SpNOX dehydrogenase domain, mutant F397W in complex with Flavin adenine dinucleotide (FAD)

Experimental Data Snapshot

  • Resolution: 1.94 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

Starting Model: in silico
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Ligand Structure Quality Assessment 

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X-ray structure and enzymatic study of a bacterial NADPH oxidase highlight the activation mechanism of eukaryotic NOX.

Petit-Hartlein, I.Vermot, A.Thepaut, M.Humm, A.S.Dupeux, F.Dupuy, J.Chaptal, V.Marquez, J.A.Smith, S.M.E.Fieschi, F.

(2024) Elife 13

  • DOI: https://doi.org/10.7554/eLife.93759
  • Primary Citation of Related Structures:  
    8QQ1, 8QQ5, 8QQ7

  • PubMed Abstract: 

    NADPH oxidases (NOX) are transmembrane proteins, widely spread in eukaryotes and prokaryotes, that produce reactive oxygen species (ROS). Eukaryotes use the ROS products for innate immune defense and signaling in critical (patho)physiological processes. Despite the recent structures of human NOX isoforms, the activation of electron transfer remains incompletely understood. SpNOX, a homolog from Streptococcus pneumoniae , can serves as a robust model for exploring electron transfers in the NOX family thanks to its constitutive activity. Crystal structures of SpNOX full-length and dehydrogenase (DH) domain constructs are revealed here. The isolated DH domain acts as a flavin reductase, and both constructs use either NADPH or NADH as substrate. Our findings suggest that hydride transfer from NAD(P)H to FAD is the rate-limiting step in electron transfer. We identify significance of F397 in nicotinamide access to flavin isoalloxazine and confirm flavin binding contributions from both DH and Transmembrane (TM) domains. Comparison with related enzymes suggests that distal access to heme may influence the final electron acceptor, while the relative position of DH and TM does not necessarily correlate with activity, contrary to previous suggestions. It rather suggests requirement of an internal rearrangement, within the DH domain, to switch from a resting to an active state. Thus, SpNOX appears to be a good model of active NOX2, which allows us to propose an explanation for NOX2's requirement for activation.

  • Organizational Affiliation

    Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
OxidoreductaseA [auth C],
B [auth F],
C [auth G]
221Streptococcus pneumoniaeMutation(s): 1 
Gene Names: ndoR
Find proteins for A0A4J2B4U9 (Streptococcus pneumoniae)
Explore A0A4J2B4U9 
Go to UniProtKB:  A0A4J2B4U9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4J2B4U9
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
D [auth C],
M [auth F],
X [auth G]
C27 H33 N9 O15 P2
Query on BR

Download Ideal Coordinates CCD File 
AA [auth G]
BA [auth G]
CA [auth G]
DA [auth G]
E [auth C]
AA [auth G],
BA [auth G],
CA [auth G],
DA [auth G],
E [auth C],
EA [auth G],
F [auth C],
FA [auth G],
G [auth C],
H [auth C],
I [auth C],
J [auth C],
K [auth C],
L [auth C],
N [auth F],
O [auth F],
P [auth F],
Q [auth F],
R [auth F],
S [auth F],
T [auth F],
U [auth F],
V [auth F],
W [auth F],
Y [auth G],
Z [auth G]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.94 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.622α = 90
b = 104.622β = 90
c = 142.688γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
Aimlessdata scaling
autoPROCdata processing
Cootmodel building
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-17-CE11-0013
Other governmentEmergence Program from University Grenoble Alpes
iNEXT-DiscoveryEuropean Union871037

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-08
    Type: Initial release