7C7E

Crystal structure of C terminal domain of Escherichia coli DgoR

Summary for 7C7E

• Entry DOI: 10.2210/pdb7c7e/pdb
• Descriptor: Putative DNA-binding transcriptional regulator, ZINC ION, SULFATE ION, ... (5 entities in total)
• Functional Keywords: d-galactonate, gntr superfamily, transcription repressor, dna binding protein
• Biological source: Escherichia coli O7:K1 (strain IAI39 / ExPEC)
• Total number of polymer chains: 1
• Total formula weight: 26797.40

Authors

Lin, W. (deposition date: 2020-05-25, release date: 2021-01-20, Last modification date: 2024-10-23)

Primary citation

Lin, Z.,Sun, Y.,Liu, Y.,Tong, S.,Shang, Z.,Cai, Y.,Lin, W.
Structural and Functional Analyses of the Transcription Repressor DgoR From Escherichia coli Reveal a Divalent Metal-Containing D-Galactonate Binding Pocket.
Front Microbiol, 11:590330-590330, 2020

PubMed Abstract: The transcription repressor of D-galactonate metabolism, DgoR, from belongs to the FadR family of the GntR superfamily. In the presence of D-galactonate, DgoR binds to two inverted repeats overlapping the 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, Mg, and Ca. 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.

PubMed: 33224125
DOI: 10.3389/fmicb.2020.590330

Experimental method

X-RAY DIFFRACTION (2.047 Å)