9W8G | pdb_00009w8g

Crystal structure of Staphylococcus aureus cysteine-free ScdA with bound iron, determined by molecular replacement and Fe anomalous signal


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 
    0.238 (Depositor), 0.238 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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Literature

Structure and Nitrite Reductase Activity of the Di-iron Protein ScdA in Staphylococcus aureus.

Chen, H.Y.Tsai, R.F.Lu, Y.S.Cheng, Y.C.Fan-Chiang, H.Y.Wu, C.Y.Lo, F.C.Kuo, H.W.Yang, W.K.Liao, W.Y.Hu, N.J.Sue, S.C.Chiang, Y.W.

(2025) J Am Chem Soc 147: 31558-31569

  • DOI: https://doi.org/10.1021/jacs.5c05573
  • Primary Citation of Related Structures:  
    9J47, 9W8G

  • PubMed Abstract: 

    Pathogenic Staphylococcus aureus endures bursts of host-derived reactive nitrogen species, yet the molecular defenses that enable this resilience have remained unclear. We now show that the previously enigmatic di-iron enzyme ScdA functions as a nitrite reductase, converting nitrite to nitric oxide (NO), and we elucidate the structural elements that support this activity. Using an integrative toolkit─X-ray crystallography, solution NMR, AlphaFold modeling, and pulsed EPR/DEER─we solved the full-length homodimeric structure of ScdA and identified a robust di-iron center that forms stable iron-nitrosyl intermediates. Targeted mutagenesis reveals that redox-active cysteines and dimerization state tune catalytic output, whereas steady-state kinetics confirm efficient nitrite-to-NO turnover. In vivo, ScdA overexpression in Escherichia coli suppresses growth under nitrite-rich conditions, highlighting the cytotoxic potency of the NO it generates. By coupling structure to function, our work clarifies S. aureus strategies for managing nitrosylative stress and points to ScdA as a potential vulnerability in antibiotic-resistant pathogens.


  • Organizational Affiliation
    • Department of Chemistry, National Tsing Hua University, Hsinchu 300-044, Taiwan.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Iron-sulfur cluster repair protein ScdA
A, B
224Staphylococcus aureusMutation(s): 3 
Gene Names: scdASAUSA300_0253
UniProt
Find proteins for P72360 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore P72360 
Go to UniProtKB:  P72360
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP72360
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
I [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
FE (Subject of Investigation/LOI)
Query on FE

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
F [auth B],
G [auth B]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
O (Subject of Investigation/LOI)
Query on O

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
OXYGEN ATOM
O
XLYOFNOQVPJJNP-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free:  0.238 (Depositor), 0.238 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.02α = 90
b = 92.535β = 90
c = 110.921γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2025-09-17 
  • Deposition Author(s): Yang, W.K.

Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, Taiwan)Taiwan--

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-17
    Type: Initial release