6A83

Crystal structure of the C-terminal periplasmic domain of EcEptC from Escherichia coli complex with Zn


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural and mechanistic insights into polymyxin resistance mediated by EptC originating from Escherichia coli.

Zhao, Y.Meng, Q.Lai, Y.Wang, L.Zhou, D.Dou, C.Gu, Y.Nie, C.Wei, Y.Cheng, W.

(2019) FEBS J 286: 750-764

  • DOI: https://doi.org/10.1111/febs.14719
  • Primary Citation of Related Structures:  
    6A82, 6A83

  • PubMed Abstract: 

    Gram-negative bacteria defend against the toxicity of polymyxins by modifying their outer membrane lipopolysaccharide (LPS). This modification mainly occurs through the addition of cationic molecules such as phosphoethanolamine (PEA). EcEptC is a PEA transferase from Escherichia coli (E. coli). However, unlike its homologs CjEptC (Campylobacter jejuni) and MCR-1, EcEptC is unable to mediate polymyxin resistance when overexpressed in E. coli. Here, we report crystal structures of the C-terminal putative catalytic domain (EcEptCΔN, 205-577 aa) of EcEptC in apo and Zn 2+ -bound states at 2.10 and 2.60 Å, respectively. EcEptCΔN is arranged into an α-β-α fold and equipped with the zinc ion in a conserved mode. Coupled with isothermal titration calorimetry (ITC) data, we provide insights into the mechanism by which EcEptC recognizes Zn 2+ . Furthermore, structure comparison analysis indicated that disulfide bonds, which play a key role in polymyxin resistance, were absent in EcEptCΔN. Supported by structural and biochemical evidence, we reveal mechanistic implications for disulfide bonds in PEA transferase-mediated polymyxin resistance. Significantly, because the structural effects exhibited by disulfide bonds are absent in EcEptC, it is impossible for this protein to participate in polymyxin resistance in E. coli. DATABASE: Structural data are available in the PDB under the accession numbers 6A82 and 6A83. ENZYME: EC 2.7.8.43.


  • Organizational Affiliation

    Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphoethanolamine transferase EptC394Escherichia coli K-12Mutation(s): 0 
Gene Names: eptCcptAyijPb3955JW3927
EC: 2.7
UniProt
Find proteins for P0CB39 (Escherichia coli (strain K12))
Explore P0CB39 
Go to UniProtKB:  P0CB39
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CB39
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.568α = 90
b = 103.568β = 90
c = 122.294γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31570842

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-26
    Type: Initial release
  • Version 1.1: 2019-03-06
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description