5YLF

MCR-1 complex with D-glucose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.140 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Substrate analog interaction with MCR-1 offers insight into the rising threat of the plasmid-mediated transferable colistin resistance.

Wei, P.Song, G.Shi, M.Zhou, Y.Liu, Y.Lei, J.Chen, P.Yin, L.

(2018) FASEB J. 32: 1085-1098

  • DOI: 10.1096/fj.201700705R
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Colistin is considered a last-resort antibiotic against most gram-negative bacteria. Recent discoveries of a plasmid-mediated, transferable colistin-resistance gene (mcr-1) on all continents have heralded the imminent emergence of pan-drug-resistant ...

    Colistin is considered a last-resort antibiotic against most gram-negative bacteria. Recent discoveries of a plasmid-mediated, transferable colistin-resistance gene (mcr-1) on all continents have heralded the imminent emergence of pan-drug-resistant superbacteria. The inner-membrane protein MCR-1 can catalyze the transfer of phosphoethanolamine (PEA) to lipid A, resulting in colistin resistance. However, little is known about the mechanism, and few drugs exist to address this issue. We present crystal structures revealing the MCR-1 catalytic domain (cMCR-1) as a monozinc metalloprotein with ethanolamine (ETA) and d-glucose, respectively, thus highlighting 2 possible substrate-binding pockets in the MCR-1-catalyzed PEA transfer reaction. Mutation of the residues involved in ETA and d-glucose binding impairs colistin resistance in recombinant Escherichia coli containing full-length MCR-1. Partial analogs of the substrate are used for cocrystallization with cMCR-1, providing valuable information about the family of PEA transferases. One of the analogs, ETA, causes clear inhibition of polymyxin B resistance, highlighting its potential for drug development. These data demonstrate the crucial role of the PEA- and lipid A-binding pockets and provide novel insights into the structure-based mechanisms, important drug-target hot spots, and a drug template for further drug development to combat the urgent, rising threat of MCR-1-mediated antibiotic resistance.-Wei, P., Song, G., Shi, M., Zhou, Y., Liu, Y., Lei, J., Chen, P., Yin, L. Substrate analog interaction with MCR-1 offers insight into the rising threat of the plasmid-mediated transferable colistin resistance.


    Organizational Affiliation

    State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Probable phosphatidylethanolamine transferase Mcr-1
A
334Escherichia coliMutation(s): 0 
Gene Names: mcr1 (mcr-1)
EC: 2.7.-.-
Find proteins for A0A0R6L508 (Escherichia coli)
Go to UniProtKB:  A0A0R6L508
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
BGC
Query on BGC

Download SDF File 
Download CCD File 
A
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.140 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.750α = 90.00
b = 72.820β = 90.00
c = 82.330γ = 90.00
Software Package:
Software NamePurpose
iMOSFLMdata reduction
PHASERphasing
PHENIXrefinement
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Basic Research Program of ChinaChina2014CB910103
National Natural Science Foundation of ChinaChina31470738
National Thousand (Young) Talents ProgramChina--

Revision History 

  • Version 1.0: 2017-11-08
    Type: Initial release
  • Version 1.1: 2018-02-21
    Type: Database references
  • Version 1.2: 2018-03-07
    Type: Database references