ArticleThe Journal of biological chemistry2015
YbiB from Escherichia coli, the Defining Member of the Novel TrpD2 Family of Prokaryotic DNA-binding Proteins.
Article in The Journal of biological chemistry, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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7 citing papers in PubMed.
- Ectopic overexpression and CRISPRi-based knockdown ofJournal of bacteriology · 2025Article
- Experimental evolution ofMicrobiology spectrum · 2025Article
- Article
- YbiB: a novel interactor of the GTPase ObgE.Nucleic acids research · 2023Article
- Structure, mechanism and inhibition of anthranilate phosphoribosyltransferase.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2023Review
- Deciphering Microbial Metal Toxicity Responses via Random Bar Code Transposon Site Sequencing and Activity-Based Metabolomics.Applied and environmental microbiology · 2021Article
- AGeNNT: annotation of enzyme families by means of refined neighborhood networks.BMC bioinformatics · 2017Article
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6 authors.
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Abstract
We present the crystal structure and biochemical characterization of Escherichia coli YbiB, a member of the hitherto uncharacterized TrpD2 protein family. Our results demonstrate that the functional diversity of proteins with a common fold can be far greater than predictable by computational annotation. The TrpD2 proteins show high structural homology to anthranilate phosphoribosyltransferase (TrpD) and nucleoside phosphorylase class II enzymes but bind with high affinity (KD = 10-100 nM) to nucleic acids without detectable sequence specificity. The difference in affinity between single- and double-stranded DNA is minor. Results suggest that multiple YbiB molecules bind to one longer DNA molecule in a cooperative manner. The YbiB protein is a homodimer that, therefore, has two electropositive DNA binding grooves. But due to negative cooperativity within the dimer, only one groove binds DNA in in vitro experiments. A monomerized variant remains able to bind DNA with similar affinity, but the negative cooperative effect is eliminated. The ybiB gene forms an operon with the DNA helicase gene dinG and is under LexA control, being induced by DNA-damaging agents. Thus, speculatively, the TrpD2 proteins may be part of the LexA-controlled SOS response in bacteria.
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