4OQP

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


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

  • DOI: https://doi.org/10.1111/febs.12856
  • Primary Citation of Related Structures:  
    4OQP, 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.


  • 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Deoxyribonucleoside regulator264Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: deoRyxxCBSU39430
UniProt
Find proteins for P39140 (Bacillus subtilis (strain 168))
Explore P39140 
Go to UniProtKB:  P39140
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39140
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PED
Query on PED

Download Ideal Coordinates CCD File 
B [auth A]PENTANE-3,4-DIOL-5-PHOSPHATE
C5 H13 O6 P
FQKLTSRHTQGSQZ-CRCLSJGQSA-N
CD
Query on CD

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C [auth A]CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
CO
Query on CO

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G [auth A]COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
NI
Query on NI

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D [auth A],
E [auth A],
F [auth A]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
H [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.995α = 90
b = 78.983β = 90
c = 91.338γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-06-04
    Type: Initial release
  • Version 1.1: 2014-06-18
    Changes: Database references
  • Version 1.2: 2014-10-01
    Changes: Database references
  • Version 1.3: 2019-11-20
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description