4HQM | pdb_00004hqm

The crystal structure of QsrR-menadione complex

• PDB DOI: https://doi.org/10.2210/pdb4HQM/pdb

• Classification: TRANSCRIPTION regulator
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-10-25 Released: 2013-03-06 
• Deposition Author(s): Ji, Q., Zhang, L., Jones, M.B., Sun, F., Deng, X., Liang, H., Brugarolas, P., Gao, N., Peterson, S.N., Lan, L., Bae, T., He, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.296 (Depositor), 0.299 (DCC) 
• R-Value Work: 
  0.284 (Depositor), 0.277 (DCC) 
• R-Value Observed: 
  0.285 (Depositor) 

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

• PubMed: 23479646 
• DOI: https://doi.org/10.1073/pnas.1219446110
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 26.49 kDa 
• Atom Count: 1,621 
• Modeled Residue Count: 199 
• Deposited Residue Count: 230 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
QsrR protein	A, B	115	Staphylococcus aureus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
17Z	C [auth A], D [auth B]	2-methylnaphthalene-1,4-diol C11 H10 O2 ZJTLZYDQJHKRMQ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.296 (Depositor), 0.299 (DCC) 
• R-Value Work:  0.284 (Depositor), 0.277 (DCC) 
• R-Value Observed: 0.285 (Depositor) 

Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.758	α = 90
b = 124.758	β = 90
c = 30.633	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-06 
Deposition Author(s): Ji, Q., Zhang, L., Jones, M.B., Sun, F., Deng, X., Liang, H., Brugarolas, P., Gao, N., Peterson, S.N., Lan, L., Bae, T., He, C.

Revision History  

• Version 1.0: 2013-03-06
  Type: Initial release
  
• Version 1.1: 2013-05-22
  Changes: Database references
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary