9NFE | pdb_00009nfe

Active conformation of a redox-regulated glycoside hydrolase (CapGH2b) from the GH2 family


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.62 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A disulfide redox switch mechanism regulates glycoside hydrolase function.

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.

(2026) Nat Commun 17: 45-45

  • DOI: https://doi.org/10.1038/s41467-025-67225-2
  • Primary Citation of Related Structures:  
    9NFE, 9NP8, 9NP9, 9NPA, 9NPB, 9NPC, 9NPD, 9NPE, 9NPF, 9NPL, 9NPN

  • 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.


  • Organizational Affiliation
    • Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, Brazil.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycoside hydrolase family 2
A, B, C
798metagenomeMutation(s): 0 
EC: 3.2.1.25
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.62 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil2021/04891-3
Sao Paulo Research Foundation (FAPESP)Brazil2021/09793-0

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-12
    Type: Initial release
  • Version 1.1: 2026-01-21
    Changes: Data collection, Database references