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The transcription repressor of  D -galactonate metabolism, DgoR, from  Escherichia coli  belongs to the FadR family of the GntR superfamily. In the presence of  D -galactonate, DgoR binds to two inverted repeats overlapping the  dgo  cis-acting promoter repressing the expression of genes involved in  D -galactonate metabolism. To further understand the structural and molecular details of ligand and effector interactions between  D -galactonate and this FadR family member, herein we solved the crystal structure of C-terminal domain of DgoR (DgoR_C), which revealed a unique divalent metal-containing substrate binding pocket. The metal ion is required for  D -galactonate binding, as evidenced by the dramatically decreased affinity between  D -galactonate and DgoR in the presence of EDTA, which can be reverted by the addition of Zn 2+ , Mg 2+ , and Ca 2+ . The key amino acid residues involved in the interactions between  D -galactonate and DgoR were revealed by molecular docking studies and further validated with biochemical studies by site-directed mutagenesis. It was found that changes to alanine in residues R102, W181, T191, and R224 resulted in significantly decreased binding affinities for  D -galactonate, as determined by EMSA and MST assays. These results suggest that the molecular modifications induced by a  D -galactonate and a metal binding in the DgoR are required for DNA binding activity and consequently, transcriptional inhibition.

frontiers in microbiology

Structural and Functional Analyses of the Transcription Repressor DgoR From Escherichia coli Reveal a Divalent Metal-Containing D-Galactonate Binding Pocket