7WAA

Crystal structure of MCR-1-S treated by AgNO3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Re-sensitization of mcr carrying multidrug resistant bacteria to colistin by silver.

Zhang, Q.Wang, R.Wang, M.Liu, C.Koohi-Moghadam, M.Wang, H.Ho, P.L.Li, H.Sun, H.

(2022) Proc Natl Acad Sci U S A 119: e2119417119-e2119417119

  • DOI: https://doi.org/10.1073/pnas.2119417119
  • Primary Citation of Related Structures:  
    7WAA

  • PubMed Abstract: 

    Colistin is considered the last-line antimicrobial for the treatment of multidrug-resistant gram-negative bacterial infections. The emergence and spread of superbugs carrying the mobile colistin resistance gene ( mcr ) have become the most serious and urgent threat to healthcare. Here, we discover that silver (Ag + ), including silver nanoparticles, could restore colistin efficacy against mcr -positive bacteria. We show that Ag + inhibits the activity of the MCR-1 enzyme via substitution of Zn 2+ in the active site. Unexpectedly, a tetra-silver center was found in the active-site pocket of MCR-1 as revealed by the X-ray structure of the Ag-bound MCR-1, resulting in the prevention of substrate binding. Moreover, Ag + effectively slows down the development of higher-level resistance and reduces mutation frequency. Importantly, the combined use of Ag + at a low concentration with colistin could relieve dermonecrotic lesions and reduce the bacterial load of mice infected with mcr -1–carrying pathogens. This study depicts a mechanism of Ag + inhibition of MCR enzymes and demonstrates the potentials of Ag + as broad-spectrum inhibitors for the treatment of mcr -positive bacterial infection in combination with colistin.


  • Organizational Affiliation

    Department of Chemistry, State Key Laboratory of Synthetic Chemistry, and CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Hong Kong SAR, 999077, People's Republic of China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable phosphatidylethanolamine transferase Mcr-1
A, B
336Escherichia coliMutation(s): 0 
Gene Names: mcr1mcr-1APZ14_31440
EC: 2.7
UniProt
Find proteins for A0A0R6L508 (Escherichia coli)
Explore A0A0R6L508 
Go to UniProtKB:  A0A0R6L508
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0R6L508
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AG (Subject of Investigation/LOI)
Query on AG

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B]
SILVER ION
Ag
FOIXSVOLVBLSDH-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
A, B
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.2α = 90
b = 84.42β = 98.67
c = 81.76γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-16
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Data collection, Structure summary