5Y42

Native-crystal structure of three chain non-toxic type II ribosome inactivating protein purified from the seeds of Trichosanthes anguina

Summary for 5Y42

• Entry DOI: 10.2210/pdb5y42/pdb
• Descriptor: Lectin, Seed lectin, 2-acetamido-2-deoxy-beta-D-glucopyranose, ... (5 entities in total)
• Functional Keywords: beta-trefoil, lectin, plant protein
• Biological source: Trichosanthes anguina (Snake gourd); More
• Total number of polymer chains: 6
• Total formula weight: 114347.11

Authors

Chandran, T.,Vijayan, M. (deposition date: 2017-07-31, release date: 2018-08-08, Last modification date: 2024-11-06)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (2.9 Å)