6T99

Crystal structrue of RSL W31YW76Y lectin mutant in complex with alpha-methylfucoside

Summary for 6T99

• Entry DOI: 10.2210/pdb6t99/pdb
• Descriptor: Fucose-binding lectin protein, methyl alpha-L-fucopyranoside, SODIUM ION, ... (4 entities in total)
• Functional Keywords: lectin, beta-propeller, fucose-binding, sugar binding protein
• Biological source: Ralstonia solanacearum
• Total number of polymer chains: 9
• Total formula weight: 90440.69

Authors

Houser, J.,Kozmon, S.,Wimmerova, M. (deposition date: 2019-10-26, release date: 2020-04-22, Last modification date: 2024-01-24)

Primary citation

Houser, J.,Kozmon, S.,Mishra, D.,Hammerova, Z.,Wimmerova, M.,Koca, J.
The CH-pi Interaction in Protein-Carbohydrate Binding: Bioinformatics and In Vitro Quantification.
Chemistry, 26:10769-10780, 2020

PubMed Abstract: The molecular recognition of carbohydrates by proteins plays a key role in many biological processes including immune response, pathogen entry into a cell, and cell-cell adhesion (e.g., in cancer metastasis). Carbohydrates interact with proteins mainly through hydrogen bonding, metal-ion-mediated interaction, and non-polar dispersion interactions. The role of dispersion-driven CH-π interactions (stacking) in protein-carbohydrate recognition has been underestimated for a long time considering the polar interactions to be the main forces for saccharide interactions. However, over the last few years it turns out that non-polar interactions are equally important. In this study, we analyzed the CH-π interactions employing bioinformatics (data mining, structural analysis), several experimental (isothermal titration calorimetry (ITC), X-ray crystallography), and computational techniques. The Protein Data Bank (PDB) has been used as a source of structural data. The PDB contains over 12 000 protein complexes with carbohydrates. Stacking interactions are very frequently present in such complexes (about 39 % of identified structures). The calculations and the ITC measurement results suggest that the CH-π stacking contribution to the overall binding energy ranges from 4 up to 8 kcal mol . All the results show that the stacking CH-π interactions in protein-carbohydrate complexes can be considered to be a driving force of the binding in such complexes.

PubMed: 32208534
DOI: 10.1002/chem.202000593

Experimental method

X-RAY DIFFRACTION (2.7 Å)