8V6R

Crystal structure of EcThsA in complex with ADPR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural characterization of macro domain-containing Thoeris antiphage defense systems.

Shi, Y.Masic, V.Mosaiab, T.Rajaratman, P.Hartley-Tassell, L.Sorbello, M.Goulart, C.C.Vasquez, E.Mishra, B.P.Holt, S.Gu, W.Kobe, B.Ve, T.

(2024) Sci Adv 10: eadn3310-eadn3310

  • DOI: https://doi.org/10.1126/sciadv.adn3310
  • Primary Citation of Related Structures:  
    8V6Q, 8V6R, 8V6S, 8V6T

  • PubMed Abstract: 

    Thoeris defense systems protect bacteria from infection by phages via abortive infection. In these systems, ThsB proteins serve as sensors of infection and generate signaling nucleotides that activate ThsA effectors. Silent information regulator and SMF/DprA-LOG (SIR2-SLOG) containing ThsA effectors are activated by cyclic ADP-ribose (ADPR) isomers 2'cADPR and 3'cADPR, triggering abortive infection via nicotinamide adenine dinucleotide (NAD + ) depletion. Here, we characterize Thoeris systems with transmembrane and macro domain (TM-macro)-containing ThsA effectors. We demonstrate that ThsA macro domains bind ADPR and imidazole adenine dinucleotide (IAD), but not 2'cADPR or 3'cADPR. Combining crystallography, in silico predictions, and site-directed mutagenesis, we show that ThsA macro domains form nucleotide-induced higher-order oligomers, enabling TM domain clustering. We demonstrate that ThsB can produce both ADPR and IAD, and we identify a ThsA TM-macro-specific ThsB subfamily with an active site resembling deoxy-nucleotide and deoxy-nucleoside processing enzymes. Collectively, our study demonstrates that Thoeris systems with SIR2-SLOG and TM-macro ThsA effectors trigger abortive infection via distinct mechanisms.


  • Organizational Affiliation

    Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thoeris protein ThsA Macro domain-containing protein
A, B
241Escherichia coliMutation(s): 0 
Gene Names: FPI65_12015
UniProt
Find proteins for A0A178STJ6 (Escherichia coli)
Explore A0A178STJ6 
Go to UniProtKB:  A0A178STJ6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A178STJ6
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AR6 (Subject of Investigation/LOI)
Query on AR6

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE
C15 H23 N5 O14 P2
SRNWOUGRCWSEMX-ZQSHOCFMSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.52α = 90
b = 92.598β = 90
c = 139.976γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaFT200100572

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-12
    Type: Initial release
  • Version 1.1: 2024-07-10
    Changes: Database references