8C8E

Crystal structure of phi3T_93 L23D mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Antagonistic interactions between phage and host factors control arbitrium lysis-lysogeny decision.

Zamora-Caballero, S.Chmielowska, C.Quiles-Puchalt, N.Brady, A.Del Sol, F.G.Mancheno-Bonillo, J.Felipe-Ruiz, A.Meijer, W.J.J.Penades, J.R.Marina, A.

(2024) Nat Microbiol 9: 161-172

  • DOI: https://doi.org/10.1038/s41564-023-01550-4
  • Primary Citation of Related Structures:  
    8ANT, 8ANU, 8ANV, 8C8E

  • PubMed Abstract: 

    Phages can use a small-molecule communication arbitrium system to coordinate lysis-lysogeny decisions, but the underlying mechanism remains unknown. Here we determined that the arbitrium system in Bacillus subtilis phage phi3T modulates the bacterial toxin-antitoxin system MazE-MazF to regulate the phage life cycle. We show that phi3T expresses AimX and YosL, which bind to and inactivate MazF. AimX also inhibits the function of phi3T_93, a protein that promotes lysogeny by binding to MazE and releasing MazF. Overall, these mutually exclusive interactions promote the lytic cycle of the phage. After several rounds of infection, the phage-encoded AimP peptide accumulates intracellularly and inactivates the phage antiterminator AimR, a process that eliminates aimX expression from the aimP promoter. Therefore, when AimP increases, MazF activity promotes reversion back to lysogeny, since AimX is absent. Altogether, our study reveals the evolutionary strategy used by arbitrium to control lysis-lysogeny by domesticating and fine-tuning a phage-defence mechanism.


  • Organizational Affiliation

    Instituto de Biomedicina de Valencia (IBV)-CSIC and CIBER de Enfermedades Raras (CIBERER)-ISCIII, Valencia, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phi3T YopNA [auth C],
B [auth A]
82Bacillus phage phi3TMutation(s): 1 
Gene Names: phi3T_93
UniProt
Find proteins for A0A1P8CWW1 (Bacillus phage phi3T)
Explore A0A1P8CWW1 
Go to UniProtKB:  A0A1P8CWW1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1P8CWW1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.89α = 90
b = 71.89β = 90
c = 68.341γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
iMOSFLMdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministerio de Ciencia e Innovacion (MCIN)SpainPID2019-108541GB-100

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-25
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Database references