8QMG

Tobacco lectin Nictaba in apo state including I and Eu SAD datasets.

Summary for 8QMG

• Entry DOI: 10.2210/pdb8qmg/pdb
• Related: 8ad2
• Descriptor: Nictaba, ZINC ION (3 entities in total)
• Functional Keywords: lectin, jelly-roll, nag-binding, secreted, nuclear, sugar binding protein
• Biological source: Nicotiana tabacum (common tobacco)
• Total number of polymer chains: 8
• Total formula weight: 154704.96

Authors

Bloch, Y.,Savvides, S.N. (deposition date: 2023-09-22, release date: 2023-11-08, Last modification date: 2024-12-25)

Primary citation

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, 34:-, 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

Experimental method

X-RAY DIFFRACTION (2.3 Å)