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- PDB-9nfe: Active conformation of a redox-regulated glycoside hydrolase (Cap... -

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Entry
Database: PDB / ID: 9nfe
TitleActive conformation of a redox-regulated glycoside hydrolase (CapGH2b) from the GH2 family
ComponentsGlycoside hydrolase family 2
KeywordsHYDROLASE / redox-regulation / glycosyl hydrolase / mannosidase / redox-switch / metagenome / disulfide bond
Biological speciesmetagenome (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.62 Å
AuthorsMartins, M.P. / Santos, C.R. / Dolce, L.G. / Murakami, M.T.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2021/04891-3 Brazil
Sao Paulo Research Foundation (FAPESP)2021/09793-0 Brazil
CitationJournal: Nat Commun / Year: 2026
Title: A disulfide redox switch mechanism regulates glycoside hydrolase function.
Authors: Marcele Pandeló Martins / Gustavo Henrique Martins / Felipe Jun Fuzita / João Paulo Menezes Spadeto / Renan Yuji Miyamoto / Felippe Mariano Colombari / Fabiane Stoffel / Luciano Graciani ...Authors: Marcele Pandeló Martins / Gustavo Henrique Martins / Felipe Jun Fuzita / João Paulo Menezes Spadeto / Renan Yuji Miyamoto / Felippe Mariano Colombari / Fabiane Stoffel / Luciano Graciani Dolce / Camila Ramos Dos Santos / Rodrigo Silva Araujo Streit / Antônio Carlos Borges / Rafael Henrique Galinari / Yoshihisa Yoshimi / Paul Dupree / Gabriela Felix Persinoti / Mariana Abrahão Bueno Morais / Mario Tyago Murakami /
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 ...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.
History
DepositionFeb 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycoside hydrolase family 2
B: Glycoside hydrolase family 2
C: Glycoside hydrolase family 2


Theoretical massNumber of molelcules
Total (without water)272,4503
Polymers272,4503
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Glycoside hydrolase family 2


Mass: 90816.594 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: beta-mannosidase
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: glycoside hydrolase from the GH2 family / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: metagenome (others)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2800 nm / Nominal defocus min: 1800 nm
Image recordingElectron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 109636 / Symmetry type: POINT
RefinementHighest resolution: 2.62 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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