8BJ6

Crystal structure of YopR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 

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This is version 1.1 of the entry. See complete history


Literature

Characterization of a unique repression system present in arbitrium phages of the SPbeta family.

Brady, A.Cabello-Yeves, E.Gallego Del Sol, F.Chmielowska, C.Mancheno-Bonillo, J.Zamora-Caballero, S.Omer, S.B.Torres-Puente, M.Eldar, A.Quiles-Puchalt, N.Marina, A.Penades, J.R.

(2023) Cell Host Microbe 31: 2023-2037.e8

  • DOI: https://doi.org/10.1016/j.chom.2023.11.003
  • Primary Citation of Related Structures:  
    8BJ6, 8BJV, 8BPZ

  • PubMed Abstract: 

    Arbitrium-coding phages use peptides to communicate and coordinate the decision between lysis and lysogeny. However, the mechanism by which these phages establish lysogeny remains unknown. Here, focusing on the SPbeta phage family's model phages phi3T and SPβ, we report that a six-gene operon called the "SPbeta phages repressor operon" (sro) expresses not one but two master repressors, SroE and SroF, the latter of which folds like a classical phage integrase. To promote lysogeny, these repressors bind to multiple sites in the phage genome. SroD serves as an auxiliary repressor that, with SroEF, forms the repression module necessary for lysogeny establishment and maintenance. Additionally, the proteins SroABC within the operon are proposed to constitute the transducer module, connecting the arbitrium communication system to the activity of the repression module. Overall, this research sheds light on the intricate and specialized repression system employed by arbitrium SPβ-like phages in making lysis-lysogeny decisions.


  • Organizational Affiliation

    Centre for Bacterial Resistance Biology, Imperial College London, London SW7 2AZ, UK; Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8TA, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SPbeta prophage-derived uncharacterized protein YopR
A, B, C
321Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: yopRBSU20790
UniProt
Find proteins for O34558 (Bacillus subtilis (strain 168))
Explore O34558 
Go to UniProtKB:  O34558
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO34558
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 189.682α = 90
b = 108.007β = 90.36
c = 53.601γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
XDSdata reduction
CRANK2phasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministerio de Ciencia e Innovacion (MCIN)Spain--

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-15
    Type: Initial release
  • Version 1.1: 2024-05-29
    Changes: Database references