6NSR

TetR family transcriptional regulator CifR C99T-C181R cysteine mutant complexed with 26bp double-strand operator DNA and apo-CifR C99T-C181R

  • Classification: TRANSCRIPTION/DNA
  • Organism(s): Pseudomonas aeruginosa
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2019-01-25 Released: 2020-01-29 
  • Deposition Author(s): He, S., Taher, N.M., Simard, A.R., Madden, D.R.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), Cystic Fibrosis Foundation

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.246 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.219 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.222 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Molecular basis for the transcriptional regulation of an epoxide-based virulence circuit in Pseudomonas aeruginosa.

He, S.Taher, N.M.Simard, A.R.Hvorecny, K.L.Ragusa, M.J.Bahl, C.D.Hickman, A.B.Dyda, F.Madden, D.R.

(2024) Nucleic Acids Res 

  • DOI: https://doi.org/10.1093/nar/gkae889
  • Primary Citation of Related Structures:  
    6NSM, 6NSN, 6NSR

  • PubMed Abstract: 

    The opportunistic pathogen Pseudomonas aeruginosa infects the airways of people with cystic fibrosis (CF) and produces a virulence factor Cif that is associated with worse outcomes. Cif is an epoxide hydrolase that reduces cell-surface abundance of the cystic fibrosis transmembrane conductance regulator (CFTR) and sabotages pro-resolving signals. Its expression is regulated by a divergently transcribed TetR family transcriptional repressor. CifR represents the first reported epoxide-sensing bacterial transcriptional regulator, but neither its interaction with cognate operator sequences nor the mechanism of activation has been investigated. Using biochemical and structural approaches, we uncovered the molecular mechanisms controlling this complex virulence operon. We present here the first molecular structures of CifR alone and in complex with operator DNA, resolved in a single crystal lattice. Significant conformational changes between these two structures suggest how CifR regulates the expression of the virulence gene cif. Interactions between the N-terminal extension of CifR with the DNA minor groove of the operator play a significant role in the operator recognition of CifR. We also determined that cysteine residue Cys107 is critical for epoxide sensing and DNA release. These results offer new insights into the stereochemical regulation of an epoxide-based virulence circuit in a critically important clinical pathogen.


  • Organizational Affiliation

    Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CifR
A, B, E
198Pseudomonas aeruginosaMutation(s): 2 
Gene Names: cifRPA2931
UniProt
Find proteins for Q9HZR6 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9HZR6 
Go to UniProtKB:  Q9HZR6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HZR6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, E
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.246 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.219 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.222 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.517α = 90
b = 165.569β = 90
c = 81.529γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI091699
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP20 GM113132
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesP30 DK117469
Cystic Fibrosis FoundationUnited StatesSTANTO19R0
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesT32 AI007519

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-29
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Advisory, Data collection, Database references, Refinement description, Source and taxonomy, Structure summary
  • Version 1.2: 2024-02-14
    Changes: Source and taxonomy, Structure summary
  • Version 2.0: 2024-07-17
    Type: Coordinate replacement
    Reason: Real space R-factor
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
  • Version 2.1: 2024-10-23
    Changes: Database references, Structure summary