9NPN

Crystal structure of the inactive conformation of a glycoside hydrolase (CapGH2b - E465A Mutant) from the GH2 family in the space group P1 at 3.1 A

Summary for 9NPN

• Entry DOI: 10.2210/pdb9npn/pdb
• Descriptor: Glycoside hydrolase family 2, PHOSPHATE ION, 1,2-ETHANEDIOL, ... (4 entities in total)
• Functional Keywords: redox-regulation, glycosyl hydrolase, mannosidase, redox-switch, metagenome, disulfide bond, hydrolase
• Biological source: metagenome
• Total number of polymer chains: 6
• Total formula weight: 547261.37

Authors

Martins, M.P.,Spadeto, J.P.M.,Miyamoto, R.Y.,Morais, M.A.B.,Murakami, M.T. (deposition date: 2025-03-11, release date: 2025-11-12, Last modification date: 2026-01-21)

Primary citation

Martins, M.P.,Martins, G.H.,Fuzita, F.J.,Spadeto, J.P.M.,Miyamoto, R.Y.,Colombari, F.M.,Stoffel, F.,Dolce, L.G.,Santos, C.R.D.,Streit, R.S.A.,Borges, A.C.,Galinari, R.H.,Yoshimi, Y.,Dupree, P.,Persinoti, G.F.,Morais, M.A.B.,Murakami, M.T.
A disulfide redox switch mechanism regulates glycoside hydrolase function.
Nat Commun, 17:45-45, 2026

PubMed Abstract: 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.

PubMed: 41491304
DOI: 10.1038/s41467-025-67225-2

Experimental method

X-RAY DIFFRACTION (3.1 Å)