5A70

Structure of the LecB lectin from Pseudomonas aeruginosa strain PA14 in complex with lewis x tetrasaccharide

5A70 の概要

• エントリーDOI: 10.2210/pdb5a70/pdb
• 関連するPDBエントリー: 5A6Q 5A6X 5A6Y 5A6Z
• 分子名称: LECB, alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose, CALCIUM ION, ... (5 entities in total)
• 機能のキーワード: sugar binding protein, lectin, lecb lewis x antigen
• 由来する生物種: PSEUDOMONAS AERUGINOSA
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 49986.11

構造登録者

Sommer, R.,Wagner, S.,Varrot, A.,Khaledi, A.,Haussler, S.,Imberty, A.,Titz, A. (登録日: 2015-07-02, 公開日: 2016-07-27, 最終更新日: 2024-01-10)

主引用文献

Lepsik, M.,Sommer, R.,Kuhaudomlarp, S.,Lelimousin, M.,Paci, E.,Varrot, A.,Titz, A.,Imberty, A.
Induction of rare conformation of oligosaccharide by binding to calcium-dependent bacterial lectin: X-ray crystallography and modelling study.
Eur.J.Med.Chem., 177:212-220, 2019

PubMed Abstract: Pathogenic micro-organisms utilize protein receptors (lectins) in adhesion to host tissues, a process that in some cases relies on the interaction between lectins and human glycoconjugates. Oligosaccharide epitopes are recognized through their three-dimensional structure and their flexibility is a key issue in specificity. In this paper, we analysed by X-ray crystallography the structures of the LecB lectin from two strains of Pseudomonas aeruginosa in complex with Lewis x oligosaccharide present on cell surfaces of human tissues. An unusual conformation of the glycan was observed in all binding sites with a non-canonical syn orientation of the N-acetyl group of N-acetyl-glucosamine. A PDB-wide search revealed that such an orientation occurs only in 4% of protein/carbohydrate complexes. Theoretical chemistry calculations showed that the observed conformation is unstable in solution but stabilised by the lectin. A reliable description of LecB/Lewis x complex by force field-based methods had proven especially challenging due to the special feature of the binding site, two closely apposed Ca ions which induce strong charge delocalisation. By comparing various force-field parametrisations, we propose a general strategy which will be useful in near future for designing carbohydrate-based ligands (glycodrugs) against other calcium-dependent protein receptors.

PubMed: 31146126
DOI: 10.1016/j.ejmech.2019.05.049

実験手法

X-RAY DIFFRACTION (1.6 Å)