6PIK

Tetrameric cryo-EM ArnA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Cryo-electron microscopy structures of ArnA, a key enzyme for polymyxin resistance, revealed unexpected oligomerizations and domain movements.

Yang, M.Chen, Y.S.Ichikawa, M.Calles-Garcia, D.Basu, K.Fakih, R.Bui, K.H.Gehring, K.

(2019) J.Struct.Biol. 208: 43-50

  • DOI: 10.1016/j.jsb.2019.07.009
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Gram-negative bacteria evade the attack of cationic antimicrobial peptides through modifying their lipid A structure in their outer membranes with 4-amino-4-deoxy-L-arabinose (Ara4N). ArnA is a crucial enzyme in the lipid A modification pathway and i ...

    Gram-negative bacteria evade the attack of cationic antimicrobial peptides through modifying their lipid A structure in their outer membranes with 4-amino-4-deoxy-L-arabinose (Ara4N). ArnA is a crucial enzyme in the lipid A modification pathway and its deletion abolishes the polymyxin resistance of gram-negative bacteria. Previous studies by X-ray crystallography have shown that full-length ArnA forms a three-bladed propeller-shaped hexamer. Here, the structures of ArnA determined by cryo-electron microscopy (cryo-EM) reveal that ArnA exists in two 3D architectures, hexamer and tetramer. This is the first observation of a tetrameric ArnA. The hexameric cryo-EM structure is similar to previous crystal structures but shows differences in domain movements and conformational changes. We propose that ArnA oligomeric states are in a dynamic equilibrium, where the hexamer state is energetically more favorable, and its domain movements are important for cooperating with downstream enzymes in the lipid A-Ara4N modification pathway. The results provide us with new possibilities to explore inhibitors targeting ArnA.


    Organizational Affiliation

    Department of Biochemistry & Centre for Structural Biology, McGill University, Montreal, QC H3G 0B1, Canada. Electronic address: kalle.gehring@mcgill.ca.,Department of Anatomy and Cell Biology, McGill University, Montreal, QC H3A 0C7, Canada.,Department of Biochemistry & Centre for Structural Biology, McGill University, Montreal, QC H3G 0B1, Canada.,Department of Biochemistry & Centre for Structural Biology, McGill University, Montreal, QC H3G 0B1, Canada. Electronic address: meng.yang@mcgill.ca.,Facility for Electron Microscopy Research, McGill University, Montreal, QC H3A 0C7, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bifunctional polymyxin resistance protein ArnA
A, B, C, D
300Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: arnA (pmrI, yfbG)
Find proteins for P77398 (Escherichia coli (strain K12))
Go to UniProtKB:  P77398
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
UDP-4-amino-4-deoxy-L-arabinose formyltransferase
E, F, G, H
345Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: arnA (pmrI, yfbG)
Find proteins for P77398 (Escherichia coli (strain K12))
Go to UniProtKB:  P77398
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-06-26 
  • Released Date: 2019-07-31 
  • Deposition Author(s): Yang, M., Gehring, K.

Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada152569

Revision History 

  • Version 1.0: 2019-07-31
    Type: Initial release
  • Version 1.1: 2019-08-07
    Type: Data collection, Database references
  • Version 1.2: 2019-10-02
    Type: Data collection, Database references
  • Version 1.3: 2020-01-15
    Type: Author supporting evidence