8PQM

The DNA-binding domain of L-lactate utilization repressor (LutR-DBD) from Bacillus subtilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 
    0.237 (Depositor), 0.239 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Using environment-sensitive tetramethylated thiophene-BODIPY fluorophores in DNA probes for studying effector-induced conformational changes of protein-DNA complexes.

Soltysova, M.Guixens-Gallardo, P.Sieglova, I.Soldanova, A.Krejcirikova, V.Fabry, M.Brynda, J.Khoroshyy, P.Hocek, M.Rezacova, P.

(2025) RSC Chem Biol 

  • DOI: https://doi.org/10.1039/d4cb00260a
  • Primary Citation of Related Structures:  
    8PQM

  • PubMed Abstract: 

    The LutR protein represses the transcription of genes encoding enzymes for the utilization of l-lactate in Bacillus subtilis through binding to a specific DNA region. In this study, we employed oligonucleotide probes modified by viscosity-sensitive tetramethylated thiophene-BODIPY fluorophores to investigate the impact of selected metabolites on the LutR-DNA complex. Our goal was to identify the effector molecule whose binding alters the protein-DNA affinity, thereby enabling gene transcription. The designed DNA probes exhibited distinctive responses to the binding and release of the protein, characterized by significant alterations in fluorescence lifetime. Through this method, we have identified l-lactate as the sole metabolite exerting a substantial modulating effect on the protein-DNA interaction and thus confirmed its role as an effector molecule. Moreover, we showed that our approach was able to follow conformation changes affecting affinity, which were not captured by other methods commonly used to study the protein-DNA interaction, such as electro-mobility shift assays and florescence anisotropy binding studies. This work underlines the potential of environment-sensitive fluorophore-linked nucleotide modifications, i.e. dC TBdp , for studying the dynamics and subtle changes of protein-DNA interactions.


  • Organizational Affiliation

    Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences Flemingovo n. 2 Prague 6 Czechia hocek@uochb.cas.cz rezacova@uochb.cas.cz.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FadR family transcriptional regulator82Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: D9C10_16260
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free:  0.237 (Depositor), 0.239 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 28.31α = 90
b = 38.37β = 90
c = 66.71γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Youth and Sports of the Czech RepublicCzech RepublicLX22NPO5102

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-29
    Type: Initial release
  • Version 1.1: 2025-02-26
    Changes: Database references