Functional Analysis of the Carboxy-Terminal Region of Bacillus subtilis TnrA, a MerR Family Protein

Structures of regulatory machinery reveal novel molecular mechanisms controlling B. subtilis nitrogen homeostasis

“…In fact, this finding is consonant with previous genetic screens and alanine scanning studies, which indicated that substitution of GS residues in the catalytic E flap, Gly59 from the D509 loop, and Glu424 inhibited TnrA binding (Wray et al 2001;Fisher et al 2002;Fisher and Wray 2006;Wray and Fisher 2007;Kayumov et al 2011;Murray et al 2013). However, because most of these mutations were in the active site, it has been unclear whether they directly affect TnrA binding or have indirect effects (i.e., alter Gln binding).…”

“…5C; Supplemental Fig. S12; Wray et al 2001;Wray and Fisher 2007;Kayumov et al 2011). Each GS side cavity binds two noninteracting TnrA molecules, and each TnrAbinding pocket is constructed from three different GS subunits: two from one heptamer and the third from a subunit in the adjacent stacked heptamer (Fig.…”

“…The tight apposition of TnrA and the E flap necessitates that TnrA residue 99 and GS E flap residue 302 are both glycines, which explains why mutation of either residue abolishes binding ( Fig. 5D; Wray et al 2001;Wray and Fisher 2007). The helical face of TnrA opposite to that interacting with the E flap contacts the D509 loop; Gln100 interacts with the backbone atoms of residues 50-52, and Phe105 packs against Phe60 and Val61, while TnrA residue Met96 interacts with Ile63 (Fig.…”

Inactivation of the general transcription factor TnrA in Bacillus subtilis by proteolysis

“…The most effective feedback inhibitors of GS biosynthetic activity are glutamine and AMP, while partial inhibition has been observed with alanine, glycine, serine and tryptophan (Deuel & Prusiner, 1974). Mutations in TnrA that result in constitutive expression of the TnrA-activated amtB promoter all lie within the carboxy-terminal region of TnrA and impair the interaction between GS and TnrA (Wray et al, 2001;Wray & Fisher, 2006). Thus, the feedback inhibitors of GS are the metabolic signals that cause inhibition of TnrA through its GS interaction.…”

Protein structure prediction and conformational transitions

“…It allows structural alignments based on secondary structure topology , provides certain structural understanding of proteins when homologous tertiary structures are not available in the PDB (Wray and Fisher, 2007) (especially for membrane proteins (Kashlan et al, 2006)), and leads to more accurate tertiary structure predictions (Meiler and Baker, 2003;Jayaram et al, 2006). For tertiary structure predictions, we encounter two main limitations: (1) for certain proteins, tertiary structure prediction methods cannot provide reliable 3D models, (2) when a model can be built, the model resolution can vary widely from 2-3 Å to tens of Angstroms (Moult, 2006).…”