5Y97

Crystal structure of snake gourd seed lectin in complex with lactose

5Y97 の概要

• エントリーDOI: 10.2210/pdb5y97/pdb
• 関連するBIRD辞書のPRD_ID: PRD_900004
• 分子名称: Seed lectin, beta-D-galactopyranose-(1-4)-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose, ... (6 entities in total)
• 機能のキーワード: beta-trefoil, lectin, plant protein
• 由来する生物種: Trichosanthes anguina (Snake gourd); 詳細
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 58227.97

構造登録者

Chandran, T.,Vijayan, M.,Sivaji, N.,Surolia, A. (登録日: 2017-08-23, 公開日: 2018-08-29, 最終更新日: 2024-10-23)

主引用文献

Chandran, T.,Sivaji, N.,Surolia, A.,Vijayan, M.
Ligand binding and retention in snake gourd seed lectin (SGSL). A crystallographic, thermodynamic and molecular dynamics study
Glycobiology, 28:968-977, 2018

PubMed Abstract: Snake gourd seed lectin (SGSL) is a non-toxic homolog of type II ribosome-inactivating proteins (RIPs) which contain a catalytic domain and a lectin domain. Isothermal titration calorimetry (ITC) measurements of the interactions of the protein with LacNAc, Lac, Gal, Me-α-Gal were carried out and the crystal structures of the native protein and its complex with Lac were determined. The crystal structure of the Me-α-Gal complex has already been determined. While the crystal structure showed the presence of two-sugar-binding sites, one on each of the two domains of the lectin chain, ITC measurements indicated the presence of only one binding site. In order to resolve this anomaly, molecular dynamics (MD) simulations were carried out on the native protein and on its complexes with Me-α-Gal and Lac. Simulations were also performed on the protein after reducing the inter-chain disulfide bridge between the two chains. The crystal structures and the simulations confirmed the robustness of the protein structure, irrespective of the presence or absence of the disulfide bridge. The simulations indicated that although two sites can bind sugar, only the ligand at one site is retained in a dynamic situation. The studies thus bring out the subtle relationship between binding and retention of the ligand.

PubMed: 30099481
DOI: 10.1093/glycob/cwy072

実験手法

X-RAY DIFFRACTION (3.05 Å)