Coenzyme F420 is a redox cofactor found in methanogens and in various actinobacteria. Despite the major biological importance of this cofactor, the biosynthesis of its deazaflavin core (8-hydroxy-5-deazaflavin, F(o)) is still poorly understood. F(o) synthase, the enzyme involved, is an unusual multidomain radical SAM enzyme that uses two separate 5'-deoxyadenosyl radicals to catalyze F(o) formation. In this paper, we report a detailed mechanistic study on this complex enzyme that led us to identify (1) the hydrogen atoms abstracted from the substrate by the two radical SAM domains, (2) the second tyrosine-derived product, (3) the reaction product of the CofH-catalyzed reaction, (4) the demonstration that this product is a substrate for CofG, and (5) a stereochemical study that is consistent with the formation of a p-hydroxybenzyl radical at the CofH active site. These results enable us to propose a mechanism for F(o) synthase and uncover a new catalytic motif in radical SAM enzymology involving the use of two 5'-deoxyadenosyl radicals to mediate the formation of a complex heterocycle.
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http://dx.doi.org/10.1021/ja513287k | DOI Listing |
J Am Chem Soc
November 2024
Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States.
Dynobactins are recently discovered ribosomally synthesized and post-translationally modified peptide (RiPP) antibiotics that selectively kill Gram-negative pathogens by inhibiting the β-barrel assembly machinery (Bam) located on their outer membranes. Such activity of dynobactins derives from their unique cross-links between Trp1-Asn4 and His6-Tyr8. In particular, the His6-Tyr8 cross-link is formed between N of His6 and C of Tyr8, an unprecedented type of cross-link in RiPP natural products.
View Article and Find Full Text PDFRadicals are highly reactive, short-lived chemical species that normally react indiscriminately with biological materials, and yet, nature has evolved thousands of enzymes that employ radicals to catalyze thermodynamically challenging chemistry. How these enzymes harness highly reactive radical intermediates to steer the catalysis to the correct outcome is a topic of intense investigation. Here, the results of detailed QM/MM calculations on archetype radical B-enzymes are presented that provide new insights into how these enzymes control the reactivity of radicals within their active sites.
View Article and Find Full Text PDFJ Am Chem Soc
August 2024
Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
Arsinothricin is a potent antibiotic secreted by soil bacteria. The biosynthesis of arsinothricin was proposed to involve a C-As bond formation between trivalent As and the 3-amino-3-carboxypropyl (ACP) group of -adenosyl-l-methionine (SAM), which is catalyzed by the protein ArsL. However, ArsL has not been characterized in detail.
View Article and Find Full Text PDFPhys Chem Chem Phys
July 2024
J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18200 Prague, Czech Republic.
This study investigates the factors modulating the reactivity of 5'-deoxyadenosyl (5'dAdo˙) radical, a potent hydrogen atom abstractor that forms in the active sites of radical SAM enzymes and that otherwise undergoes a rapid self-decay in aqueous solution. Here, we compare hydrogen atom abstraction (HAA) reactions between native substrates of radical SAM enzymes and 5'dAdo˙ in aqueous solution and in two enzymatic microenvironments. With that we reveal that HAA efficiency of 5'dAdo˙ is due to (i) the formation of 5'dAdo˙ in a pre-ordered complex with a substrate, which attenuates the unfavorable effect of substrate:5'dAdo˙ complex formation, and (ii) the prevention of the conformational changes associated with self-decay by a tight active-site cavity.
View Article and Find Full Text PDFJ Am Chem Soc
March 2024
Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France.
PylB is a radical -adenosyl-l-methionine (SAM) enzyme predicted to convert l-lysine into (3)-3-methyl-d-ornithine, a precursor in the biosynthesis of the 22nd proteogenic amino acid pyrrolysine. This protein highly resembles that of the radical SAM tyrosine and tryptophan lyases, which activate their substrate by abstracting a H atom from the amino-nitrogen position. Here, combining assays, analytical methods, electron paramagnetic resonance spectroscopy, and theoretical methods, we demonstrated that instead, PylB activates its substrate by abstracting a H atom from the Cγ position of l-lysine to afford the radical-based β-scission.
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