7YJT | pdb_00007yjt

Crystal structure of MCR-1-S treated by aurothioglucose

• PDB DOI: https://doi.org/10.2210/pdb7YJT/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-07-20 Released: 2023-02-01 
• Deposition Author(s): Zhang, Q., Sun, H., Wang, M.
• Funding Organization(s): The University Grants Committee, Research Grants Council (RGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.254 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.193 (Depositor) 
• R-Value Observed: 
  0.196 (Depositor) 

Literature

Gold drugs as colistin adjuvants in the fight against MCR-1 producing bacteria.

Zhang, Q., Wang, M., Hu, X., Yan, A., Ho, P.L., Li, H., Sun, H.

(2023) J Biol Inorg Chem 28: 225-234

• PubMed: 36662362 
• DOI: https://doi.org/10.1007/s00775-022-01983-y
• Primary Citation Related Structures: 
  7YJP, 7YJQ, 7YJR, 7YJS, 7YJT


• PubMed Abstract: 
  

  The emergence and rapid spread of the mobile colistin resistance gene mcr-1 among bacterial species and hosts significantly challenge the efficacy of "last-line" antibiotic colistin. Previously, we reported silver nitrate and auranofin serve as colistin adjuvants for combating mcr-1-positive bacteria. Herein, we uncovered more gold-based drugs and nanoparticles, and found that they exhibited varying degree of synergisms with colistin on killing mcr-1-positive bacteria. However, pre-activation of the drugs by either glutathione or N-acetyl cysteine, thus releasing and accumulating gold ions, is perquisite for their abilities to substitute zinc cofactor from MCR-1 enzyme. X-ray crystallography and biophysical studies further supported the proposed mechanism. This study not only provides basis for combining gold-based drugs and colistin for combating mcr-1-positive bacterial infections, but also undoubtedly opens a new horizon for metabolism details of gold-based drugs in overcoming antimicrobial resistance.

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Organizational Affiliation: 
• Department of Chemistry and CAS-HKU Joint Laboratory of Metallomics On Health and Environment, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China.
School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China.
School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China.
Carol Yu Centre for Infection, The University of Hong Kong, Sassoon Road, Hong Kong SAR, China.
Department of Microbiology, The University of Hong Kong, Sassoon Road, Hong Kong SAR, China.
Department of Chemistry and CAS-HKU Joint Laboratory of Metallomics On Health and Environment, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China. [e-mail].
Department of Chemistry and CAS-HKU Joint Laboratory of Metallomics On Health and Environment, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 74.86 kDa 
• Atom Count: 5,174 
• Modeled Residue Count: 646 
• Deposited Residue Count: 672 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable phosphatidylethanolamine transferase Mcr-1	A, B	336	Escherichia coli	Mutation(s): 0  Gene Names: mcr1, mcr-1, APZ14_31440 EC: 2.7 (PDB Primary Data), 2.7.8.43 (UniProt)
UniProt
Find proteins for A0A0R6L508 (Escherichia coli) Explore A0A0R6L508  Go to UniProtKB:  A0A0R6L508

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AU (Subject of Investigation/LOI)	C [auth A], D [auth B]	GOLD ION Au ZBKIUFWVEIBQRT-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	A, B	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.254 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.193 (Depositor) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.23	α = 90
b = 84.614	β = 98.6
c = 81.901	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data scaling
PHENIX	phasing
autoPROC	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-02-01 
Deposition Author(s): Zhang, Q., Sun, H., Wang, M.

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Funding Organization	Location	Grant Number
The University Grants Committee, Research Grants Council (RGC)	Hong Kong	R7070-18

Revision History  

• Version 1.0: 2023-02-01
  Type: Initial release
  
• Version 1.1: 2023-03-15
  Changes: Database references
• Version 1.2: 2024-10-09
  Changes: Data collection, Structure summary