6T3H

Structure of the Rap conjugation gene regulator of the plasmid pLS20 in apo form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.04 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Inactivation of the dimeric RappLS20 anti-repressor of the conjugation operon is mediated by peptide-induced tetramerization.

Crespo, I.Bernardo, N.Miguel-Arribas, A.Singh, P.K.Luque-Ortega, J.R.Alfonso, C.Malfois, M.Meijer, W.J.J.Boer, D.R.

(2020) Nucleic Acids Res 48: 8113-8127

  • DOI: https://doi.org/10.1093/nar/gkaa540
  • Primary Citation of Related Structures:  
    6T3H, 6T46

  • PubMed Abstract: 

    Quorum sensing allows bacterial cells to communicate through the release of soluble signaling molecules into the surrounding medium. It plays a pivotal role in controlling bacterial conjugation in Gram-positive cells, a process that has tremendous impact on health. Intracellular regulatory proteins of the RRNPP family are common targets of these signaling molecules. The RRNPP family of gene regulators bind signaling molecules at their C-terminal domain (CTD), but have highly divergent functionalities at their N-terminal effector domains (NTD). This divergence is also reflected in the functional states of the proteins, and is highly interesting from an evolutionary perspective. RappLS20 is an RRNPP encoded on the Bacillus subtilis plasmid pLS20. It relieves the gene repression effectuated by RcopLS20 in the absence of the mature pLS20 signaling peptide Phr*pLS20. We report here an in-depth structural study of apo and Phr*pLS20-bound states of RappLS20 at various levels of atomic detail. We show that apo-RappLS20 is dimeric and that Phr*pLS20-bound Rap forms NTD-mediated tetramers. In addition, we show that RappLS20 binds RcopLS20 directly in the absence of Phr*pLS20 and that addition of Phr*pLS20 releases RcopLS20 from RappLS20. This allows RcopLS20 to bind the promotor region of crucial conjugation genes blocking their expression.


  • Organizational Affiliation

    ALBA Synchrotron Light Source, C. de la Llum 2-26, Cerdanyola del Vallès, 08290 Barcelona, Spain.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Response regulator aspartate phosphatase
A, B
376Bacillus subtilis subsp. nattoMutation(s): 0 
Gene Names: rapA
UniProt
Find proteins for E9RIY6 (Bacillus subtilis subsp. natto)
Explore E9RIY6 
Go to UniProtKB:  E9RIY6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE9RIY6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.04 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.79α = 90
b = 174.487β = 90
c = 49.879γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Economy and CompetitivenessSpainBIO2016-77883-C2-2-P
Ministry of Economy and CompetitivenessSpainBIO2016-77883-C2-2-P
Ministry of Economy and CompetitivenessSpainFIS2015-72574-EXP

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-24
    Type: Initial release
  • Version 1.1: 2020-07-22
    Changes: Database references, Refinement description
  • Version 1.2: 2020-08-26
    Changes: Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Refinement description