8V6S

Crystal structure of PcThsA in complex with Imidazole Adenine Dinucleotide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

Starting Model: in silico
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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
240Pseudomonas corrugataMutation(s): 0 
Gene Names: HNO91_03675
UniProt
Find proteins for A0A7Y5Z1U6 (Pseudomonas corrugata)
Explore A0A7Y5Z1U6 
Go to UniProtKB:  A0A7Y5Z1U6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7Y5Z1U6
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YG8 (Subject of Investigation/LOI)
Query on YG8

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-imidazol-1-yl-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate
C18 H25 N7 O13 P2
CBBKIMDNCBIDSI-ZZJFPLALSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.856α = 90
b = 87.705β = 97.13
c = 65.262γ = 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