The PqqD homologous domain of the radical SAM enzyme ThnB is required for thioether bond formation during thurincin H maturation

Wieckowski, Beata M.; Hegemann, Julian D.; Mielcarek, Andreas; Boss, Linda; Burghaus, Olaf; Marahiel, Mohamed A.

doi:10.1016/j.febslet.2015.05.032

Cited by 63 publications

(82 citation statements)

References 28 publications

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“…A second small region within the N-terminal domain spanning residues Gln201 through Leu286 likely harbors the leader-binding domain, as observed in the NisB cocrystal structure (Ortega et al, 2015) (Figure S3D). This structural element is also present in additional RiPP biosynthetic enzymes and it was recently shown to be a prevalent motif important for leader peptide recognition across several classes of RiPPs (Burkhart et al, 2015, Dong et al, 2015, Koehnke et al, 2015, Latham et al, 2015, Wieckowski et al, 2015). …”

Section: Resultsmentioning

confidence: 99%

Structure and tRNA Specificity of MibB, a Lantibiotic Dehydratase from Actinobacteria Involved in NAI-107 Biosynthesis

Ortega

Hao

Walker

et al. 2016

Cell Chemical Biology

126

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Summary Class I lantibiotic dehydratases dehydrate selected Ser/Thr residues of a precursor peptide. Recent studies demonstrated the requirement of glutamyl-tRNAGlu for Ser/Thr activation by one of these enzymes (NisB) from the Firmicute Lactococcus lactis. However, the generality of glutamyl-tRNAGlu usage and the tRNA specificity of lantibiotic dehydratases have not been established. Here we report the 2.7-Å resolution crystal structure, along with the glutamyl-tRNAGlu utilization of MibB, a lantibiotic dehydratase from the Actinobacterium Microbispora sp. 107891 involved in the biosynthesis of the clinical candidate NAI-107. Biochemical assays revealed nucleotides A73 and U72 within the tRNAGlu acceptor stem to be important for MibB glutamyl-tRNAGlu usage. Using this knowledge, an expression system for the production of NAI-107 analogs in Escherichia coli was developed overcoming the inability of MibB to utilize E. coli tRNAGlu. Our work provides evidence for a common tRNAGlu-dependent dehydration mechanism, paving the way for the characterization of lantibiotics from various phyla.

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Section: Resultsmentioning

confidence: 99%

Structure and tRNA Specificity of MibB, a Lantibiotic Dehydratase from Actinobacteria Involved in NAI-107 Biosynthesis

Ortega

Hao

Walker

et al. 2016

Cell Chemical Biology

126

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“…Recent investigations on the biosynthesis of thurincin H, subtilosin A, and sporulation killing factor (SKF, Figure 1B) have revealed a common biosynthetic route for the generation of the thioether linkage (Flühe et al, 2013, Flühe et al, 2012, Wieckowski et al, 2015). A common feature among sactipeptide gene clusters is the presence of a gene encoding a radical-SAM enzyme (SkfB in SKF biosynthesis).…”

Section: Introductionmentioning

confidence: 99%

“…Mutations within the RRE precluded the recognition of the corresponding precursor peptides (Burkhart et al, 2015), thus validating RREs as a general scaffold needed for precursor peptide recognition during RiPP biosynthesis. Mutational studies using the sactipeptide RiPP biosynthetic machinery has also been performed, revealing the importance of the RRE for sactipeptide maturation (Wieckowski et al, 2015). Interestingly, the RRE domain sometimes may exist as a stand-alone protein and not as a subdomain within a RiPP biosynthetic enzyme as recently observed for lasso peptides and thiazole/oxazole-modified peptide gene clusters (Burkhart et al, 2015, Dunbar et al, 2015, Elsayed et al, 2015, Gavrish et al, 2014, Inokoshi et al, 2012, Li et al, 2015, Metelev et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

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

Ortega

Donk

2016

Cell Chemical Biology

251

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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“…In the mycofactocin biosynthetic pathway, the peptide chaperone is a stand-alone protein (MftB), and in the thurincin H biosynthetic pathway, the peptide chaperone is fused to the N terminus of the RS protein (ThnB). Although morphologically different, it was shown in both systems that the peptide chaperone protein/domain is required for catalytic turnover by the RS protein (28,29,35). These findings led us to the hypothesis that the PqqD domain is ubiquitous among the remaining characterized RS-SPASM proteins (excluding AnSME).…”

Section: Minireview: Free Radical Enzymology Of Peptidesmentioning

confidence: 99%

“…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 PqqD homologous domain of the radical SAM enzyme ThnB is required for thioether bond formation during thurincin H maturation

Cited by 63 publications

References 28 publications

Structure and tRNA Specificity of MibB, a Lantibiotic Dehydratase from Actinobacteria Involved in NAI-107 Biosynthesis

Structure and tRNA Specificity of MibB, a Lantibiotic Dehydratase from Actinobacteria Involved in NAI-107 Biosynthesis

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

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

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