8HJ8 image
Entry Detail
PDB ID:
8HJ8
Keywords:
Title:
Crystal structure of barley exohydrolase isoform ExoI E220A mutant in complex with 2-deoxy-2-fluoro-D-glucopyranosides
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2022-11-22
Release Date:
2024-12-25
Method Details:
Experimental Method:
Resolution:
1.95 Å
R-Value Free:
0.18
R-Value Work:
0.14
R-Value Observed:
0.14
Space Group:
P 43 21 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Glyco_hydro_3 domain-containing protein
Mutations:E220A
Chain IDs:A
Chain Length:609
Number of Molecules:1
Biological Source:Hordeum vulgare
Primary Citation
The structure and dynamics of water molecule networks underlie catalytic efficiency in a glycoside exo-hydrolase.
Commun Biol 8 729 729 (2025)
PMID: 40348901 DOI: 10.1038/s42003-025-08113-9

Abstact

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.

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