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The three-dimensional structure of the vicilin storage protein canavalin, from
Canavalia ensiformis, has been determined in a hexagonal crystal by x-ray
diffraction methods. The model has been refined at 2.6 A resolution to an R
factor of 0.197 with acceptable geometry. Because of proteolysis, 58 of 419
amino acids of the canavalin polypeptide are not visible in the electron density
map. The canavalin subunit is composed of two extremely similar structural
domains that reflect the tandem duplication observed in the cDNA and in the
amino acid sequence. Each domain consists of two elements, a compact,
eight-stranded beta-barrel having the "Swiss roll" topology and an extended loop
containing several short alpha-helices. The root mean square deviation between
84 pairs of corresponding C alpha atoms making up the strands of the two
beta-barrels in a subunit is 0.78 A, and for 112 pairs of structurally
equivalent C alpha atoms of the two domains the deviation is 1.37 A. The
interface between domains arises from the apposition of broad hydrophobic
surfaces formed by side chains originating from one side of the beta-barrels,
supplemented by at least four salt bridges. The interfaces between subunits in
the trimer are supplied by the extended loop elements. These interfaces are also
composed primarily of hydrophobic residues supplemented by six salt bridges. The
canavalin subunits have dimensions about 40 x 40 x 86 A, and the oligomer is a
disk-shaped molecule about 88 A in diameter with a thickness of about 40 A. The
distribution of domains lends a high degree of pseudo-32-point group symmetry to
the molecule. There is a large channel of 18 A diameter, lined predominantly by
hydrophilic and charged amino acids, running through the molecule along the
3-fold axis. The majority of residues conserved between domains and among
vicilins occur at the interface between subunits but appear otherwise
arbitrarily distributed within the subunit, although predominantly on its
exterior.
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