8BFR

The E. coli TrpD2 protein YbiB at 1.3 A resolution

Summary for 8BFR

• Entry DOI: 10.2210/pdb8bfr/pdb
• Descriptor: Protein YbiB, GLYCEROL (3 entities in total)
• Functional Keywords: trpd2, ybib, dna-binding, dna binding protein
• Biological source: Escherichia coli
• Total number of polymer chains: 1
• Total formula weight: 37737.42

Authors

Deckers, B.,Galicia, C.,Versees, W. (deposition date: 2022-10-26, release date: 2023-02-22, Last modification date: 2024-02-07)

Primary citation

Deckers, B.,Vercauteren, S.,De Kock, V.,Martin, C.,Lazar, T.,Herpels, P.,Dewachter, L.,Verstraeten, N.,Peeters, E.,Ballet, S.,Michiels, J.,Galicia, C.,Versees, W.
YbiB: a novel interactor of the GTPase ObgE.
Nucleic Acids Res., 51:3420-3435, 2023

PubMed Abstract: Obg is a widely conserved and essential GTPase in bacteria, which plays a central role in a large range of important cellular processes, such as ribosome biogenesis, DNA replication, cell division and bacterial persistence. Nevertheless, the exact function of Obg in these processes and the interactions it makes within the associated pathways remain largely unknown. Here, we identify the DNA-binding TrpD2 protein YbiB as an interactor of the Escherichia coli Obg (ObgE). We show that both proteins interact with high affinity in a peculiar biphasic fashion, and pinpoint the intrinsically disordered and highly negatively charged C-terminal domain of ObgE as a main driver for this interaction. Molecular docking and X-ray crystallography, together with site-directed mutagenesis, are used to map the binding site of this ObgE C-terminal domain within a highly positively charged groove on the surface of the YbiB homodimer. Correspondingly, ObgE efficiently inhibits the binding of DNA to YbiB, indicating that ObgE competes with DNA for binding in the positive clefts of YbiB. This study thus forms an important step for the further elucidation of the interactome and cellular role of the essential bacterial protein Obg.

PubMed: 36864742
DOI: 10.1093/nar/gkad127

Experimental method

X-RAY DIFFRACTION (1.3 Å)