ArticleJournal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry2019
Solution structure and biochemical characterization of a spare part protein that restores activity to an oxygen-damaged glycyl radical enzyme.
Article in Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 11 citations in OpenAlex.
- Nature's Anaerobic Toolkit: Glycyl Radical Enzymes and Their Expanding Functional and Mechanistic Diversity.Biochemistry · 2026Review
- In vivo evidence for glycyl radical insertion into a catalytically inactive variant of pyruvate formate-lyase.FEBS letters · 2025Article
- Modeling the Initiation Phase of the Catalytic Cycle in the Glycyl-Radical Enzyme Benzylsuccinate Synthase.The journal of physical chemistry. B · 2024Article
- Type III secretion system effector YfiD inhibits the activation of host poly(ADP-ribose) polymerase-1 to promote bacterial infection.Communications biology · 2024Article
- Pyruvate formate-lyase activating enzyme: The catalytically active 5'-deoxyadenosyl radical caught in the act of H-atom abstraction.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Development of in-line anoxic small-angle X-ray scattering and structural characterization of an oxygen-sensing transcriptional regulator.bioRxiv : the preprint server for biology · 2023Article
- Genomic evaluation of novel Kenyan virulent phage isolates infecting carbapenemase-producing Klebsiella pneumoniae and safety determination of their lysates in Balb/c mice.Archives of microbiology · 2022Article
- Activation of Glycyl Radical Enzymes─Multiscale Modeling Insights into Catalysis and Radical Control in a Pyruvate Formate-Lyase-Activating Enzyme.Journal of chemical information and modeling · 2022Article
- The Autonomous Glycyl Radical Protein GrcA Restores Activity to Inactive Full-Length Pyruvate Formate-LyaseJournal of bacteriology · 2022Article
- When anaerobes encounter oxygen: mechanisms of oxygen toxicity, tolerance and defence.Nature reviews. Microbiology · 2021Review
- Rescuing activity of oxygen-damaged pyruvate formate-lyase by a spare part protein.The Journal of biological chemistry · 2021Article
- Prokaryotic Organelles: Bacterial Microcompartments inEcoSal Plus · 2020Review
- The PhoPQ Two-Component System Is the Major Regulator of Cell Surface Properties, Stress Responses and Plant-Derived Substrate Utilisation During Development ofFrontiers in microbiology · 2020Article
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8 authors at 4 institutions in 1 country.
Funding
Abstract
Glycyl radical enzymes (GREs) utilize a glycyl radical cofactor to carry out a diverse array of chemically challenging enzymatic reactions in anaerobic bacteria. Although the glycyl radical is a powerful catalyst, it is also oxygen sensitive such that oxygen exposure causes cleavage of the GRE at the site of the radical. This oxygen sensitivity presents a challenge to facultative anaerobes dwelling in areas prone to oxygen exposure. Once GREs are irreversibly oxygen damaged, cells either need to make new GREs or somehow repair the damaged one. One particular GRE, pyruvate formate lyase (PFL), can be repaired through the binding of a 14.3 kDa protein, termed YfiD, which is constitutively expressed in E. coli. Herein, we have solved a solution structure of this 'spare part' protein using nuclear magnetic resonance spectroscopy. These data, coupled with data from circular dichroism, indicate that YfiD has an inherently flexible N-terminal region (residues 1-60) that is followed by a C-terminal region (residues 72-127) that has high similarity to the glycyl radical domain of PFL. Reconstitution of PFL activity requires that YfiD binds within the core of the PFL barrel fold; however, modeling suggests that oxygen-damaged, i.e. cleaved, PFL cannot fully accommodate YfiD. We further report that a PFL variant that mimics the oxygen-damaged enzyme is highly susceptible to proteolysis, yielding additionally truncated forms of PFL. One such PFL variant of ~ 77 kDa makes an ideal scaffold for the accommodation of YfiD. A molecular model for the rescue of PFL activity by YfiD is presented.
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