The Radical S-Adenosyl-l-methionine Enzyme QhpD Catalyzes Sequential Formation of Intra-protein Sulfur-to-Methylene Carbon Thioether Bonds

Nakai, Tadashi; Ito, Hiroto; Kobayashi, Kazuo; Takahashi, Yasuhiro; Hori, Hiroshi; Tsubaki, Motonari; Tanizawa, Katsuyuki; Okajima, Toshihide

doi:10.1074/jbc.m115.638320

Cited by 42 publications

(71 citation statements)

References 57 publications

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“…While there are reports of rSAM enzymes that install thioether linkages within protein substrates (e.g. QhpD acting on QhpC), 46 these are not considered RiPPs; thus, they will not be mentioned further.…”

Section: Ripp Biosynthetic Reactions Catalyzed By Rsam Enzymesmentioning

confidence: 99%

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: 99%

Radical S-Adenosylmethionine Enzymes Involved in RiPP Biosynthesis

2017

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“…21,35,46,47 Since the characterization of these three enzymes, additional members of the RS superfamily, including QhpD, were observed to contain a Cys rich C-terminal domain that binds auxiliary [4Fe-4S] clusters. 38 BLAST search of Tte1186 revealed that it was homologous to both anSME and AlbA, suggesting that it contains the C-terminal SPASM domain. Both the bioinformatic analysis of Tte1186 and the excess Fe and S observed in both the wild-type and ΔRC variant discussed above suggested that Tte1186, by analogy to PqqE, AlbA, QhpD, and anSME, contains at least one auxiliary cluster.…”

Section: Resultsmentioning

confidence: 99%

“…Thioether crosslinks have been observed previously in the maturation of subtilosin A, sporulation killing factor, thurincin H, and the γ subunit of quinohemoprotein amine dehydrogenase. 35,36,37,38 …”

Section: Resultsmentioning

confidence: 99%

“…35–38 Additionally, the RS enzymes ThrC and ThrD were proposed to catalyze the formation of thioether crosslinks in the RiPPs Trnα and Trnβ, which together form the bacteriocin thuricin CD 9 . However, recent bioinformatic investigations have identified numerous instances where a gene encoding for a RS enzyme was clustered with a gene encoding for a putative RiPP precursor indicating that the enzyme may act as a RiPP maturase.…”

mentioning

confidence: 99%

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Biochemical and Spectroscopic Characterization of a Radical S-Adenosyl-l-methionine Enzyme Involved in the Formation of a Peptide Thioether Cross-Link

et al. 2016

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Peptide-derived natural products are a class of metabolites that afford the producing organism a selective advantage over other organisms in their biological niche. While the polypeptide antibiotic produced by the non-ribosomal polypeptide synthetases (NRPS) are the most widely recognized, the ribosomally-synthesized and post-translationally-modified peptides (RiPPs) are an emerging group of natural products with diverse structures and biological functions. Both the NRPS derived peptides and the RiPPs undergo extensive post-translational modifications to produce structural diversity. Here we report the first characterization of the six cysteines in forty-five (SCIFF) [Haft, D.H. and Basu M.K. (2011) J Bacteriol 193, 2745–2755] peptide maturase Tte1186, which is a member of the radical SAM superfamily. Tte1186 catalyzes the formation of a thioether crosslink in the peptide Tte1186a encoded by an orf located upstream of the maturase, under reducing conditions in the presence of SAM. Tte1186 contains three [4Fe-4S] clusters that are indispensable for thioether crosslink formation; however, only one cluster catalyzes the reductive cleavage of SAM. Mechanistic imperatives for the reaction catalyzed by the thioether forming radical SAM maturases will be discussed.

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“…The resulting alkyl radical forms a bond with a thiol of a nearby cysteine resulting in a cyclized peptide. Interestingly, most members of this group (AlbA, QhpD, ThnB, CteB, and SkfB) have been found to carry out multiple modifications on the same peptide, distinguishing them from the rest of the enzymes in Table 1, which modify only a single site in their substrates (33)(34)(35)(36)(37). In addition, the diverse physiological functions for the products of these RS enzymes, which include antibiotics (e.g.…”

Section: Carbon-carbon Bond Creation: Pqqe Strb and Mftcmentioning

confidence: 99%

At the confluence of ribosomally synthesized peptide modification and radical S-adenosylmethionine (SAM) enzymology

Latham

Barr

Klinman

2017

Journal of Biological Chemistry

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Radical S-adenosylmethionine (RS) enzymology has emerged as a major biochemical strategy for the homolytic cleavage of unactivated C-H bonds. At the same time, the post-translational modification of ribosomally synthesized peptides is a rapidly expanding area of investigation. We discuss the functional cross-section of these two disciplines, highlighting the recently uncovered importance of protein-protein interactions, especially between the peptide substrate and its chaperone, which functions either as a stand-alone protein or as an N-terminal fusion to the respective RS enzyme. The need for further work on this class of enzymes is emphasized, given the poorly understood roles performed by multiple, auxiliary iron-sulfur clusters and the paucity of protein X-ray structural data.Modern biochemistry has seen the exponential growth of two exciting areas of research that focus individually on the post-translational modification of ribosomally synthesized and post-translationally modified peptides (RiPPs) 2 (1) and on the structure and mechanism of free radical conversions catalyzed by radical S-adenosylmethionine (RS) enzymes (2, 3). These separate fields have recently converged within a growing family of enzymes that bring about free radical-based, post-translational modifications on ribosomally produced peptide substrates. RS enzymes function by cleavage of a [4Fe-4S] clusterbound S-adenosylmethionine to form methionine and a deoxyadenosyl radical. This radical then initiates the reaction by abstracting a hydrogen atom from the substrate. The [4Fe-4S] cluster that accomplishes this reaction has a characteristic CX 3 CXC motif, with each of the cysteines coordinated to a single iron, leaving an open coordination sphere where SAM binds and is cleaved. A subset of RS enzymes belongs to a family that contains an additional conserved structural motif annotated as a SPASM domain and referred to as RS-SPASM proteins. Although the exact function of the SPASM domain is unknown, it has been shown that it houses generally two additional iron-sulfur clusters that are critical in RS-SPASM chemistry. Using the perspective of the pathway for production of the bacterial cofactor pyrroloquinoline quinone (PQQ), we compare and highlight some of the unique properties among these RS-SPASM-dependent RiPP systems. Bioinformatics analyses suggest that the family members will extend far beyond the examples presented herein.

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The Radical S-Adenosyl-l-methionine Enzyme QhpD Catalyzes Sequential Formation of Intra-protein Sulfur-to-Methylene Carbon Thioether Bonds

Cited by 42 publications

References 57 publications

Radical S-Adenosylmethionine Enzymes Involved in RiPP Biosynthesis

Radical S-Adenosylmethionine Enzymes Involved in RiPP Biosynthesis

Biochemical and Spectroscopic Characterization of a Radical S-Adenosyl-l-methionine Enzyme Involved in the Formation of a Peptide Thioether Cross-Link

At the confluence of ribosomally synthesized peptide modification and radical S-adenosylmethionine (SAM) enzymology

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