6IO4

Silver-bound Glyceraldehyde-3-phosphate dehydrogenase A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.178 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Antimicrobial silver targets glyceraldehyde-3-phosphate dehydrogenase in glycolysis ofE. coli.

Wang, H.Wang, M.Yang, X.Xu, X.Hao, Q.Yan, A.Hu, M.Lobinski, R.Li, H.Sun, H.

(2019) Chem Sci 10: 7193-7199

  • DOI: 10.1039/c9sc02032b
  • Primary Citation of Related Structures:  
    6IO4, 6IO6, 6IOJ

  • PubMed Abstract: 
  • Silver has long been used as an antibacterial agent, yet its molecular targets remain largely unknown. Using a custom-designed coupling of gel electrophoresis with inductively coupled plasma mass spectrometry (GE-ICP-MS), we identified six silver-binding proteins in E ...

    Silver has long been used as an antibacterial agent, yet its molecular targets remain largely unknown. Using a custom-designed coupling of gel electrophoresis with inductively coupled plasma mass spectrometry (GE-ICP-MS), we identified six silver-binding proteins in E. coli . The majority of the identified proteins are associated with the central carbon metabolism of E. coli . Among them, we unveil that GAPDH, an essential enzyme in glycolysis, serves as a vital target of Ag + in E. coli for the first time. We demonstrate that silver inhibits the enzymatic function of GAPDH through targeting Cys149 in its catalytic site. The X-ray structure reveals that Ag + coordinates to Cys149 and His176 with a quasi-linear geometry (S-Ag-N angle of 157°). And unexpectedly, two Ag + ions coordinate to Cys288 in the non-catalytic site with weak argentophilic interaction (Ag···Ag distance of 2.9 Å). This is the first report on antimicrobial Ag + targeting a key enzyme in the glycolytic pathway of E. coli . The findings expand our knowledge on the mode of action and bio-coordination chemistry of silver, particularly silver-targeting residues in proteins at the atomic level.


    Organizational Affiliation

    Department of Chemistry , The University of Hong Kong , Hong Kong , P. R. China . Email: hsun@hku.hk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glyceraldehyde-3-phosphate dehydrogenase A
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
329Escherichia coli K-12Mutation(s): 1 
Gene Names: gapAb1779JW1768
EC: 1.2.1.12
UniProt
Find proteins for P0A9B2 (Escherichia coli (strain K12))
Explore P0A9B2 
Go to UniProtKB:  P0A9B2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A9B2
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.178 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.991α = 87.66
b = 110.019β = 86.94
c = 139.712γ = 87.26
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
xia2data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The University Grants Committee, Research Grants Council (RGC)Hong Kong17305415P

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-03
    Type: Initial release
  • Version 1.1: 2019-08-14
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-20
    Changes: Database references