6Z5H | pdb_00006z5h

Crystal structure of Aeromonas exotoxin A

• PDB DOI: https://doi.org/10.2210/pdb6Z5H/pdb

• Classification: TOXIN
• Organism(s): Aeromonas hydrophila
• Expression System: Escherichia coli K-12
• Mutation(s): Yes 


• Deposited: 2020-05-26 Released: 2020-06-24 
• Deposition Author(s): Masuyer, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.247 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.208 (DCC) 

Starting Model: experimental

Literature

Crystal Structure of Exotoxin A from Aeromonas Pathogenic Species.

Masuyer, G.

(2020) Toxins (Basel) 12

• PubMed: 32549399 
• DOI: https://doi.org/10.3390/toxins12060397
• Primary Citation Related Structures: 
  6Z5H


• PubMed Abstract: 
  

  Aeromonas exotoxin A (AE) is a bacterial virulence factor recently discovered in a clinical case of necrotising fasciitis caused by the flesh-eating Aeromonas hydrophila . Here, database mining shows that AE is present in the genome of several emerging Aeromonas pathogenic species. The X-ray crystal structure of AE was solved at 2.3 Å and presents all the hallmarks common to diphthamide-specific mono-ADP-ribosylating toxins, suggesting AE is a fourth member of this family alongside the diphtheria toxin, Pseudomonas exotoxin A and cholix. Structural homology indicates AE may use a similar mechanism of cytotoxicity that targets eukaryotic elongation factor 2 and thus inhibition of protein synthesis. The structure of AE also highlights unique features including a metal binding site, and a negatively charged cleft that could play a role in interdomain interactions and may affect toxicity. This study raises new opportunities to engineer alternative toxin-based molecules with pharmaceutical potential.

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Organizational Affiliation: 
• Department of Pharmacy and Pharmacology, Centre for Therapeutic Innovation, University of Bath, Bath BA2 7AY, UK.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 136.71 kDa 
• Atom Count: 9,568 
• Modeled Residue Count: 1,207 
• Deposited Residue Count: 1,256 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Exotoxin	A [auth AAA], B [auth BBB]	628	Aeromonas hydrophila	Mutation(s): 1  Gene Names: BFW41_14015

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	D [auth AAA], G [auth BBB]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
ACT	E [auth AAA]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA (Subject of Investigation/LOI)	C [auth AAA], F [auth BBB]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.247 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.208 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.371	α = 90
b = 140.215	β = 101.793
c = 96.821	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-06-24 
Deposition Author(s): Masuyer, G.

Revision History  

• Version 1.0: 2020-06-24
  Type: Initial release
  
• Version 1.1: 2020-07-01
  Changes: Database references
• Version 1.2: 2020-09-30
  Changes: Database references, Derived calculations
• Version 1.3: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary