ArticlePloS one2017
Molecular dynamics simulation unveils the conformational flexibility of the interdomain linker in the bacterial transcriptional regulator GabR from Bacillus subtilis bound to pyridoxal 5'-phosphate.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 14 citations in OpenAlex.
- Bioisosteric replacement of pyridoxal-5'-phosphate to pyridoxal-5'-tetrazole targeting Bacillus subtilis GabR.Protein science : a publication of the Protein Society · 2025Article
- Piperine's potential in treating polycystic ovarian syndrome explored through in-silico docking.Scientific reports · 2024Article
- Structural insights into the DNA recognition mechanism by the bacterial transcription factor PdxR.Nucleic acids research · 2023Article
- "Conformational dynamics of C1r inhibitor proteins from Lyme disease and relapsing fever spirochetes".bioRxiv : the preprint server for biology · 2023Article
- Molecular Cloning, Purification and Characterization of Mce1R of Mycobacterium tuberculosis.Molecular biotechnology · 2021Article
- Conformational transitions induced by γ-amino butyrate binding in GabR, a bacterial transcriptional regulator.Scientific reports · 2019Article
- Computational classification of MocR transcriptional regulators into subgroups as a support for experimental and functional characterization.Bioinformation · 2019Article
- A Survey of Pyridoxal 5'-Phosphate-Dependent Proteins in the Gram-Positive Model BacteriumFrontiers in molecular biosciences · 2019Review
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
GabR from Bacillus subtilis is a transcriptional regulator belonging to the MocR subfamily of the GntR regulators. The structure of the MocR regulators is characterized by the presence of two domains: i) a N-terminal domain, about 60 residue long, possessing the winged-Helix-Turn-Helix (wHTH) architecture with DNA recognition and binding capability; ii) a C-terminal domain (about 350 residue) folded as the pyridoxal 5'-phosphate (PLP) dependent aspartate aminotransferase (AAT) with dimerization and effector binding functions. The two domains are linked to each other by a peptide bridge. Although structural and functional characterization of MocRs is proceeding at a fast pace, virtually nothing is know about the molecular changes induced by the effector binding and on how these modifications influence the properties of the regulator. An extensive molecular dynamics simulation on the crystallographic structure of the homodimeric B. subtilis GabR has been undertaken with the aim to envisage the role and the importance of conformational flexibility in the action of GabR. Molecular dynamics has been calculated for the apo (without PLP) and holo (with PLP bound) forms of the GabR. A comparison between the molecular dynamics trajectories calculated for the two GabR forms suggested that one of the wHTH domain detaches from the AAT-like domain in the GabR PLP-bound form. The most evident conformational change in the holo PLP-bound form is represented by the rotation and the subsequent detachment from the subunit surface of one of the wHTH domains. The movement is mediated by a rearrangement of the linker connecting the AAT domain possibly triggered by the presence of the negative charge of the PLP cofactor. This is the second most significant conformational modification. The C-terminal section of the linker docks into the "active site" pocket and establish stabilizing contacts consisting of hydrogen-bonds, salt-bridges and hydrophobic interactions.
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