X-ray study of the pea lectin- carbohydrate complex at 2.4 Å resolution. II. Metal- and carbohydrate binding sites. A model of lectin-carbohydrate interaction
Yu. D. Lobsanov, V. Z. Pletnev, M. A. Mokulskii
Institute of Molecular Genetics, Academy of Sciences of the USSR, Moscow
Abstract: The organization of the metal- and carbohydrate binding sites of pea lectin has been determined by the X-ray method. The first, octahedric coordination sphere of manganese ion is formed by the following ligands: carboxyl oxygens of the side chains of Glu119, Asp121, Asp129, nitrogen atom of imidazole ring of His136 and oxygen atoms of two water molecules. Calcium ion is coordinated by carboxyl oxygens of the side chains of Asp121, Asn125, Asp129, carbonyl oxygen of Phe123, and two oxygens of water molecules. The seventh ligand, OD1 of Asp121, which is also ligand for Mn, slightly distorts ideality of octahedric coordination of calcium ion. The saccharide molecule (benzyl-2-acetamido-2,3-dideoxy-3-iodo-α-D-glucopyranoside) in Cl conformation is bound by the protein in a shallow cleft on the surface of the molecule near to the metal binding site. There are two hydrogen bonds connecting saccharide oxygens O4 and O6 with the Ca-coordinating water molecule oxygen and with the nitrogen atom of the Ala127 amino group, respectively. The non-polar part of the pyranose ring lying in the plane of carbon atoms C3, C4, C5 forms pseudostacking interaction with aromatic side chains of Phe123 and Tyr100. In the case of the native saccharide, oxygen 03 presumably forms two more hydrogen bonds with carbonyl oxygen of cis-peptide Ala80 – Asp81 and with carboxyl oxygen OD1 of Asp81. The saccharide binding site lies in the middle of the rouleau of six aromatic side chains of Tyr77, Tyr124, Phe123, Tyr100, Trp128, and Tyr109. It suggests that these groups orm an extended olygosaccharide binding region with preference to the biantennary olygosaccharides. The proposed model of binding carbohydrates by the pea lectin molecule is in good accordance with biochemical data.
Russian Journal of Bioorganic Chemistry 1990, 16 (12):1599-1606