5GRR | pdb_00005grr

Crystal structure of MCR-1

• PDB DOI: https://doi.org/10.2210/pdb5GRR/pdb

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


• Deposited: 2016-08-12 Released: 2017-01-04 
• Deposition Author(s): Ma, G., Zhu, Y., Yu, Z., Zhang, H.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.177 (Depositor), 0.187 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.161 (DCC) 
• R-Value Observed: 
  0.153 (Depositor) 

Starting Model: experimental

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

• PubMed: 28000749 
• DOI: https://doi.org/10.1038/srep39540
• Primary Citation 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.

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

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 36.56 kDa 
• Atom Count: 3,080 
• Modeled Residue Count: 323 
• Deposited Residue Count: 325 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable phosphatidylethanolamine transferase Mcr-1	A	325	Escherichia coli	Mutation(s): 0  Gene Names: mcr1, mcr-1 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	B [auth A], C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.177 (Depositor), 0.187 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.161 (DCC) 
• R-Value Observed: 0.153 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.314	α = 90
b = 62.696	β = 90
c = 104.831	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data collection
HKL-3000	data scaling
Coot	model building
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-01-04 
Deposition Author(s): Ma, G., Zhu, Y., Yu, Z., Zhang, H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31670753

Revision History  

• 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