Primary structure of wheat germ agglutinin isolectin 2. Peptide order deduced from x-ray structure

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Abstract
The complete amino acid sequence of wheat germ agglutinin isolectin 2 was determined by the method of sequential Edman degradation and with the aid of the 3-dimensional structure known from X-ray crystallography. Peptides ranging from 2-18 residues in length were obtained by thermolysin digestion of the S-carboxymethylated protein and purified by gel filtration and high-performance liquid chromatography. The peptide order was established primarily by matching (carboxymethyl)cysteines with the clearly defined half-cystine positions in the X-ray structure, thereby satisfying the disulfide repeat pattern observed in all 4 isostructural domains (A, B, C and D) of wheat germ agglutinin, and by examination of amino acid compositions and terminal sequences of 10 tryptic peptides. The unique assignment of peptides to these domains was consistent with all invariant half-cystines and glycines, as well as the single tryptophan, the 2 closely spaced histidines and a number of other residues clearly identified in the X-ray structure analysis. Discrepancies between the chemical and X-ray sequencies lie exclusively in poorly defined regions of the electron density map, at the N- and C-termini, and at the 1st intercystine loop of each domain. The latter loop was 8 instead of 6 residues in length, thus extending the size of domains A, B and C from 41 to 43 residues and that of domain D to 42 residues. Regions of extensive interdomain homology, in addition to that of the half-cystines, are clustered at the central portion of each domain fold and are likely to be important for the integrity of the 3-dimensional structure of the dimer molecule.