9RO8 | pdb_00009ro8

Pantoea ananatis encodes an antibacterial and anti-eukaryotic human CD38 homologue T6SS ADP-ribosyl cyclase polymorphic toxin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 
    0.216 (Depositor), 0.216 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 
    0.185 (Depositor) 

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

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This is version 1.2 of the entry. See complete history

Literature

Widespread deployment of the human CD38 ADP-ribosyl cyclase fold in antibacterial and anti-eukaryotic polymorphic toxins.

Martinkus, J.Terradot, L.Jurenas, D.Cascales, E.

(2025) J Biological Chem 301: 110775-110775

  • DOI: https://doi.org/10.1016/j.jbc.2025.110775
  • Primary Citation Related Structures: 
    9RO8

  • PubMed Abstract: 

    Bacterial polymorphic toxins are modular weapons that mediate inter-microbial competition and host interactions by delivering diverse cytotoxic domains through specialized secretion systems. Here, we identify and characterize a novel toxin domain in Pantoea ananatis that displays remarkable structural and functional conservation with the human enzyme CD38. This bacterial toxin, fused to a type VI secretion system (T6SS) PAAR domain, harbors a C-terminal ADP-ribosyl cyclase (ARC) domain that hydrolyzes NAD + and NADP + in vitro and in vivo, leading to growth inhibition in both bacterial and eukaryotic cells. The 1.6-Å resolution structure of ARC reveals that it adopts a globular fold nearly identical to the human CD38 ADP ribosyl cyclase, with key catalytic residues conserved. Comparative genomics reveals that CD38-like ARC domains are widespread in bacteria, fused to diverse delivery modules including T6SS, T7SS, and CDI systems. Functional assays demonstrate that these domains act as NAD-depleting toxins, with cross-immunity observed between non-cognate toxin-immunity pairs. Taken together, our findings identify a bacterial NAD + hydrolase fold with strong similarity to human CD38 and define a novel class of metabolic toxins, expanding the functional scope of polymorphic effectors and illustrating how enzymes can be co-opted for microbial warfare.


  • Organizational Affiliation
    • Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Aix-Marseille Université, CNRS, UMR 7255, Marseille, France.

Macromolecule Content 

  • Total Structure Weight: 32.85 kDa 
  • Atom Count: 2,308 
  • Modeled Residue Count: 258 
  • Deposited Residue Count: 298 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ADP-ribosylcyclase toxin
A, B
149Pantoea ananatis LMG 20103Mutation(s): 0 
Gene Names: PANA_2924
UniProt
Find proteins for D4GKQ2 (Pantoea ananatis (strain LMG 20103))
Explore D4GKQ2 
Go to UniProtKB:  D4GKQ2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD4GKQ2
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free:  0.216 (Depositor), 0.216 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 0.185 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.23α = 90
b = 70.213β = 90
c = 96.119γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Fonds National de la Recherche Scientifique (FNRS)BelgiumFNRS-MIS F4526.23
Walloon Excellence in Lifesciences & BIOtechnology (WELBIO)BelgiumSTG-X.251
Agence Nationale de la Recherche (ANR)FranceANR-20-CE11-0017
Fondation pour la Recherche Medicale (FRM)FranceDEQ20180339165

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-01
    Type: Initial release
  • Version 1.1: 2025-10-08
    Changes: Database references
  • Version 1.2: 2025-11-12
    Changes: Database references