6PIK

Tetrameric cryo-EM ArnA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.80 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:  
    6PIH, 6PIK

  • 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 its deletion abolishes the polymyxin resistance of gram-negative bacteria ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bifunctional polymyxin resistance protein ArnAA, B, C, D300Escherichia coli DH5[alpha]Mutation(s): 0 
Gene Names: arnAEIT12_05710
EC: 2.1.2.13 (PDB Primary Data), 1.1.1.305 (PDB Primary Data)
UniProt
Find proteins for P77398 (Escherichia coli (strain K12))
Explore P77398 
Go to UniProtKB:  P77398
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
UDP-4-amino-4-deoxy-L-arabinose formyltransferaseE, F, G, H345Escherichia coli DH5[alpha]Mutation(s): 0 
Gene Names: arnABvCmsC61A_03676
EC: 2.1.2.13 (UniProt), 1.1.1.305 (UniProt)
UniProt
Find proteins for P77398 (Escherichia coli (strain K12))
Explore P77398 
Go to UniProtKB:  P77398
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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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  (Full details and data files)

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