The crystal structure of Nictaba reveals its carbohydrate-binding properties and a new lectin dimerization mode.

IF 3.4 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Glycobiology Pub Date : 2024-10-22 DOI:10.1093/glycob/cwae087
Yehudi Bloch, Vinicius J S Osterne, Savvas N Savvides, Els J M Van Damme
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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.

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Nictaba 的晶体结构揭示了其碳水化合物结合特性和一种新的凝集素二聚化模式。
Nictaba 是来自烟草(Nicotiana tabacum)的一种(GlcNAc)n 结合型胁迫诱导凝集素,是 Nictaba 相关凝集素的代表,该凝集素是一组在植物防御机制和胁迫响应途径中发挥关键作用的蛋白质。尽管对该凝集素的生物活性和生理作用进行了广泛的研究,但 Nictaba 的三维结构在很大程度上仍然未知。在此,我们报告了 Nictaba 的 apo 形式和与壳三糖结合的晶体结构。这些结构揭示了 Nictaba 的原体具有果冻状折叠,与黄瓜凝集素 Cus17 相似,但表现出一种独特的、以前从未见过的二聚化模式。与 Cus17 相似,壳三糖的结合模式也是以中心 GlcNAc 残基为中心,这为了解 Nictaba 对碳水化合物结构的特异性提供了线索。通过将这些结构见解与来自糖阵列、分子对接和分子动力学模拟的输入信息相结合,我们提出 Nictaba 在二聚体的两个亚基中的每一个都利用了单个碳水化合物识别域,从而对含 GlcNAc 的碳水化合物表现出明显的特异性。此外,我们还确定了参与扩展结合位点的氨基酸残基,该位点能够容纳结构多样的高甘露糖和复杂的 N-聚糖。聚糖阵列和硅学分析揭示了以保守的 Man3GlcNAc2 核心为中心的相互作用,从而解释了对 N-聚糖结构的广泛识别。总之,本文提出的结构和生化见解填补了凝集素结构-功能关系图谱的空白,为植物胁迫生物学和基于凝集素的应用的未来发展铺平了道路。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
Glycobiology
Glycobiology 生物-生化与分子生物学
CiteScore
7.50
自引率
4.70%
发文量
73
审稿时长
3 months
期刊介绍: Established as the leading journal in the field, Glycobiology provides a unique forum dedicated to research into the biological functions of glycans, including glycoproteins, glycolipids, proteoglycans and free oligosaccharides, and on proteins that specifically interact with glycans (including lectins, glycosyltransferases, and glycosidases). Glycobiology is essential reading for researchers in biomedicine, basic science, and the biotechnology industries. By providing a single forum, the journal aims to improve communication between glycobiologists working in different disciplines and to increase the overall visibility of the field.
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