6GED

Adhesin domain of PrgB from Enterococcus faecalis bound to DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

PrgB promotes aggregation, biofilm formation, and conjugation through DNA binding and compaction.

Schmitt, A., Jiang, K., Camacho, M.I., Jonna, V.R., Hofer, A., Westerlund, F., Christie, P.J., Berntsson, R.P.

(2018) Mol Microbiol 109: 291-305

  • DOI: 10.1111/mmi.13980
  • Primary Citation of Related Structures:  
    6EVU, 6GED

  • PubMed Abstract: 

    • Gram-positive bacteria deploy type IV secretion systems (T4SSs) to facilitate horizontal gene transfer. The T4SSs of Gram-positive bacteria rely on surface adhesins as opposed to conjugative pili to facilitate mating. Enterococcus faecalis PrgB is a ...

    Gram-positive bacteria deploy type IV secretion systems (T4SSs) to facilitate horizontal gene transfer. The T4SSs of Gram-positive bacteria rely on surface adhesins as opposed to conjugative pili to facilitate mating. Enterococcus faecalis PrgB is a surface adhesin that promotes mating pair formation and robust biofilm development in an extracellular DNA (eDNA) dependent manner. Here, we report the structure of the adhesin domain of PrgB. The adhesin domain binds and compacts DNA in vitro. In vivo PrgB deleted of its adhesin domain does not support cellular aggregation, biofilm development and conjugative DNA transfer. PrgB also binds lipoteichoic acid (LTA), which competes with DNA binding. We propose that PrgB binding and compaction of eDNA facilitates cell aggregation and plays an important role in establishment of early biofilms in mono- or polyspecies settings. Within these biofilms, PrgB mediates formation and stabilization of direct cell-cell contacts through alternative binding of cell-bound LTA, which in turn promotes establishment of productive mating junctions and efficient intra- or inter-species T4SS-mediated gene transfer.

    Organizational Affiliation: 

    Department of Medical Biochemistry and Biophysics, Umeå University, SE-90187 Umeå, Sweden.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PrgBA315Enterococcus faecalisMutation(s): 0 
Gene Names: prgB
Find proteins for Q04112 (Enterococcus faecalis)
Explore Q04112 
Go to UniProtKB:  Q04112
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*GP*GP*GP*CP*GP*GP*CP*CP*CP*G)-3')C10synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(P*CP*GP*GP*GP*CP*CP*GP*CP*CP*C)-3')D10synthetic construct
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      EDO
      Query on EDO
      Download Ideal Coordinates CCD File 
      A
      		1,2-ETHANEDIOL
      C2 H6 O2
      LYCAIKOWRPUZTN-UHFFFAOYSA-N      		 Ligand Interaction
      NA
      Query on NA
      Download Ideal Coordinates CCD File 
      A
      		SODIUM ION
      Na
      FKNQFGJONOIPTF-UHFFFAOYSA-N      		 Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.79 Å
      • R-Value Free: 0.212 
      • R-Value Work: 0.174 
      • R-Value Observed: 0.176 
      • Space Group: P 21 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 32.017α = 90
      b = 93.026β = 90
      c = 99.097γ = 90
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      XDSdata reduction
      XSCALEdata scaling
      PHASERphasing
      PDB_EXTRACTdata extraction

      Structure Validation

      View Full Validation Report


      View more in-depth experimental data

      Entry History & Funding Information

      Deposition Data

      Funding OrganizationLocationGrant Number
      Swedish Research CouncilSweden2016-03599
      KempestiftelsernaSwedenJCK-1524

      Revision History 

      • Version 1.0: 2018-05-16
        Type: Initial release
      • Version 1.1: 2018-10-03
        Changes: Data collection, Database references
      • Version 1.2: 2019-08-14
        Changes: Data collection