5GRR

Crystal structure of MCR-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.153 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

High resolution crystal structure of the catalytic domain of MCR-1

Ma, G.Zhu, Y.Yu, Z.Ahmad, A.Zhang, H.

(2016) Sci Rep 6: 39540-39540

  • DOI: https://doi.org/10.1038/srep39540
  • Primary Citation of Related Structures:  
    5GRR

  • PubMed Abstract: 

    The newly identified mobile colistin resistant gene (mcr-1) rapidly spread among different bacterial strains and confers colistin resistance to its host, which has become a global concern. Based on sequence alignment, MCR-1 should be a phosphoethanolamine transferase, members of the YhjW/YjdB/YijP superfamily and catalyze the addition of phosphoethanolamine to lipid A, which needs to be validated experimentally. Here we report the first high-resolution crystal structure of the C-terminal catalytic domain of MCR-1 (MCR-1C) in its native state. The active pocket of native MCR-1C depicts unphosphorylated nucleophilic residue Thr285 in coordination with two Zinc ions and water molecules. A flexible adjacent active site loop (aa: Lys348-365) pose an open conformation compared to its structural homologues, suggesting of an open substrate entry channel. Taken together, this structure sets ground for further study of substrate binding and MCR-1 catalytic mechanism in development of potential therapeutic agents.


  • Organizational Affiliation

    Department of Biology and Shenzhen Key Laboratory of Cell Microenvironment, Southern University of Science and Technology, Shenzhen 518055, China.


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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.153 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.314α = 90
b = 62.696β = 90
c = 104.831γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data collection
HKL-3000data scaling
Cootmodel building
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31670753

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-04
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.2: 2024-11-13
    Changes: Structure summary