4ZA6 | pdb_00004za6

Structure of the R. erythropolis transcriptional repressor QsdR from TetR family


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 
    0.228 (Depositor), 0.195 (DCC) 
  • R-Value Work: 
    0.206 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 4ZA6

This is version 1.2 of the entry. See complete history

Literature

Natural Guided Genome Engineering Reveals Transcriptional Regulators Controlling Quorum-Sensing Signal Degradation.

El Sahili, A.Kwasiborski, A.Mothe, N.Velours, C.Legrand, P.Morera, S.Faure, D.

(2015) PLoS One 10: e0141718-e0141718

  • DOI: https://doi.org/10.1371/journal.pone.0141718
  • Primary Citation Related Structures: 
    4ZA6

  • PubMed Abstract: 

    Quorum-quenching (QQ) are natural or engineered processes disrupting the quorum-sensing (QS) signalling which controls virulence and persistence (e.g. biofilm) in numerous bacteria. QQ involves different enzymes including lactonases, amidases, oxidases and reductases which degrade the QS molecules such as N-acylhomoserine lactones (NAHL). Rhodococcus erythropolis known to efficiently degrade NAHL is proposed as a biocontrol agent and a reservoir of QQ-enzymes for biotechnology. In R. erythropolis, regulation of QQ-enzymes remains unclear. In this work, we performed genome engineering on R. erythropolis, which is recalcitrant to reverse genetics, in order to investigate regulation of QQ-enzymes at a molecular and structural level with the aim to improve the QQ activity. Deep-sequencing of the R. erythropolis enhanced variants allowed identification of a punctual mutation in a key-transcriptional factor QsdR (Quorum sensing degradation Regulation) which regulates the sole QQ-lactonase QsdA identified so far. Using biophysical and structural studies on QsdR, we demonstrate that QQ activity can be improved by modifying the regulation of QQ-enzymes degrading QS signal. This modification requiring the change of only one amino-acid in a transcriptional factor leads to an enhanced R. erythropolis in which the QS-signal degradation pathway is strongly activated.


  • Organizational Affiliation
    • Institute for Integrative Biology of the Cell (I2BC), CNRS, CEA, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette Cedex, France.

Macromolecule Content 

  • Total Structure Weight: 43.51 kDa 
  • Atom Count: 3,277 
  • Modeled Residue Count: 376 
  • Deposited Residue Count: 384 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
TetR family transcriptional regulator
A, B
192Rhodococcus erythropolisMutation(s): 0 
Gene Names: QV65_28910
UniProt
Find proteins for A0A0C2W9F0 (Rhodococcus erythropolis)
Explore A0A0C2W9F0 
Go to UniProtKB:  A0A0C2W9F0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0C2W9F0
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MPD

Query on MPD



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
I [auth B]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
I [auth B],
K [auth B]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
G [auth A],
J [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA

Query on CA



Download:Ideal Coordinates CCD File
H [auth A],
L [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free:  0.228 (Depositor), 0.195 (DCC) 
  • R-Value Work:  0.206 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.63α = 90
b = 91.63β = 90
c = 145.22γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PHASERphasing
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-21
    Type: Initial release
  • Version 1.1: 2015-11-25
    Changes: Database references
  • Version 1.2: 2024-05-01
    Changes: Data collection, Database references, Derived calculations, Refinement description