Surprise! A hidden B12 cofactor catalyzes a radical methylation

Jarrett, Joseph T.

doi:10.1074/jbc.h119.009976

Cited by 4 publications

(3 citation statements)

References 8 publications

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“…4a ). A prevalence of B 12 -binding domains identified in biosynthetic genes raises the possibility of B 12 -dependent methylation during synthesis or post-translational modification of biosynthesized peptides 61 , 64 . Phosphopantetheine attachment site domains were also ubiquitous in Cariaco BGCs.…”

Section: Resultsmentioning

confidence: 99%

Diverse secondary metabolites are expressed in particle-associated and free-living microorganisms of the permanently anoxic Cariaco Basin

et al. 2023

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Secondary metabolites play essential roles in ecological interactions and nutrient acquisition, and are of interest for their potential uses in medicine and biotechnology. Genome mining for biosynthetic gene clusters (BGCs) can be used for the discovery of new compounds. Here, we use metagenomics and metatranscriptomics to analyze BGCs in free-living and particle-associated microbial communities through the stratified water column of the Cariaco Basin, Venezuela. We recovered 565 bacterial and archaeal metagenome-assembled genomes (MAGs) and identified 1154 diverse BGCs. We show that differences in water redox potential and microbial lifestyle (particle-associated vs. free-living) are associated with variations in the predicted composition and production of secondary metabolites. Our results indicate that microbes, including understudied clades such as Planctomycetota, potentially produce a wide range of secondary metabolites in these anoxic/euxinic waters.

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Section: Resultsmentioning

confidence: 99%

Diverse secondary metabolites are expressed in particle-associated and free-living microorganisms of the permanently anoxic Cariaco Basin

et al. 2023

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“…Tokk is involved in consecutive methylations to install an isopropyl group on the C6 carbon of the carbapenem antibiotic asparenomycin A [62,63], while Mmp10 catalyzes the posttranslational methylation of the C δ position of arginine residue R285 of methyl-coenzyme M reductase [64][65][66]. Even though TsrM, Tokk and Mmp10 all use the Cbl cofactor as an intermediate methyl carrier, they employ very different mechanisms to catalyze the methyl transfer reaction [67]. Strikingly, TsrM is an unprecedented exception to the radical SAM enzyme mechanistic paradigm that normally proceeds through 5 -dA • radical generation [58,68,69].…”

Section: Cobalamin-dependent Rsmases: Similar Domains Different Mecha...mentioning

confidence: 99%

Structure and Catalytic Mechanism of Radical SAM Methylases

Nguyen

Nicolet

2022

Life

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Methyl transfer is essential in myriad biological pathways found across all domains of life. Unlike conventional methyltransferases that catalyze this reaction through nucleophilic substitution, many members of the radical S-adenosyl-L-methionine (SAM) enzyme superfamily use radical-based chemistry to methylate unreactive carbon centers. These radical SAM methylases reductively cleave SAM to generate a highly reactive 5′-deoxyadenosyl radical, which initiates a broad range of transformations. Recently, crystal structures of several radical SAM methylases have been determined, shedding light on the unprecedented catalytic mechanisms used by these enzymes to overcome the substantial activation energy barrier of weakly nucleophilic substrates. Here, we review some of the discoveries on this topic over the last decade, focusing on enzymes for which three-dimensional structures are available to identify the key players in the mechanisms, highlighting the dual function of SAM as a methyl donor and a 5’-deoxyadenosyl radical or deprotonating base source. We also describe the role of the protein matrix in orchestrating the reaction through different strategies to catalyze such challenging methylations.

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“…So far, none of the rSAM MTs in bottromycin biosynthesis are reconstituted and characterized in vitro. Based on the previous reports on similar enzymes, a proposed mechanism 45 for these enzymes in bottromycin pathway is shown in Scheme 2. At first, co(I)balamin (9) will react with SAM-1 (10) via S N 2 reaction to give methyl co(III)balamin (11) and SAH (12).…”

Section: Account Synlettmentioning

confidence: 99%

Recent Advancements in Bottromycin Biosynthesis

Mahanta¹,

PH²,

KS³

et al. 2022

Synlett

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Bottromycin is a structurally complex cyclic peptidic compound isolated from Streptomyces bottropensis and related organisms and belongs to the RiPP family of natural products (ribosomally synthesized and post-translationally modified peptides). It exhibits potent antibacterial properties against gram-positive pathogens (including drug resistant strains such as MRSA, MIC 1 μg/mL and VRE, MIC 0.5 μg/mL) and mycoplasma. Bottromycin blocks the binding of the aminoacyl-tRNA to the A-site on the 50S ribosome and hence inhibits protein synthesis. Bottromycins contain structurally diverse post-translational modifications (PTMs) on a small peptide (GPVVVFDC) including a unique macrocyclic amidine, rare β-methylation, terminal thiazole heterocycle, oxidative decarboxylation, and Asp epimerization, among others. It exhibits a precursor peptide organization with a C-terminal follower peptide and a N-terminal core peptide. There are several new studies reported recently which gave detailed insights into the bottromycin biosynthesis pathway. This Account highlights the current advancements in understanding the biosynthetic pathway of bottromycin focusing mainly on the biochemically and structurally characterized enzymes and intricate details of the peptide–protein biophysical interactions. These studies have provided a strong foundation for conducting combinatorial biosynthesis and synthetic biological studies to create novel bottromycin variants for therapeutic applications.1 Introduction2 Biosynthetic Pathway for Bottromycin3 Enzymology of Bottromycin Biosynthesis3.1 Cleavage of Methionine (BotP)3.2 Radical SAM Methyltransferases (BotRMT1, BotRMT2, BotRMT3)3.3 ATP-Dependent YcaO Enzymes3.3.1 Thiazoline Formation by BotC3.3.2 Macrolactamidine Formation by BotCD3.4 Follower Peptide Hydrolysis (BotAH)3.5 Aspartate Epimerization (BotH)3.6 Oxidative Decarboxylation (BotCYP)3.7 O-Methyltransferase (BotOMT)4 Heterologous Bottromycin Production and Analogue Preparation5 Summary and Outlook

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Surprise! A hidden B12 cofactor catalyzes a radical methylation

Cited by 4 publications

References 8 publications

Diverse secondary metabolites are expressed in particle-associated and free-living microorganisms of the permanently anoxic Cariaco Basin

Diverse secondary metabolites are expressed in particle-associated and free-living microorganisms of the permanently anoxic Cariaco Basin

Structure and Catalytic Mechanism of Radical SAM Methylases

Recent Advancements in Bottromycin Biosynthesis

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