8AD2

Tobacco lectin Nictaba in complex with triacetylchitotriose

8AD2 の概要

• エントリーDOI: 10.2210/pdb8ad2/pdb
• 関連するBIRD辞書のPRD_ID: PRD_900017
• 分子名称: Nictaba, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ZINC ION, ... (5 entities in total)
• 機能のキーワード: lectin, jelly-roll, nag-binding, secreted, nuclear, sugar binding protein
• 由来する生物種: Nicotiana tabacum (common tobacco)
• タンパク質・核酸の鎖数: 8
• 化学式量合計: 157185.38

構造登録者

Bloch, Y.,Savvides, S.N. (登録日: 2022-07-07, 公開日: 2023-01-18, 最終更新日: 2024-11-20)

主引用文献

Bloch, Y.,Osterne, V.J.S.,Savvides, S.N.,Van Damme, E.J.M.
The crystal structure of Nictaba reveals its carbohydrate-binding properties and a new lectin dimerization mode.
Glycobiology, 2024

PubMed Abstract: Nictaba is a (GlcNAc)n-binding, stress-inducible lectin from Nicotiana tabacum that serves as a representative for the Nictaba-related lectins, a group of proteins that play pivotal roles in plant defense mechanisms and stress response pathways. Despite extensive research into biological activities and physiological role(s) of the lectin, the three-dimensional structure of Nictaba remained largely unknown. Here, we report crystal structures for Nictaba in the apo form and bound to chitotriose. The structures reveal that the Nictaba protomer has a jelly-roll fold, similar to the cucumber lectin Cus17, but exhibit a unique and previously unseen mode of dimerization. The chitotriose binding mode, similar to Cus17, centers around the central GlcNAc residue, providing insights into the determinants of specificity of Nictaba towards carbohydrate structures. By integrating these structural insights with inputs from glycan arrays, molecular docking, and molecular dynamics simulations, we propose that Nictaba employs a single carbohydrate-recognition domain within each of the two subunits in the dimer to display pronounced specificity towards GlcNAc-containing carbohydrates. Furthermore, we identified amino acid residues involved in the extended binding site capable of accommodating structurally diverse high-mannose and complex N-glycans. Glycan array and in silico analyses revealed interactions centered around the conserved Man3GlcNAc2 core, explaining the broad recognition of N-glycan structures. Collectively, the structural and biochemical insights presented here fill a void into the atlas of lectin structure-function relationships and pave the way for future developments in plant stress biology and lectin-based applications.

PubMed: 39437181
DOI: 10.1093/glycob/cwae087

実験手法

X-RAY DIFFRACTION (2 Å)