9NPD image
Deposition Date 2025-03-11
Release Date 2025-11-12
Last Version Date 2026-01-21
Entry Detail
PDB ID:
9NPD
Keywords:
Title:
Crystal structure of the inactive conformation of a glycoside hydrolase (CapGH2b - E553Q Mutant) from the GH2 family in the space group P3121 at 3.05 A
Biological Source:
Source Organism(s):
metagenome (Taxon ID: 256318)
Expression System(s):
Method Details:
Experimental Method:
Resolution:
3.05 Å
R-Value Free:
0.23
R-Value Work:
0.21
R-Value Observed:
0.21
Space Group:
P 31 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Glycoside hydrolase family 2
Mutagens:E553Q
Chain IDs:A, B, C
Chain Length:798
Number of Molecules:3
Biological Source:metagenome
Primary Citation

Abstact

Disulfide bonds are a key post-translational modification involved in protein folding, structural stability, and functional regulation. Here, we demonstrate that a glycoside hydrolase from the GH2 family undergoes reversible redox regulation through an intramolecular disulfide bond. The enzyme is inactive in its oxidized state and becomes active when reduced through a fully reversible process. Under oxidative conditions, multiple crystallographic and cryo-EM structures revealed a pronounced structural disorder in the active site, most prominent in the regulatory and catalytic loops, which disrupts the substrate binding site and, remarkably, the configuration of the acidic catalytic residues. Conversely, a high-resolution cryo-EM structure of the active (reduced) state unveiled a well-ordered active site with catalytic residues properly positioned for a classical Koshland retaining mechanism. This reversible order-disorder process based on a disulfide switch provides a mechanism for redox-dependent control of glycoside hydrolase activity, with potential implications for carbohydrate metabolism, microbial adaptation and biotechnological applications.

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Primary Citation of related structures
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