4HQE

The crystal structure of QsrR-DNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular mechanism of quinone signaling mediated through S-quinonization of a YodB family repressor QsrR.

Ji, Q.Zhang, L.Jones, M.B.Sun, F.Deng, X.Liang, H.Cho, H.Brugarolas, P.Gao, Y.N.Peterson, S.N.Lan, L.Bae, T.He, C.

(2013) Proc Natl Acad Sci U S A 110: 5010-5015

  • DOI: https://doi.org/10.1073/pnas.1219446110
  • Primary Citation of Related Structures:  
    4HQE, 4HQM

  • PubMed Abstract: 

    Quinone molecules are intracellular electron-transport carriers, as well as critical intra- and extracellular signals. However, transcriptional regulation of quinone signaling and its molecular basis are poorly understood. Here, we identify a thiol-stress-sensing regulator YodB family transcriptional regulator as a central component of quinone stress response of Staphylococcus aureus, which we have termed the quinone-sensing and response repressor (QsrR). We also identify and confirm an unprecedented quinone-sensing mechanism based on the S-quinonization of the essential residue Cys-5. Structural characterizations of the QsrR-DNA and QsrR-menadione complexes further reveal that the covalent association of menadione directly leads to the release of QsrR from operator DNA following a 10° rigid-body rotation as well as a 9-Å elongation between the dimeric subunits. The molecular level characterization of this quinone-sensing transcriptional regulator provides critical insights into quinone-mediated gene regulation in human pathogens.


  • Organizational Affiliation

    Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional regulator QsrR
A, B
115Staphylococcus aureusMutation(s): 0 
Gene Names: SAV2123
UniProt
Find proteins for A0A0H3JWI0 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
Explore A0A0H3JWI0 
Go to UniProtKB:  A0A0H3JWI0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3JWI0
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*GP*TP*AP*TP*AP*AP*TP*AP*AP*TP*TP*AP*TP*AP*CP*T)-3')17synthetic construct
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*GP*TP*AP*TP*AP*AP*TP*TP*AP*TP*TP*AP*TP*AP*CP*C)-3')17synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.189α = 90
b = 48.189β = 90
c = 156.807γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASESphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-06
    Type: Initial release
  • Version 1.1: 2013-05-22
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references