8S2N | pdb_00008s2n

Xenorhabdus bovienii Rhs toxin TreTu complex with TrxA and TriTu immunity protein

• PDB DOI: https://doi.org/10.2210/pdb8S2N/pdb

• Classification: TOXIN
• Organism(s): Xenorhabdus bovienii SS-2004, Escherichia coli str. K-12 substr. MG1655
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-02-18 Released: 2024-12-04 
• Deposition Author(s): Jurenas, D., Terradot, L.
• Funding Organization(s): Fonds National de la Recherche Scientifique (FNRS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 
  0.232 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Models: experimental, in silico

Literature

Thioredoxin 1 moonlights as a chaperone for an interbacterial ADP-ribosyltransferase toxin.

Dumont, B., Terradot, L., Cascales, E., Van Melderen, L., Jurenas, D.

(2024) Nat Commun 15: 10388-10388

• PubMed: 39613764 
• DOI: https://doi.org/10.1038/s41467-024-54892-w
• Primary Citation of Related Structures:  
  8S2M, 8S2N, 9GCO


• PubMed Abstract: 
  

  Formation and breakage of disulfide bridges strongly impacts folding and activity of proteins. Thioredoxin 1 (TrxA) is a small, conserved enzyme that reduces disulfide bonds in the bacterial cytosol. In this study, we provide an example of the emergence of a chaperone role for TrxA, which is independent of redox catalysis. We show that the activity of the secreted bacterial ADP-ribosyltransferase (ART) toxin TreX, which does not contain any cysteines, is dependent on TrxA. TreX binds to the reduced form of TrxA via its carboxy-terminal extension to form a soluble and active complex. Structural studies revealed that TreX-like toxins are homologous to Scabin-like ART toxins which possess cysteine residues and form disulfide bridges at the position that superimposes the TrxA binding site in TreX. Our study therefore suggests that thioredoxin 1 evolved alternative functions by maintaining the interaction with cysteine-free substrates.

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Organizational Affiliation: 
• Bacterial Genetics and Physiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Gosselies, Belgium.
Unité Biodiversité et Amélioration des Plantes et Forêts, Centre Wallon de Recherches Agronomiques (CRA-W), Bâtiment Emile Marchal, Gembloux, Belgium.
Laboratory of Molecular Microbiology and Structural Biochemistry, Institut de Biologie et Chimie des Protéines (IBCP), Université de Lyon, Lyon, France.
Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie de la Méditerranée (IMM), Aix-Marseille Université, Marseille, France.
Bacterial Genetics and Physiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Gosselies, Belgium. [e-mail].
Bacterial Genetics and Physiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Gosselies, Belgium. [e-mail].
WEL Research Institute, Wavre, Belgique. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 44.27 kDa 
• Atom Count: 3,019 
• Modeled Residue Count: 372 
• Deposited Residue Count: 393 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunity Protein TriX	A	142	Xenorhabdus bovienii SS-2004	Mutation(s): 0  Gene Names: XBJ1_1304
UniProt
Find proteins for D3UXR2 (Xenorhabdus bovienii (strain SS-2004)) Explore D3UXR2  Go to UniProtKB:  D3UXR2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Complete genome segment 11/17	B	140	Xenorhabdus bovienii SS-2004	Mutation(s): 0  Gene Names: XBJ1_1305
UniProt
Find proteins for D3UXR3 (Xenorhabdus bovienii (strain SS-2004)) Explore D3UXR3  Go to UniProtKB:  D3UXR3

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioredoxin 1	C	111	Escherichia coli str. K-12 substr. MG1655	Mutation(s): 0  Gene Names: trxA, fipA, tsnC, b3781, JW5856
UniProt
Find proteins for P0AA25 (Escherichia coli (strain K12)) Explore P0AA25  Go to UniProtKB:  P0AA25

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	D [auth A], E [auth A], F [auth C]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	G [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free:  0.232 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.6	α = 90
b = 74.6	β = 90
c = 190.703	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
XDS	data reduction
Aimless	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-04 
Deposition Author(s): Jurenas, D., Terradot, L.

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Funding Organization	Location	Grant Number
Fonds National de la Recherche Scientifique (FNRS)	Belgium	F4526.23

Revision History  

• Version 1.0: 2024-12-04
  Type: Initial release
  
• Version 1.1: 2024-12-11
  Changes: Database references