2VUZ

Crystal structure of Codakine in complex with biantennary nonasaccharide at 1.7A resolution

2VUZ の概要

• エントリーDOI: 10.2210/pdb2vuz/pdb
• 関連するPDBエントリー: 2VUV
• 分子名称: CODAKINE, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CALCIUM ION, ... (5 entities in total)
• 機能のキーワード: nonasaccharide, codakia orbicularis, sugar-binding protein, c-type, lectin, codakine, biantennary, invertebrate, sugar binding protein
• 由来する生物種: CODAKIA ORBICULARIS
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 15821.04

構造登録者

Gourdine, J.P.,Cioci, G.C.,Miguet, L.,Unverzagt, C.,Varrot, A.,Gauthier, C.,Smith-Ravin, E.J.,Imberty, A. (登録日: 2008-06-02, 公開日: 2008-08-05, 最終更新日: 2023-12-13)

主引用文献

Gourdine, J.P.,Cioci, G.C.,Miguet, L.,Unverzagt, C.,Silva, D.V.,Varrot, A.,Gautier, C.,Smith-Ravin, E.J.,Imberty, A.
High Affinity Interaction between a Bivalve C-Type Lectin and a Biantennary Complex-Type N-Glycan Revealed by Crystallography and Microcalorimetry.
J.Biol.Chem., 283:30112-, 2008

PubMed Abstract: Codakine is an abundant 14-kDa mannose-binding C-type lectin isolated from the gills of the sea bivalve Codakia orbicularis. Binding studies using inhibition of hemagglutination indicated specificity for mannose and fucose monosaccharides. Further experiments using a glycan array demonstrated, however, a very fine specificity for N-linked biantennary complex-type glycans. An unusually high affinity was measured by titration microcalorimetry performed with a biantennary Asn-linked nonasaccharide. The crystal structure of the native lectin at 1.3A resolution revealed a new type of disulfide-bridged homodimer. Each monomer displays three intramolecular disulfide bridges and contains only one calcium ion located in the canonical binding site that is occupied by a glycerol molecule. The structure of the complex between Asn-linked nonasaccharide and codakine has been solved at 1.7A resolution. All residues could be located in the electron density map, except for the capping beta1-4-linked galactosides. The alpha1-6-linked mannose binds to calcium by coordinating the O3 and O4 hydroxyl groups. The GlcNAc moiety of the alpha1,6 arm engages in several hydrogen bonds with the protein, whereas the GlcNAc on the other antenna is stacked against Trp(108), forming an extended binding site. This is the first structural report for a bivalve lectin.

PubMed: 18687680
DOI: 10.1074/JBC.M804353200

実験手法

X-RAY DIFFRACTION (1.7 Å)