7N10

Co-crystal structure of Prx with ComR DNA binding domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Molecular mechanism of quorum sensing inhibition in Streptococcus by the phage protein paratox.

Rutbeek, N.R.Rezasoltani, H.Patel, T.R.Khajehpour, M.Prehna, G.

(2021) J Biol Chem 297: 100992-100992

  • DOI: https://doi.org/10.1016/j.jbc.2021.100992
  • Primary Citation of Related Structures:  
    7N10, 7N1N

  • PubMed Abstract: 

    Streptococcus pyogenes, or Group A Streptococcus, is a Gram-positive bacterium that can be both a human commensal and a pathogen. Central to this dichotomy are temperate bacteriophages that incorporate into the bacterial genome as prophages. These genetic elements encode both the phage proteins and the toxins harmful to the human host. One such conserved phage protein, paratox (Prx), is always found encoded adjacent to the toxin genes, and this linkage is preserved during all stages of the phage life cycle. Within S. pyogenes, Prx functions to inhibit the quorum-sensing receptor-signal pair ComRS, the master regulator of natural competence, or the ability to uptake endogenous DNA. However, the mechanism by which Prx directly binds and inhibits the receptor ComR is unknown. To understand how Prx inhibits ComR at the molecular level, we pursued an X-ray crystal structure of Prx bound to ComR. The structural data supported by solution X-ray scattering data demonstrate that Prx induces a conformational change in ComR to directly access its DNA-binding domain. Furthermore, electromobility shift assays and competition binding assays reveal that Prx effectively uncouples the interdomain conformational change required for activation of ComR via the signaling molecule XIP. Although to our knowledge the molecular mechanism of quorum-sensing inhibition by Prx is unique, it is analogous to the mechanism employed by the phage protein Aqs1 in Pseudomonas aeruginosa. Together, this demonstrates an example of convergent evolution between Gram-positive and Gram-negative phages to inhibit quorum-sensing and highlights the versatility of small phage proteins.


  • Organizational Affiliation

    Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Prx
A, C
68Streptococcus pyogenes MGAS315Mutation(s): 0 
Gene Names: SpyM3_1300
UniProt
Find proteins for A0A0H2UWN8 (Streptococcus pyogenes serotype M3 (strain ATCC BAA-595 / MGAS315))
Explore A0A0H2UWN8 
Go to UniProtKB:  A0A0H2UWN8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2UWN8
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ComR69Streptococcus mutans UA159Mutation(s): 0 
Gene Names: SMU_61
UniProt
Find proteins for Q8DWI6 (Streptococcus mutans serotype c (strain ATCC 700610 / UA159))
Explore Q8DWI6 
Go to UniProtKB:  Q8DWI6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DWI6
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.556α = 90
b = 41.918β = 90
c = 90γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
PHENIXphasing
XDSdata reduction
XDSdata scaling
Aimlessdata scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)CanadaRGPIN-2018-04968

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-28
    Type: Initial release
  • Version 1.1: 2021-08-25
    Changes: Database references
  • Version 1.2: 2021-09-08
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description