Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 29943.30 
• Atom Count: 2115 
• Residue Count: 264 
• Unique protein chains: 1

4OQP

Structure of the effector-binding domain of deoxyribonucleoside regulator DeoR from Bacillus subtilis in complex with deoxyribose-5-phosphate

• DOI: 10.2210/pdb4OQP/pdb

• Classification: TRANSCRIPTION
• Organism(s): Bacillus subtilis (strain 168)
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2014-02-10 Released: 2014-06-04 
• Deposition Author(s): Rezacova, P., Skerlova, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.6 Å
• R-Value Free: 0.191 
• R-Value Work: 0.154 

Literature

Structure of the effector-binding domain of deoxyribonucleoside regulator DeoR from Bacillus subtilis.

Skerlova, J., Fabry, M., Hubalek, M., Otwinowski, Z., Rezacova, P.

(2014) Febs J. 281: 4280-4292

• PubMed: 24863636 
• DOI: 10.1111/febs.12856
• Primary Citation of Related Structures:  
  4OQQ


• PubMed Abstract: 
  

Deoxyribonucleoside regulator (DeoR) from Bacillus subtilis negatively regulates expression of enzymes involved in the catabolism of deoxyribonucleosides and deoxyribose. The DeoR protein is homologous to the sorbitol operon regulator family of metabolic regulators and comprises an N-terminal DNA-binding domain and a C-terminal effector-binding domain. We have determined the crystal structure of the effector-binding domain of DeoR (C-DeoR) in free form and in covalent complex with its effector deoxyribose-5-phosphate (dR5P). This is the first case of a covalently attached effector molecule captured in the structure of a bacterial transcriptional regulator. The dR5P molecule is attached through a Schiff base linkage to residue Lys141. The crucial role of Lys141 in effector binding was confirmed by mutational analysis and mass spectrometry of Schiff base adducts formed in solution. Structural analyses of the free and effector-bound C-DeoR structures provided a structural explanation for the mechanism of DeoR function as a molecular switch.

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Related Citations: 

• Crystal structures of the effector-binding domain of repressor Central glycolytic gene Regulator from Bacillus subtilis reveal ligand-induced structural changes upon binding of several glycolytic intermediates.
  Rezacova, P.,Kozisek, M.,Moy, S.F.,Sieglova, I.,Joachimiak, A.,Machius, M.,Otwinowski, Z.
  (2008) Mol.Microbiol. 69: 895
• Crystallization of the Effector-Binding Domain of Repressor DeoR from Bacillus subtilis
  Pisackova, J.,Prochazkova, K.,Fabry, M.,Rezacova, P.
  (2013) Cryst.GrowthDes. 13: 844




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Organizational Affiliation: 

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic; Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Deoxyribonucleoside regulator	A	264	Bacillus subtilis (strain 168)	Mutation(s): 0  Gene Names: deoR (yxxC)
Find proteins for P39140 (Bacillus subtilis (strain 168)) Go to UniProtKB:  P39140

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
PED	A	PENTANE-3,4-DIOL-5-PHOSPHATE OPEN FORM OF 1'-2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE C5 H13 O6 P FQKLTSRHTQGSQZ-CRCLSJGQSA-N
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NI	A	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
CO	A	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N
CD	A	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.6 Å
• R-Value Free: 0.191 
• R-Value Work: 0.154 
• Space Group: C 2 2 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 76.995	α = 90.00
b = 78.983	β = 90.00
c = 91.338	γ = 90.00

Software Package:

Software Name	Purpose
MAR345dtb	data collection
HKL-3000	data reduction
HKL-3000	data scaling
REFMAC	refinement
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-02-10 
• Released Date: 2014-06-04 
• Deposition Author(s): Rezacova, P., Skerlova, J.

Revision History 

• Version 1.0: 2014-06-04
  Type: Initial release
• Version 1.1: 2014-06-18
  Type: Database references
• Version 1.2: 2014-10-01
  Type: Database references
• Version 1.3: 2019-11-20
  Type: Database references, Derived calculations