8BEG

Structure of Ig-like domains from PrgB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural foundation for the role of enterococcal PrgB in conjugation, biofilm formation, and virulence.

Sun, W.S.Lassinantti, L.Jarva, M.Schmitt, A.Ter Beek, J.Berntsson, R.P.

(2023) Elife 12

  • DOI: https://doi.org/10.7554/eLife.84427
  • Primary Citation of Related Structures:  
    8BEG

  • PubMed Abstract: 

    Type 4 Secretion Systems are a main driver for the spread of antibiotic resistance genes and virulence factors in bacteria. In Gram-positives, these secretion systems often rely on surface adhesins to enhance cellular aggregation and mating-pair formation. One of the best studied adhesins is PrgB from the conjugative plasmid pCF10 of Enterococcus faecalis , which has been shown to play major roles in conjugation, biofilm formation, and importantly also in bacterial virulence. Since prgB orthologs exist on a large number of conjugative plasmids in various different species, this makes PrgB a model protein for this widespread virulence factor. After characterizing the polymer adhesin domain of PrgB previously, we here report the structure for almost the entire remainder of PrgB, which reveals that PrgB contains four immunoglobulin (Ig)-like domains. Based on this new insight, we re-evaluate previously studied variants and present new in vivo data where specific domains or conserved residues have been removed. For the first time, we can show a decoupling of cellular aggregation from biofilm formation and conjugation in prgB mutant phenotypes. Based on the presented data, we propose a new functional model to explain how PrgB mediates its different functions. We hypothesize that the Ig-like domains act as a rigid stalk that presents the polymer adhesin domain at the right distance from the cell wall.


  • Organizational Affiliation

    Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PrgB
A, B
650Enterococcus faecalisMutation(s): 0 
Gene Names: prgB
UniProt
Find proteins for Q04112 (Enterococcus faecalis)
Explore Q04112 
Go to UniProtKB:  Q04112
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04112
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76α = 90
b = 87.5β = 90
c = 224.8γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2016-03599
Carl Trygger FoundationSwedenCTS 18:39

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-30
    Type: Initial release
  • Version 1.1: 2023-11-01
    Changes: Data collection, Database references
  • Version 1.2: 2024-05-01
    Changes: Refinement description