Tryptophan Lyase (NosL): Mechanistic Insights from Substrate Analogues and Mutagenesis

Bhandari, Dhananjay M; Xu, Hui; Nicolet, Yvain; Fontecilla‐Camps, Juan C.; Begley, Tadhg P.

doi:10.1021/acs.biochem.5b00764

Cited by 46 publications

(63 citation statements)

References 15 publications

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“…This mechanism is supported by labeling experiments that identified the origin of key atoms in the product, by trapping 66 as 3-methylindole ( 72 ), and by hydrolysis of 67 to yield glyoxalate ( 73 ). 78,81,87 The most compelling evidence for amino hydrogen abstraction comes from the crystal structure of the NosL- 1 complex 85 which is further supported by studies employing analogs of 1 . 81,87 Active site residues suspected to play a catalytic role were probed by mutagenesis.…”

Section: Ripp Biosynthetic Reactions Catalyzed By Rsam Enzymesmentioning

confidence: 95%

“…78,81,87 The most compelling evidence for amino hydrogen abstraction comes from the crystal structure of the NosL- 1 complex 85 which is further supported by studies employing analogs of 1 . 81,87 Active site residues suspected to play a catalytic role were probed by mutagenesis. 85,87 Arg323 was apparently hydrogen bonded to the amino and carboxyl groups of 1 and was suspected to control the regiochemistry of the β scission reaction and in binding 67 for subsequent reaction at C-2 of the indole.…”

Section: Ripp Biosynthetic Reactions Catalyzed By Rsam Enzymesmentioning

confidence: 95%

“…81,87 Active site residues suspected to play a catalytic role were probed by mutagenesis. 85,87 Arg323 was apparently hydrogen bonded to the amino and carboxyl groups of 1 and was suspected to control the regiochemistry of the β scission reaction and in binding 67 for subsequent reaction at C-2 of the indole. In support of this function, the replacement of Arg323 with Lys produced indole-3-pyruvic acid and no products arising from Cα-Cβ bond scission were detected.…”

Section: Ripp Biosynthetic Reactions Catalyzed By Rsam Enzymesmentioning

confidence: 99%

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Radical S-Adenosylmethionine Enzymes Involved in RiPP Biosynthesis

2017

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Ribosomally synthesized and post-translationally modified peptides (RiPPs) display a diverse range of structures and continue to expand as a natural product class. Accordingly, RiPPs exhibit a wide array of bioactivities, such as broad and narrow spectrum growth suppressors, antidiabetics, as well as antinociception and anticancer agents. Owing to these properties, and the complex repertoire of post-translational modifications (PTMs) that give rise to these molecules, RiPP biosynthesis has been intensely studied. RiPP biosynthesis often involves enzymes that perform unique chemistry with intriguing reaction mechanisms, which attract chemists and biochemists alike to study and re-engineer these pathways. One particular type of RiPP biosynthetic enzyme is the so-called radical S-adenosylmethionine (rSAM) enzyme, which utilize radical-based chemistry to install several distinct PTMs. Here, we describe the rSAM enzymes characterized over the past decade that catalyze six reactions types from several RiPP biosynthetic pathways. We present the current state of mechanistic understanding and conclude with possible directions for future characterization of this enzyme family.

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Section: Ripp Biosynthetic Reactions Catalyzed By Rsam Enzymesmentioning

confidence: 95%

Section: Ripp Biosynthetic Reactions Catalyzed By Rsam Enzymesmentioning

confidence: 95%

Section: Ripp Biosynthetic Reactions Catalyzed By Rsam Enzymesmentioning

confidence: 99%

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Radical S-Adenosylmethionine Enzymes Involved in RiPP Biosynthesis

2017

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“…However, recent structural characterization of NosL in complex with Trp and S -adenosyl-homocysteine (PDB ID 4R33) revealed that only the amino group of Trp was placed at an optimal position for hydrogen atom abstraction (Nicolet et al, 2014). Formation of a radical intermediate on the amino group is supported by the observation that tryptophan analogs containing either benzothiofuran or benzofuran moieties (Figure 3B) instead of indole were still converted to the corresponding MIA analogs, thus suggesting hydrogen abstraction does not occur from the indole nitrogen (Bhandari et al, 2015, Ji et al, 2015). Based on these results a revised mechanism was proposed.…”

Section: Introductionmentioning

confidence: 81%

New Insights into the Biosynthetic Logic of Ribosomally Synthesized and Post-translationally Modified Peptide Natural Products

Ortega

Donk

2016

Cell Chemical Biology

247

245

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Summary Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a large group of structurally diverse natural products. Their biological activities and unique biosynthetic pathways have sparked a growing interest in RiPPs. Furthermore, the relatively low genetic complexity associated with RiPP biosynthesis makes them excellent candidates for synthetic biology applications. This review highlights recent developments in the understanding of the biosynthesis of several bacterial RiPP family members, the use of the RiPP biosynthetic machinery for generating novel macrocyclic peptides, and the implementation of tools designed to guide the discovery and characterization of novel RiPPs.

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“…When the mechanism of NosL was investigated using a series of L-Trp analogs, the data suggested that H-atom abstraction occurs at the α-NH 2 group. 119–121 Based on these results, the mechanism shown at the top of Fig. 25 involving Cα–Cβ bond cleavage was proposed.…”

Section: Thih-like Enzymesmentioning

confidence: 97%

C–C bond forming radical SAM enzymes involved in the construction of carbon skeletons of cofactors and natural products

Yokoyama

Lilla

2018

Nat. Prod. Rep.

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C–C bond formations are frequently the key steps in cofactor and natural product biosynthesis. Historically, C–C bond formations were thought to proceed by two electron mechanisms, represented by Claisen condensation in fatty acids and polyketide biosynthesis. These types of mechanisms require activated substrates to create a nucleophile and an electrophile. More recently, increasing number of C–C bond formations catalyzed by radical SAM enzymes are being identified. These free radical mediated reactions can proceed between almost any sp3 and sp2 carbon centers, allowing introduction of C–C bonds at unconventional positions in metabolites. Therefore, free radical mediated C–C bond formations are frequently found in the construction of structurally unique and complex metabolites. This review discusses our current understanding of the functions and mechanisms of C–C bond forming radical SAM enzymes and highlights their important roles in the biosynthesis of structurally complex, naturally occurring organic molecules. Mechanistic consideration of C–C bond formation by radical SAM enzymes identifies the significance of three key mechanistic factors: radical initiation, acceptor substrate activation and radical quenching. Understanding the functions and mechanisms of these characteristic enzymes will be important not only in promoting our understanding of radical SAM enzymes, but also for understanding natural product and cofactor biosynthesis.

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Tryptophan Lyase (NosL): Mechanistic Insights from Substrate Analogues and Mutagenesis

Cited by 46 publications

References 15 publications

Radical S-Adenosylmethionine Enzymes Involved in RiPP Biosynthesis

Radical S-Adenosylmethionine Enzymes Involved in RiPP Biosynthesis

New Insights into the Biosynthetic Logic of Ribosomally Synthesized and Post-translationally Modified Peptide Natural Products

C–C bond forming radical SAM enzymes involved in the construction of carbon skeletons of cofactors and natural products

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