Structure of di-zinc MCR-1 in P41212 space group

Experimental Data Snapshot

  • Resolution: 1.75 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 

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Insights into the Mechanistic Basis of Plasmid-Mediated Colistin Resistance from Crystal Structures of the Catalytic Domain of MCR-1.

Hinchliffe, P.Yang, Q.E.Portal, E.Young, T.Li, H.Tooke, C.L.Carvalho, M.J.Paterson, N.G.Brem, J.Niumsup, P.R.Tansawai, U.Lei, L.Li, M.Shen, Z.Wang, Y.Schofield, C.J.Mulholland, A.J.Shen, J.Fey, N.Walsh, T.R.Spencer, J.

(2017) Sci Rep 7: 39392-39392

  • DOI: https://doi.org/10.1038/srep39392
  • Primary Citation of Related Structures:  
    5LRM, 5LRN

  • PubMed Abstract: 

    The polymixin colistin is a "last line" antibiotic against extensively-resistant Gram-negative bacteria. Recently, the mcr-1 gene was identified as a plasmid-mediated resistance mechanism in human and animal Enterobacteriaceae, with a wide geographical distribution and many producer strains resistant to multiple other antibiotics. mcr-1 encodes a membrane-bound enzyme catalysing phosphoethanolamine transfer onto bacterial lipid A. Here we present crystal structures revealing the MCR-1 periplasmic, catalytic domain to be a zinc metalloprotein with an alkaline phosphatase/sulphatase fold containing three disulphide bonds. One structure captures a phosphorylated form representing the first intermediate in the transfer reaction. Mutation of residues implicated in zinc or phosphoethanolamine binding, or catalytic activity, restores colistin susceptibility of recombinant E. coli. Zinc deprivation reduces colistin MICs in MCR-1-producing laboratory, environmental, animal and human E. coli. Conversely, over-expression of the disulphide isomerase DsbA increases the colistin MIC of laboratory E. coli. Preliminary density functional theory calculations on cluster models suggest a single zinc ion may be sufficient to support phosphoethanolamine transfer. These data demonstrate the importance of zinc and disulphide bonds to MCR-1 activity, suggest that assays under zinc-limiting conditions represent a route to phenotypic identification of MCR-1 producing E. coli, and identify key features of the likely catalytic mechanism.

  • Organizational Affiliation

    School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
phosphatidylethanolamine transferase Mcr-1325Escherichia coliMutation(s): 0 
Gene Names: mcr1mcr-1APZ14_31440
EC: 2.7
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
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.75 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.044α = 90
b = 49.044β = 90
c = 244.253γ = 90
Software Package:
Software NamePurpose
DIALSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMR/P007295/1

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-07
    Type: Initial release
  • Version 1.1: 2017-01-18
    Changes: Database references
  • Version 1.2: 2017-09-13
    Changes: Author supporting evidence
  • Version 1.3: 2018-01-24
    Changes: Source and taxonomy
  • Version 1.4: 2024-05-01
    Changes: Data collection, Database references, Derived calculations, Refinement description