8PQM
The DNA-binding domain of L-lactate utilization repressor (LutR-DBD) from Bacillus subtilis
Summary for 8PQM
| Entry DOI | 10.2210/pdb8pqm/pdb |
| Descriptor | FadR family transcriptional regulator, SODIUM ION (3 entities in total) |
| Functional Keywords | transcription, metabolic repressor, bacillus subtilis, dna binding protein |
| Biological source | Bacillus subtilis subsp. subtilis str. 168 |
| Total number of polymer chains | 1 |
| Total formula weight | 9239.05 |
| Authors | Soltysova, M. (deposition date: 2023-07-11, release date: 2025-01-29, Last modification date: 2025-03-19) |
| Primary citation | Soltysova, M.,Guixens-Gallardo, P.,Sieglova, I.,Soldanova, A.,Krejcirikova, V.,Fabry, M.,Brynda, J.,Khoroshyy, P.,Hocek, M.,Rezacova, P. Using environment-sensitive tetramethylated thiophene-BODIPY fluorophores in DNA probes for studying effector-induced conformational changes of protein-DNA complexes. Rsc Chem Biol, 6:376-386, 2025 Cited by PubMed Abstract: The LutR protein represses the transcription of genes encoding enzymes for the utilization of l-lactate in 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, dC, for studying the dynamics and subtle changes of protein-DNA interactions. PubMed: 39822774DOI: 10.1039/d4cb00260a PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.46 Å) |
Structure validation
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