Crystal structure of Bacillus subtilis GabR, an autorepressor and transcriptional activator of gabT

Abstract

Significance GabR is a member of the MocR/GabR subfamily of the GntR family of bacterial transcription regulators. It regulates the metabolism of γ-aminobutyric acid, an important nitrogen and carbon source in many bacteria. The crystal structures reported here show that this protein has evolved from the fusion of a type I aminotransferase and a winged helix-turn-helix DNA-binding protein to form a chimeric protein that adopts a dimeric head-to-tail configuration. The pyridoxal 5′-phosphate–binding regulatory domain of GabR is therefore an example of a coenzyme playing a role in transcription regulation rather than in enzymatic catalysis. Our structural and biochemical studies lay the mechanistic foundation for understanding the regulatory functions of the MocR/GabR subfamily of transcription regulators.

Molecular mechanism of PdxR – a transcriptional activator involved in the regulation of vitamin B6 biosynthesis in the probiotic bacterium Bacillus clausii

“…2) sequences, used as seed for model building, revealed that they sharẽ 36% sequence identity: this result is in line with the previously reported average sequence conservation within Firmicutes MocRs [13]. The alignment shows the conservation of the DNA-binding domain sequence and, in particular, of residues Arg43, Ser52 and Lys75, which is predicted to constitute the major DNA-binding surface in GabR [18]. Also, the key PLP interacting residues Asp276 and Lys309 (numbering referred to bcPdxR sequence), which hydrogen-bonds to the nitrogen atom of the pyridine ring and reacts with the cofactor aldehyde group at the 5 0 position of PLP forming a Schiff-base, respectively, are conserved.…”

Negative Regulation of Ectoine Uptake and Catabolism in Sinorhizobium meliloti: Characterization of the EhuR Gene

“…In addition, members of the MocR family have a highly conserved aspartate (class I) aminotransferase domain at their C terminus, which can bind pyridoxal 5=-phosphate (PLP) as a cofactor (3,5,13,14). PLP, alone or with other small molecules, proved to modulate the DNA-binding activities of MocR family regulators (5,(13)(14)(15)(16). Since the putative PLP-binding site is highly conserved in EhuR (data not shown), we analyzed EhuR-mediated mobility shifts in the presence of PLP as well as ectoine, DABA (a catabolic end product), and aspartate (Fig.…”

The aspartate aminotransferase-like domain of Firmicutes MocR transcriptional regulators

“…7). No significant enzyme activity has been detected in GabR (Belitsky, 2004) although the protein is able to bind GABA (Edayathumangalam et al, 2013). Second, proteins belonging to clade 1 display a surface patch (positions 362-375) rich of basic residues localized on an exposed a-helix (Edayathumangalam et al, 2013) which may suggests the presence of a DNA or protein interaction site (Supplementary Fig.…”

“…Only a few members of the MocR family have been structurally and functionally characterized: for example, GabR that regulates the utilization of g-aminobutyric acid (GABA) in B. subtilis (Belitsky, 2004) and PdxR from Listeria monocytogenes and Corynebacterium glutamicum, involved in the regulation of PLP biosynthesis (Belitsky, 2014;Jochmann et al, 2011). Recently, the crystallographic structure of the GabR protein, deposited in the Protein Data Bank (PDB) with the codes 4MGR, 4N0B, and 4TV7 (Edayathumangalam et al, 2013;Okuda et al, 2015), confirmed the presence of a fold type-I domain at the C-terminus of the regulator and opened new perspectives in deciphering the mechanism of action of MocRs. GabR is a domain swap homodimer in which the HTH domain of one subunit interacts with the PLP-binding domain of the other subunit; this is possible thanks to a very long linker that connects the two domains.…”