Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 62.64 kDa 
• Atom Count: 3805 
• Modelled Residue Count: 411 
• Deposited Residue Count: 524 
• Unique protein chains: 1

4A5N

Redoxregulator HypR in its reduced form

• PDB DOI: 10.2210/pdb4A5N/pdb

• Classification: TRANSCRIPTION
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2011-10-26 Released: 2012-01-11 
• Deposition Author(s): Palm, G.J., Waack, P., Read, R.J., Hinrichs, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 0.223 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 

Literature

Structural Insights Into the Redox-Switch Mechanism of the Marr/Duf24-Type Regulator Hypr

Palm, G.J., Chi, B.K., Waack, P., Gronau, K., Becher, D., Albrecht, D., Hinrichs, W., Read, R.J., Antelmann, H.

(2012) Nucleic Acids Res 40: 4178

• PubMed: 22238377 
• DOI: 10.1093/nar/gkr1316
• Primary Citation of Related Structures:  
  4A5M, 4A5N


• PubMed Abstract: 
  

Bacillus subtilis encodes redox-sensing MarR-type regulators of the OhrR and DUF24-families that sense organic hydroperoxides, diamide, quinones or aldehydes via thiol-based redox-switches. In this article, we characterize the novel redox-sensing MarR/DUF24-family regulator HypR (YybR) that is activated by disulphide stress caused by diamide and NaOCl in B. subtilis. HypR controls positively a flavin oxidoreductase HypO that confers protection against NaOCl stress. The conserved N-terminal Cys14 residue of HypR has a lower pK(a) of 6.36 and is essential for activation of hypO transcription by disulphide stress. HypR resembles a 2-Cys-type regulator that is activated by Cys14-Cys49' intersubunit disulphide formation. The crystal structures of reduced and oxidized HypR proteins were resolved revealing structural changes of HypR upon oxidation. In reduced HypR a hydrogen-bonding network stabilizes the reactive Cys14 thiolate that is 8-9 Å apart from Cys49'. HypR oxidation breaks these H-bonds, reorients the monomers and moves the major groove recognition α4 and α4' helices ∼4 Å towards each other. This is the first crystal structure of a redox-sensing MarR/DUF24 family protein in bacteria that is activated by NaOCl stress. Since hypochloric acid is released by activated macrophages, related HypR-like regulators could function to protect pathogens against the host immune defense.

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Organizational Affiliation: 

Institute for Biochemistry, Ernst-Moritz-Arndt-University of Greifswald, D-17487 Greifswald, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UNCHARACTERIZED HTH-TYPE TRANSCRIPTIONAL REGULATOR YYBR	A, B, C, D	131	Bacillus subtilis	Mutation(s): 1
UniProt
Find proteins for P37486 (Bacillus subtilis (strain 168)) Explore P37486  Go to UniProtKB:  P37486

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BME	E [auth A], F [auth B], G [auth C], H [auth D]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
EDO	I [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 0.223 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.93	α = 90
b = 68.03	β = 97.45
c = 60.42	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-10-26 
• Released Date: 2012-01-11 
Deposition Author(s): Palm, G.J., Waack, P., Read, R.J., Hinrichs, W.

Revision History  

• Version 1.0: 2012-01-11
  Type: Initial release
  
• Version 1.1: 2012-01-25
  Changes: Other
• Version 1.2: 2012-05-23
  Changes: Other