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.
Highlights
The proteins of the transcription factor family named GntR, are characterized by the presence of two domains [1, 2]: the N-terminal domain, 60 residue long on average, possesses the winged-Helix-Turn-Helix architecture to which DNA recognition and binding [3, 4] functions are associated; the larger, C-terminal domain can belong to at least four different structural families and has oligomerization and effector binding functions
For example: TauR which activates the expression of taurine utilization genes in Rhodobacter capsulatus [12]; Bacillus subtilis GabR [13] which with pyridoxal 5’-phosphate (PLP) and γ-amino butyric acid (GABA) bound as external aldimine, activates transcription of genes coding for GABA aminotransferase and succinic semi-aldehyde dehydrogenase; PtsJ regulates the production of pyridoxal kinase in Salmonella typhimurium [14] while PdxR is involved in the regulation of the PLP synthesis in several bacteria such as Corynebacterium glutamicum [15], Streptococcus pneumoniae [16], Listeria monocytogenes [17], Streptococcus mutans [18], Bacillus clausii [19]
Molecular dynamics trajectories have been calculated for GabR apo forms, namely GabR without any ligand, and for GabR holo form, i.e. GabR with PLP bound through a Schiff base to each subunit of the homo dimer (PDB code 4N0B)
Summary
The proteins of the transcription factor family named GntR, are characterized by the presence of two domains [1, 2]: the N-terminal domain, 60 residue long on average, possesses the winged-Helix-Turn-Helix architecture (wHTH) to which DNA recognition and binding [3, 4] functions are associated; the larger, C-terminal domain can belong to at least four different structural families and has oligomerization and effector binding functions. A GntR subfamily, named MocR [5, 6] after designation of the regulator of expression of rhizopine catabolism genes [7], is characterized by possessing a large C-terminal domain (350 residue on average) folded as type-I pyridoxal 5’-phosphate (PLP)-dependent enzymes [8]. The two wHTH and AAT domains are linked to each other by a peptide bridge which can be of various lengths in different MocRs [10, 11]. Since their discovery, several MocR regulators have been studied and characterized. A new Brevibacillus brevis MocR has been demonstrated to regulate the expression of the gene coding for D-alanyl-D-alanine ligase [20]
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