9GCO | pdb_00009gco

Xenorhabdus bovienii Thioredoxin complex with Rhs toxin TreX and immunity protein TriX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.223 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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

  • 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.


  • Organizational Affiliation
    • Bacterial Genetics and Physiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Gosselies, Belgium.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thioredoxin
A, D
115Xenorhabdus bovienii SS-2004Mutation(s): 0 
Gene Names: trxAXBJ1_4182
UniProt
Find proteins for D3V6L5 (Xenorhabdus bovienii (strain SS-2004))
Explore D3V6L5 
Go to UniProtKB:  D3V6L5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD3V6L5
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Toxin TreX
B, E
140Xenorhabdus bovienii SS-2004Mutation(s): 0 
Gene Names: XBJ1_1305
UniProt
Find proteins for D3UXR3 (Xenorhabdus bovienii (strain SS-2004))
Explore D3UXR3 
Go to UniProtKB:  D3UXR3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD3UXR3
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Immunity Protein TriX
C, F
142Xenorhabdus bovienii SS-2004Mutation(s): 0 
Gene Names: XBJ1_1304
UniProt
Find proteins for D3UXR2 (Xenorhabdus bovienii (strain SS-2004))
Explore D3UXR2 
Go to UniProtKB:  D3UXR2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD3UXR2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download Ideal Coordinates CCD File 
H [auth B],
M [auth E]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
G [auth A]
I [auth B]
J [auth C]
K [auth C]
L [auth D]
G [auth A],
I [auth B],
J [auth C],
K [auth C],
L [auth D],
N [auth F],
O [auth F]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.223 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.955α = 90
b = 82.353β = 90
c = 121.607γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Fonds National de la Recherche Scientifique (FNRS)BelgiumF4526.23

Revision History  (Full details and data files)

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