The structure and dynamics of water molecule networks underlie catalytic efficiency in a glycoside exo-hydrolase
Abstract Glycoside hydrolases break glycosidic bonds by transferring a water molecule onto the glycosidic oxygen of carbohydrates, but on the nanoscale, the dynamics of water molecules remains unclear. We investigate the role of the non-nucleophilic E220 glutamate, essential for maintaining the wate...
Saved in:
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2025-05-01
|
| Series: | Communications Biology |
| Online Access: | https://doi.org/10.1038/s42003-025-08113-9 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| Summary: | Abstract Glycoside hydrolases break glycosidic bonds by transferring a water molecule onto the glycosidic oxygen of carbohydrates, but on the nanoscale, the dynamics of water molecules remains unclear. We investigate the role of the non-nucleophilic E220 glutamate, essential for maintaining the water molecule network in a family 3 β-d-glucan glucohydrolase, but not involved directly in catalysis. Kinetic data disclose that the E220A mutant retains substrate poly-specificity but has drastically reduced catalytic efficiency compared to the wild-type. High-resolution structures in-complex with a hydrolytic product and a mechanism-based inhibitor reveal that in wild-type, the concatenated water molecules near acid/base E491 and neighbouring N219 and E220 form a harmonised network. In contrast, in the E220A mutant, this network is uncoordinated. Computational models of covalent complexes show that water flux through the wild-type protein correlates with high catalytic efficiency dissimilar to E220A, where this correlation is lost. Ancestral sequence reconstructions of family 3 enzymes divulge the evolutionary conservation of residues participating in water molecule networks, which underlie substrate-product-assisted processivity. Our findings provide a blueprint for the dynamics of catalysis mediated by hydrolytic enzymes, which could inspire bioengineering to create a sustainable bio-economy. |
|---|---|
| ISSN: | 2399-3642 |