The three-dimensional structure of canavalin at 3.0 A resolution by X-ray diffraction analysis.

The structure of the jack bean (Canavalia ensiformis) protein canavalin, which forms the classical vicillin fraction of the seed protein in this species, has been determined for the rhombohedral (R3) crystal form to 3.0-A resolution. X-ray diffraction data were collected by the screened precession method for the native protein and five heavy atom derivatives and the phases were determined by conventional isomorphous replacement. The electron density map thus obtained, and a molecularly averaged electron density map, permitted tentative tracing of the polypeptide chains that comprise the asymmetric unit. It was found that the two major fragments that make up the canavalin monomer, which are derived from the NH2- and COOH-terminal halves of a 42,000-dalton precursor polypeptide, are virtually identical in structure and are related by a near exact molecular dyad axis of symmetry. The halves of the monomer are themselves composed of two discrete domains, corresponding in one case to the secondary cleavage products of a major fragment. One domain provides the structure involved in binding the Zn2+ ion which lies near the pseudo 32 symmetry point. The other domain forms a distinct cleft on the exterior or the monomer that may be a substrate-binding region. The molecule is almost entirely beta structure, organized into a series of interrelated sheets. The proteolytic cleavage points have been identified, and a number of additional interesting features are described.