Deamination of choline catalyzed by the glycyl radical enzyme choline trimethylamine-lyase (CutC) has emerged as an important route for the production of trimethylamine, a microbial metabolite ...associated with both human disease and biological methane production. Here, we have determined five high-resolution X-ray structures of wild-type CutC and mechanistically informative mutants in the presence of choline. Within an unexpectedly polar active site, CutC orients choline through hydrogen bonding with a putative general base, and through close interactions between phenolic and carboxylate oxygen atoms of the protein scaffold and the polarized methyl groups of the trimethylammonium moiety. These structural data, along with biochemical analysis of active site mutants, support a mechanism that involves direct elimination of trimethylamine. This work broadens our understanding of radical-based enzyme catalysis and will aid in the rational design of inhibitors of bacterial trimethylamine production.
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•Molecular basis for trimethylamine production in human gut•Crystallographic snapshots of radical-based enzyme catalysis•CH—O hydrogen bonds help bind choline in an enzyme active site•Microbial mechanism and human health linkage explored
This crystallographic and biochemical study provides a molecular depiction of how trimethylamine, a metabolite associated with both liver and cardiovascular disease, is generated from choline by the human gut microbiota.
Genome sequencing of environmental bacteria allows identification of biosynthetic gene clusters encoding unusual combinations of enzymes that produce unknown natural products. We identified a pathway ...in which a ribosomally synthesized small peptide serves as a scaffold for nonribosomal peptide extension and chemical modification. Amino acids are transferred to the carboxyl terminus of the peptide through adenosine triphosphate and amino acyl-tRNA-dependent chemistry that is independent of the ribosome. Oxidative rearrangement, carboxymethylation, and proteolysis of a terminal cysteine yields an amino acid-derived small molecule. Microcrystal electron diffraction demonstrates that the resulting product is isosteric to glutamate. We show that a similar peptide extension is used during the biosynthesis of the ammosamides, which are cytotoxic pyrroloquinoline alkaloids. These results suggest an alternative paradigm for biosynthesis of amino acid-derived natural products.
Ribosomally synthesized and Post-translationally modified Peptides (RiPPs) take advantage of the ribosomal translation machinery to generate linear peptides that are subsequently modified with ...heterocycles and/or macrocycles to impose three-dimensional structure and thwart degradation by proteases. Although RiPP precursors are limited to proteinogenic amino acids, post-translational modifications (PTMs) can alter the structure of individual amino acids and thereby improve the stability and biological activity of the molecule. These “tailoring modifications” often occur on amino acid side chainsfor example, hydroxylation, methylation, halogenation, prenylation, and acylationbut can also take place within the backbone, as in epimerization, or can result in capping of the N- or C-terminus. At one extreme, these modifications can be essential to the activity of the RiPP, either as a compulsory step in reaching the final molecule or by imparting chemical functionality required for biological activity. At the other extreme, tailoring PTMs may have little effect on the activity in an in vitro settingpossibly because of test conditions that do not match the biological context in which the PTMs evolved. Establishing the molecular basis for the function of tailoring PTMs often requires a three-dimensional structure of the RiPP bound to its biological target. These structures have revealed roles for tailoring PTMs that include providing additional hydrogen bonds to targets, rigidifying the RiPP structure to reduce the entropic cost of binding, or altering the secondary structure of the peptide backbone. Bacterial RiPPs are particularly suited to structural characterization, as they are relatively easy to isolate from laboratory cultures or to produce in a heterologous host. The identification of new tailoring PTMs within bacteria is also facilitated by clustering of the genes encoding tailoring enzymes with those of the RiPP precursor and primary modification enzymes. In this Account, we describe the effects of tailoring PTMs on RiPP structure, their interactions with biological targets, and their influence on RiPP stability, with a focus on bacterial RiPP classes. We also discuss the enzymes that generate tailoring PTMs and highlight examples of and prospects for engineering of RiPPs.
Clearing the Air Funk, Michael A.; Ash, Caroline; Smith, Jesse ...
Science (American Association for the Advancement of Science),
07/2024, Letnik:
385, Številka:
6707
Journal Article
Graphene has attracted a lot of attention for ultracapacitor electrodes because of its high electrical conductivity, high surface area, and superb chemical stability. However, poor volumetric ...capacitive performance of typical graphene-based electrodes has hindered their practical applications because of the extremely low density. Herein we report a scalable synthesis method of holey graphene (h-Graphene) in a single step without using any catalysts or special chemicals. The film made of the as-synthesized h-Graphene exhibited relatively strong mechanical strength, 2D hole morphology, high density, and facile processability. This scalable one-step synthesis method for h-Graphene is time-efficient, cost-efficient, environmentally friendly, and generally applicable to other two-dimensional materials. The ultracapacitor electrodes based on the h-Graphene show a remarkably improved volumetric capacitance with about 700% increase compared to that of regular graphene electrodes. Modeling on individual h-Graphene was carried out to understand the excellent processability and improved ultracapacitor performance.
In Science Journals Smith, Jesse; Szuromi, Phil; Stajic, Jelena ...
Science (American Association for the Advancement of Science),
08/2024, Letnik:
385, Številka:
6709
Journal Article
In Science Journals Smith, Jesse; Funk, Michael A.; Stern, Peter ...
Science (American Association for the Advancement of Science),
07/2024, Letnik:
385, Številka:
6707
Journal Article
In Science Journals Grocholski, Brent; Szuromi, Phil; Yeston, Jake S. ...
Science (American Association for the Advancement of Science),
07/2024, Letnik:
385, Številka:
6706
Journal Article
In Science Journals Funk, Michael A.; Osborne, Ian S.; Szuromi, Phil ...
Science (American Association for the Advancement of Science),
07/2024, Letnik:
385, Številka:
6705
Journal Article
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