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Olivier Berteau - One of the best experts on this subject based on the ideXlab platform.
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Radical SAM enzymes in the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs)
Frontiers in Chemistry, 2017Co-Authors: Alhosna Benjdia, Clémence Balty, Olivier BerteauAbstract:Ribosomally-synthesized and post-translationally modified peptides (RiPPs) are a large and diverse family of natural products. They possess interesting biological properties such as antibiotic or anticancer activities, making them attractive for therapeutic applications. In contrast to polyketides and non-ribosomal peptides, RiPPs derive from ribosomal peptides and are post-translationally modified by diverse enzyme families. Among them, the emerging superfamily of Radical SAM enzymes has been shown to play a major role. These enzymes catalyze the formation of a wide range of post-translational modifications some of them having no counterparts in living systems or synthetic chemistry. The investigation of Radical SAM enzymes has not only illuminated unprecedented strategies used by living systems to tailor peptides into complex natural products but has also allowed to uncover novel RiPP families. In this review, we summarize the current knowledge on Radical SAM enzymes catalyzing RiPP post-translational modifications and discuss their mechanisms and growing importance notably in the context of the human microbiota.
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Carbon–sulfur bond-forming reaction catalysed by the Radical SAM enzyme HydE
Nature Chemistry, 2016Co-Authors: Roman Rohac, Patricia Amara, Alhosna Benjdia, Lydie Martin, Pauline Ruffié, Adrien Favier, Olivier Berteau, Juan C. Fontecilla-camps, Jean-marie Mouesca, Yvain NicoletAbstract:L -Cysteine-derived thiazolidines have now been shown to be artificial substrates of the Radical SAM enzyme HydE, which converts them into S -adenosyl- L -cysteine. Carbon–sulfur bonds are formed in a concerted mechanism that involves the formation of a C-centred Radical that concomitantly attacks the S atom of a thioether. This is the first example of a Radical SAM enzyme that reacts directly on a sulfur atom instead of abstracting an H-atom. Carbon–sulfur bond formation at aliphatic positions is a challenging reaction that is performed efficiently by Radical S -adenosyl- L -methionine (SAM) enzymes. Here we report that 1,3-thiazolidines can act as ligands and substrates for the Radical SAM enzyme HydE, which is involved in the assembly of the active site of [FeFe]-hydrogenase. Using X-ray crystallography, in vitro assays and NMR spectroscopy we identified a Radical-based reaction mechanism that is best described as the formation of a C-centred Radical that concomitantly attacks the sulfur atom of a thioether. To the best of our knowledge, this is the first example of a Radical SAM enzyme that reacts directly on a sulfur atom instead of abstracting a hydrogen atom. Using theoretical calculations based on our high-resolution structures we followed the evolution of the electronic structure from SAM through to the formation of S -adenosyl- L -cysteine. Our results suggest that, at least in this case, the widely proposed and highly reactive 5′-deoxyadenosyl Radical species that triggers the reaction in Radical SAM enzymes is not an isolable intermediate.
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Carbon-sulfur bond-forming reaction catalysed by the Radical SAM enzyme HydE.
Nature Chemistry, 2016Co-Authors: Roman Rohac, Patricia Amara, Alhosna Benjdia, Lydie Martin, Pauline Ruffié, Adrien Favier, Olivier Berteau, Juan C. Fontecilla-camps, Jean-marie Mouesca, Yvain NicoletAbstract:Carbon-sulfur bond formation at aliphatic positions is a challenging reaction that is performed efficiently by Radical S-adenosyl-L-methionine (SAM) enzymes. Here we report that 1,3-thiazolidines can act as ligands and substrates for the Radical SAM enzyme HydE, which is involved in the assembly of the active site of [FeFe]-hydrogenase. Using X-ray crystallography, in vitro assays and NMR spectroscopy we identified a Radical-based reaction mechanism that is best described as the formation of a C-centred Radical that concomitantly attacks the sulfur atom of a thioether. To the best of our knowledge, this is the first example of a Radical SAM enzyme that reacts directly on a sulfur atom instead of abstracting a hydrogen atom. Using theoretical calculations based on our high-resolution structures we followed the evolution of the electronic structure from SAM through to the formation of S-adenosyl-L-cysteine. Our results suggest that, at least in this case, the widely proposed and highly reactive 5'-deoxyadenosyl Radical species that triggers the reaction in Radical SAM enzymes is not an isolable intermediate.
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Thioether bond formation by SPASM domain Radical SAM enzymes: Cα H-atom abstraction in subtilosin A biosynthesis
Chemical communications (Cambridge England), 2016Co-Authors: Alhosna Benjdia, Alain Guillot, Benjamin Lefranc, Hubert Vaudry, Jérôme Leprince, Olivier BerteauAbstract:AlbA is a Radical SAM enzyme catalyzing the formation of three unusual thioether bonds in the antibiotic subtilosin A. We demonstrate here that AlbA catalyzes direct Cα H-atom abstraction and likely contains three essential [4Fe-4S] centers. This leads us to propose novel mechanistic perspectives for thioether bond catalysis by Radical SAM enzymes.
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Thioether bond formation by SPASM domain Radical SAM enzymes: C α H-atom abstraction in subtilosin A biosynthesis
Chemical Communications, 2016Co-Authors: Alhosna Benjdia, Alain Guillot, Benjamin Lefranc, Hubert Vaudry, Jérôme Leprince, Olivier BerteauAbstract:AlbA is a Radical SAM enzyme catalyzing the formation of three unusual thioether bonds in the antibiotic subtilosin A. We demonstrate here that AlbA catalyzes direct Cα H-atom abstraction and likely contains three essential [4Fe-4S] centers. This leads us to propose novel mechanistic perspectives for thioether bond catalysis by Radical SAM enzymes.
Alhosna Benjdia - One of the best experts on this subject based on the ideXlab platform.
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Radical SAM enzymes in the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs)
Frontiers in Chemistry, 2017Co-Authors: Alhosna Benjdia, Clémence Balty, Olivier BerteauAbstract:Ribosomally-synthesized and post-translationally modified peptides (RiPPs) are a large and diverse family of natural products. They possess interesting biological properties such as antibiotic or anticancer activities, making them attractive for therapeutic applications. In contrast to polyketides and non-ribosomal peptides, RiPPs derive from ribosomal peptides and are post-translationally modified by diverse enzyme families. Among them, the emerging superfamily of Radical SAM enzymes has been shown to play a major role. These enzymes catalyze the formation of a wide range of post-translational modifications some of them having no counterparts in living systems or synthetic chemistry. The investigation of Radical SAM enzymes has not only illuminated unprecedented strategies used by living systems to tailor peptides into complex natural products but has also allowed to uncover novel RiPP families. In this review, we summarize the current knowledge on Radical SAM enzymes catalyzing RiPP post-translational modifications and discuss their mechanisms and growing importance notably in the context of the human microbiota.
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Carbon–sulfur bond-forming reaction catalysed by the Radical SAM enzyme HydE
Nature Chemistry, 2016Co-Authors: Roman Rohac, Patricia Amara, Alhosna Benjdia, Lydie Martin, Pauline Ruffié, Adrien Favier, Olivier Berteau, Juan C. Fontecilla-camps, Jean-marie Mouesca, Yvain NicoletAbstract:L -Cysteine-derived thiazolidines have now been shown to be artificial substrates of the Radical SAM enzyme HydE, which converts them into S -adenosyl- L -cysteine. Carbon–sulfur bonds are formed in a concerted mechanism that involves the formation of a C-centred Radical that concomitantly attacks the S atom of a thioether. This is the first example of a Radical SAM enzyme that reacts directly on a sulfur atom instead of abstracting an H-atom. Carbon–sulfur bond formation at aliphatic positions is a challenging reaction that is performed efficiently by Radical S -adenosyl- L -methionine (SAM) enzymes. Here we report that 1,3-thiazolidines can act as ligands and substrates for the Radical SAM enzyme HydE, which is involved in the assembly of the active site of [FeFe]-hydrogenase. Using X-ray crystallography, in vitro assays and NMR spectroscopy we identified a Radical-based reaction mechanism that is best described as the formation of a C-centred Radical that concomitantly attacks the sulfur atom of a thioether. To the best of our knowledge, this is the first example of a Radical SAM enzyme that reacts directly on a sulfur atom instead of abstracting a hydrogen atom. Using theoretical calculations based on our high-resolution structures we followed the evolution of the electronic structure from SAM through to the formation of S -adenosyl- L -cysteine. Our results suggest that, at least in this case, the widely proposed and highly reactive 5′-deoxyadenosyl Radical species that triggers the reaction in Radical SAM enzymes is not an isolable intermediate.
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Carbon-sulfur bond-forming reaction catalysed by the Radical SAM enzyme HydE.
Nature Chemistry, 2016Co-Authors: Roman Rohac, Patricia Amara, Alhosna Benjdia, Lydie Martin, Pauline Ruffié, Adrien Favier, Olivier Berteau, Juan C. Fontecilla-camps, Jean-marie Mouesca, Yvain NicoletAbstract:Carbon-sulfur bond formation at aliphatic positions is a challenging reaction that is performed efficiently by Radical S-adenosyl-L-methionine (SAM) enzymes. Here we report that 1,3-thiazolidines can act as ligands and substrates for the Radical SAM enzyme HydE, which is involved in the assembly of the active site of [FeFe]-hydrogenase. Using X-ray crystallography, in vitro assays and NMR spectroscopy we identified a Radical-based reaction mechanism that is best described as the formation of a C-centred Radical that concomitantly attacks the sulfur atom of a thioether. To the best of our knowledge, this is the first example of a Radical SAM enzyme that reacts directly on a sulfur atom instead of abstracting a hydrogen atom. Using theoretical calculations based on our high-resolution structures we followed the evolution of the electronic structure from SAM through to the formation of S-adenosyl-L-cysteine. Our results suggest that, at least in this case, the widely proposed and highly reactive 5'-deoxyadenosyl Radical species that triggers the reaction in Radical SAM enzymes is not an isolable intermediate.
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Thioether bond formation by SPASM domain Radical SAM enzymes: Cα H-atom abstraction in subtilosin A biosynthesis
Chemical communications (Cambridge England), 2016Co-Authors: Alhosna Benjdia, Alain Guillot, Benjamin Lefranc, Hubert Vaudry, Jérôme Leprince, Olivier BerteauAbstract:AlbA is a Radical SAM enzyme catalyzing the formation of three unusual thioether bonds in the antibiotic subtilosin A. We demonstrate here that AlbA catalyzes direct Cα H-atom abstraction and likely contains three essential [4Fe-4S] centers. This leads us to propose novel mechanistic perspectives for thioether bond catalysis by Radical SAM enzymes.
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Thioether bond formation by SPASM domain Radical SAM enzymes: C α H-atom abstraction in subtilosin A biosynthesis
Chemical Communications, 2016Co-Authors: Alhosna Benjdia, Alain Guillot, Benjamin Lefranc, Hubert Vaudry, Jérôme Leprince, Olivier BerteauAbstract:AlbA is a Radical SAM enzyme catalyzing the formation of three unusual thioether bonds in the antibiotic subtilosin A. We demonstrate here that AlbA catalyzes direct Cα H-atom abstraction and likely contains three essential [4Fe-4S] centers. This leads us to propose novel mechanistic perspectives for thioether bond catalysis by Radical SAM enzymes.
Alain Guillot - One of the best experts on this subject based on the ideXlab platform.
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Thioether bond formation by SPASM domain Radical SAM enzymes: Cα H-atom abstraction in subtilosin A biosynthesis
Chemical communications (Cambridge England), 2016Co-Authors: Alhosna Benjdia, Alain Guillot, Benjamin Lefranc, Hubert Vaudry, Jérôme Leprince, Olivier BerteauAbstract:AlbA is a Radical SAM enzyme catalyzing the formation of three unusual thioether bonds in the antibiotic subtilosin A. We demonstrate here that AlbA catalyzes direct Cα H-atom abstraction and likely contains three essential [4Fe-4S] centers. This leads us to propose novel mechanistic perspectives for thioether bond catalysis by Radical SAM enzymes.
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Thioether bond formation by SPASM domain Radical SAM enzymes: C α H-atom abstraction in subtilosin A biosynthesis
Chemical Communications, 2016Co-Authors: Alhosna Benjdia, Alain Guillot, Benjamin Lefranc, Hubert Vaudry, Jérôme Leprince, Olivier BerteauAbstract:AlbA is a Radical SAM enzyme catalyzing the formation of three unusual thioether bonds in the antibiotic subtilosin A. We demonstrate here that AlbA catalyzes direct Cα H-atom abstraction and likely contains three essential [4Fe-4S] centers. This leads us to propose novel mechanistic perspectives for thioether bond catalysis by Radical SAM enzymes.
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thiostrepton tryptophan methyltransferase expands the chemistry of Radical SAM enzymes
Nature Chemical Biology, 2012Co-Authors: Alhosna Benjdia, Olivier Berteau, Stephane Pierre, Alain Guillot, Corine Sandstrom, Philippe LangellaAbstract:TsrM, a member of the Radical SAM enzyme family, is shown to catalyze tryptophan methylation en route to thiostrepton A with the help of a methylcobalamin cofactor and without generating the canonical 5-deoxyadenosyl Radical.
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Thiostrepton tryptophan methyltransferase expands the chemistry of Radical SAM enzymes
Nature Chemical Biology, 2012Co-Authors: Stephane Pierre, Alhosna Benjdia, Alain Guillot, Corine Sandstrom, Philippe Langella, Olivier BerteauAbstract:Methylation is among the most widespread chemical modifications encountered in biomolecules and has a pivotal role in many major biological processes. In the biosynthetic pathway of the antibiotic thiostrepton A, we identified what is to our knowledge the first tryptophan methyltransferase. We show that it uses unprecedented chemistry to methylate inactivated sp(2)-hybridized carbon atoms, despite being predicted to be a Radical SAM enzyme.
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Anaerobic Sulfatase-Maturating Enzymes: Radical SAM Enzymes Able To Catalyze in Vitro Sulfatase Post-translational Modification
Journal of the American Chemical Society, 2007Co-Authors: Alhosna Benjdia, Alain Guillot, Hubert Vaudry, Jérôme Leprince, Sylvie Rabot, Olivier BerteauAbstract:Sulfatases are widespread enzymes, found from prokaryotes to eukaryotes and involved in many biochemical processes. To be active, all known sulfatases undergo a unique post-translational modification leading to the conversion of a critical active-site residue, i.e., a serine or a cysteine, into a C alpha-formylglycine (FGly). Two different systems are involved in sulfatase maturation. One, named FGE, is an oxygen-dependent oxygenase and has been fully characterized. The other one, a member of the so-called "Radical SAM" super-family, has been only preliminary investigated. This latter system allows the maturation of sulfatases in strictly anaerobic conditions and has thus been named anSME (anaerobic Sulfatase Maturating Enzyme). Our results provide the first experimental evidence that anSME are iron-sulfur enzymes able to perform the reductive cleavage of SAM and thus belong to the Radical SAM super-family. Furthermore, they demonstrate that anSME are able to efficiently oxidize cysteine into FGly in an oxygen-independent manner.
Squire J Booker - One of the best experts on this subject based on the ideXlab platform.
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Structural basis for non-Radical catalysis by TsrM, a Radical SAM methylase
Nature Chemical Biology, 2021Co-Authors: Hayley L. Knox, Catherine L. Drennan, Tyler L. Grove, Percival Yang-ting Chen, Anthony J. Blaszczyk, Arnab Mukherjee, Erica L. Schwalm, Bo Wang, Squire J BookerAbstract:Tryptophan 2C methyltransferase (TsrM) methylates C2 of the indole ring of l -tryptophan during biosynthesis of the quinaldic acid moiety of thiostrepton. TsrM is annotated as a cobalamin-dependent Radical S -adenosylmethionine (SAM) methylase; however, TsrM does not reductively cleave SAM to the universal 5ʹ-deoxyadenosyl 5ʹ-Radical intermediate, a hallmark of Radical SAM (RS) enzymes. Herein, we report structures of TsrM from Kitasatospora setae , which are the first structures of a cobalamin-dependent Radical SAM methylase. Unexpectedly, the structures show an essential arginine residue that resides in the proximal coordination sphere of the cobalamin cofactor, and a [4Fe–4S] cluster that is ligated by a glutamyl residue and three cysteines in a canonical CXXXCXXC RS motif. Structures in the presence of substrates suggest a substrate-assisted mechanism of catalysis, wherein the carboxylate group of SAM serves as a general base to deprotonate N1 of the tryptophan substrate, facilitating the formation of a C2 carbanion. Crystal structures of a cobalamin-dependent Radical S -adenosylmethionine (SAM) methylase reveal an unexpected mechanism that involves substrate-assisted catalysis whereby the carboxylate group of the co-substrate SAM serves as a general base.
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Atlas of the Radical SAM Superfamily: Divergent Evolution of Function Using a "Plug and Play" Domain.
Methods in enzymology, 2018Co-Authors: Gemma L. Holliday, Squire J Booker, Eyal Akiva, Elaine C. Meng, Shoshana D. Brown, Sara Calhoun, Ursula Pieper, Andrej Sali, Patricia C. BabbittAbstract:Abstract The Radical SAM superfamily contains over 100,000 homologous enzymes that catalyze a remarkably broad range of reactions required for life, including metabolism, nucleic acid modification, and biogenesis of cofactors. While the highly conserved SAM-binding motif responsible for formation of the key 5′-deoxyadenosyl Radical intermediate is a key structural feature that simplifies identification of superfamily members, our understanding of their structure–function relationships is complicated by the modular nature of their structures, which exhibit varied and complex domain architectures. To gain new insight about these relationships, we classified the entire set of sequences into similarity-based subgroups that could be visualized using sequence similarity networks. This superfamily-wide analysis reveals important features that had not previously been appreciated from studies focused on one or a few members. Functional information mapped to the networks indicates which members have been experimentally or structurally characterized, their known reaction types, and their phylogenetic distribution. Despite the biological importance of Radical SAM chemistry, the vast majority of superfamily members have never been experimentally characterized in any way, suggesting that many new reactions remain to be discovered. In addition to 20 subgroups with at least one known function, we identified additional subgroups made up entirely of sequences of unknown function. Importantly, our results indicate that even general reaction types fail to track well with our sequence similarity-based subgroupings, raising major challenges for function prediction for currently identified and new members that continue to be discovered. Interactive similarity networks and other data from this analysis are available from the Structure-Function Linkage Database.
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auxiliary iron sulfur cofactors in Radical SAM enzymes
Biochimica et Biophysica Acta, 2015Co-Authors: Nicholas D. Lanz, Squire J BookerAbstract:A vast number of enzymes are now known to belong to a superfamily known as Radical SAM, which all contain a [4Fe-4S] cluster ligated by three cysteine residues. The remaining, unligated, iron ion of the cluster binds in contact with the α-amino and α-carboxylate groups of S-adenosyl-l-methionine (SAM). This binding mode facilitates inner-sphere electron transfer from the reduced form of the cluster into the sulfur atom of SAM, resulting in a reductive cleavage of SAM to methionine and a 5'-deoxyadenosyl Radical. The 5'-deoxyadenosyl Radical then abstracts a target substrate hydrogen atom, initiating a wide variety of Radical-based transformations. A subset of Radical SAM enzymes contains one or more additional iron-sulfur clusters that are required for the reactions they catalyze. However, outside of a subset of sulfur insertion reactions, very little is known about the roles of these additional clusters. This review will highlight the most recent advances in the identification and characterization of Radical SAM enzymes that harbor auxiliary iron-sulfur clusters. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
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Auxiliary iron–sulfur cofactors in Radical SAM enzymes
Biochimica et biophysica acta, 2015Co-Authors: Nicholas D. Lanz, Squire J BookerAbstract:A vast number of enzymes are now known to belong to a superfamily known as Radical SAM, which all contain a [4Fe-4S] cluster ligated by three cysteine residues. The remaining, unligated, iron ion of the cluster binds in contact with the α-amino and α-carboxylate groups of S-adenosyl-l-methionine (SAM). This binding mode facilitates inner-sphere electron transfer from the reduced form of the cluster into the sulfur atom of SAM, resulting in a reductive cleavage of SAM to methionine and a 5'-deoxyadenosyl Radical. The 5'-deoxyadenosyl Radical then abstracts a target substrate hydrogen atom, initiating a wide variety of Radical-based transformations. A subset of Radical SAM enzymes contains one or more additional iron-sulfur clusters that are required for the reactions they catalyze. However, outside of a subset of sulfur insertion reactions, very little is known about the roles of these additional clusters. This review will highlight the most recent advances in the identification and characterization of Radical SAM enzymes that harbor auxiliary iron-sulfur clusters. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
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Electrochemical Investigation of the Radical SAM Enzyme, BtrN from Bacillus Circulans
Biophysical Journal, 2013Co-Authors: Stephanie J. Maiocco, Squire J Booker, Tyler L. Grove, Lauren A. Sites, Sean J. ElliottAbstract:Radical SAM enzymes catalyze a variety of reactions involved in biological pathways including the biosynthesis of antibiotics, cofactors, and biosynthesis and repair of DNA. Measurement of the electrochemical characteristics of Radical SAM enzymes has been limited due to the typically buried location of the Radical SAM cluster within the enzyme. The midpoint potential of a Radical SAM cluster has only been determined for lysine aminomutase using spectroelectrochemical titrations with the use of mediators. This study presents the first direct electrochemical measurement of a Radical SAM enzyme using the technique of protein film voltammetry (PFV). BtrN from Bacillus circulans is an emerging class of Radical SAM dehydrogenases, which catalyze the third step in the biosynthetic pathway of the antibiotic butirosin. BtrN has been shown to contain a second [4Fe-4S] in addition to the canonical Radical SAM [4Fe-4S] cluster. Nonturnover PFV has characterized the electrochemical properties of these clusters and provided insight into the mechanism of electron transfer. Additionally, PFV has been used to characterize the effect of substrate binding on the clusters. These results provide insight into the catalytic mechanism of BtrN and the electrochemical characteristics of Radical SAM enzymes in general.
Stephane Pierre - One of the best experts on this subject based on the ideXlab platform.
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thiostrepton tryptophan methyltransferase expands the chemistry of Radical SAM enzymes
Nature Chemical Biology, 2012Co-Authors: Alhosna Benjdia, Olivier Berteau, Stephane Pierre, Alain Guillot, Corine Sandstrom, Philippe LangellaAbstract:TsrM, a member of the Radical SAM enzyme family, is shown to catalyze tryptophan methylation en route to thiostrepton A with the help of a methylcobalamin cofactor and without generating the canonical 5-deoxyadenosyl Radical.
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Thiostrepton tryptophan methyltransferase expands the chemistry of Radical SAM enzymes
Nature Chemical Biology, 2012Co-Authors: Stephane Pierre, Alhosna Benjdia, Alain Guillot, Corine Sandstrom, Philippe Langella, Olivier BerteauAbstract:Methylation is among the most widespread chemical modifications encountered in biomolecules and has a pivotal role in many major biological processes. In the biosynthetic pathway of the antibiotic thiostrepton A, we identified what is to our knowledge the first tryptophan methyltransferase. We show that it uses unprecedented chemistry to methylate inactivated sp(2)-hybridized carbon atoms, despite being predicted to be a Radical SAM enzyme.
