Å for the orthorhombic C222 crystals. Structure determination of a new crystal form of canavalin having space group P222 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 C222 and P222 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 P222 and rhombohedral crystals were also vacant, but the N terminal cupin domain of the C222 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.

PubMed: 31983433
DOI: 10.1016/j.bbrc.2020.01.101

Experimental method

X-RAY DIFFRACTION (1.4 Å)