9NPN | pdb_00009npn

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 
    0.276 (Depositor), 0.277 (DCC) 
  • R-Value Work: 
    0.245 (Depositor), 0.246 (DCC) 
  • R-Value Observed: 
    0.247 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9NPN

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 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.

Macromolecule Content 

  • Total Structure Weight: 547.26 kDa 
  • Atom Count: 35,009 
  • Modeled Residue Count: 4,312 
  • Deposited Residue Count: 4,788 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glycoside hydrolase family 2
A, B, C, D, E
A, B, C, D, E, F
798metagenomeMutation(s): 0 
EC: 3.2.1.25

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4

Query on PO4



Download:Ideal Coordinates CCD File
AA [auth E]
BA [auth E]
CA [auth E]
DA [auth E]
G [auth A]
AA [auth E],
BA [auth E],
CA [auth E],
DA [auth E],
G [auth A],
H [auth A],
HA [auth F],
I [auth A],
IA [auth F],
JA [auth F],
L [auth B],
M [auth B],
O [auth C],
P [auth C],
Q [auth C],
R [auth C],
S [auth C],
T [auth C],
V [auth D],
W [auth D],
X [auth D],
Y [auth D]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO

Query on EDO



Download:Ideal Coordinates CCD File
EA [auth E]
FA [auth E]
GA [auth E]
J [auth A]
K [auth A]
EA [auth E],
FA [auth E],
GA [auth E],
J [auth A],
K [auth A],
KA [auth F],
LA [auth F],
N [auth B],
U [auth C],
Z [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free:  0.276 (Depositor), 0.277 (DCC) 
  • R-Value Work:  0.245 (Depositor), 0.246 (DCC) 
  • R-Value Observed: 0.247 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.278α = 89.13
b = 123.715β = 117.56
c = 133.041γ = 103.51
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
XDSdata reduction
PHASERphasing

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
Sao Paulo Research Foundation (FAPESP)Brazil2022/06298-0

Revision History  (Full details and data files)

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