7CB5

The 6-phosphogluconate dehydrogenase from Staphylococcus aureus (6-phosphogluconate bound)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Multi-target mode of action of silver against Staphylococcus aureus endows it with capability to combat antibiotic resistance.

Wang, H.Wang, M.Xu, X.Gao, P.Xu, Z.Zhang, Q.Li, H.Yan, A.Kao, R.Y.Sun, H.

(2021) Nat Commun 12: 3331-3331

  • DOI: https://doi.org/10.1038/s41467-021-23659-y
  • Primary Citation of Related Structures:  
    7CB0, 7CB5, 7CB6

  • PubMed Abstract: 

    The rapid emergence of drug resistant Staphylococcus aureus (S. aureus) poses a serious threat to public health globally. Silver (Ag)-based antimicrobials are promising to combat antibiotic resistant S. aureus, yet their molecular targets are largely elusive. Herein, we separate and identify 38 authentic Ag + -binding proteins in S. aureus at the whole-cell scale. We then capture the molecular snapshot on the dynamic action of Ag + against S. aureus and further validate that Ag + could inhibit a key target 6-phosphogluconate dehydrogenase through binding to catalytic His185 by X-ray crystallography. Significantly, the multi-target mode of action of Ag + (and nanosilver) endows its sustainable antimicrobial efficacy, leading to enhanced efficacy of conventional antibiotics and resensitization of MRSA to antibiotics. Our study resolves the long-standing question of the molecular targets of silver in S. aureus and offers insights into the sustainable bacterial susceptibility of silver, providing a potential approach for combating antimicrobial resistance.


  • Organizational Affiliation

    Department of Chemistry, State Key Laboratory of Synthetic Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Hong Kong S.A.R., People's Republic of China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
6-phosphogluconate dehydrogenase, decarboxylating
A, B, C, D
468Staphylococcus aureus subsp. aureus str. NewmanMutation(s): 0 
Gene Names: gndNWMN_1417
EC: 1.1.1.44
UniProt
Find proteins for A0A0H3KGN1 (Staphylococcus aureus (strain Newman))
Explore A0A0H3KGN1 
Go to UniProtKB:  A0A0H3KGN1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3KGN1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.92α = 90
b = 132.62β = 90
c = 169.85γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
xia2data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The University Grants Committee, Research Grants Council (RGC)Hong Kong1733616P
National Science Foundation (NSF, China)China21671203

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-07
    Type: Initial release
  • Version 1.1: 2021-06-23
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Refinement description