Structure and mechanism of the tRNA-dependent lantibiotic dehydratase NisB

Ortega, Manuel; Hao, Yanling; Zhang, Qi; Walker, Mark C.; Donk, Wilfred A. van der; Nair, Satish K.

doi:10.1038/nature13888

Cited by 274 publications

(503 citation statements)

References 49 publications

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“…This has been observed in at least some of the enzymes involved in the biosynthesis of pyrroloquinoline quinone (45), lantibiotics (46), lasso peptides (44), and cyanobactins (47). In contrast, the follower peptide binding observed in PCY1 does not rely on hydrophobic interactions, but rather on hydrogenbonding interactions.…”

Section: Resultsmentioning

confidence: 88%

Characterization of the macrocyclase involved in the biosynthesis of RiPP cyclic peptides in plants

Chekan

Estrada

Covello

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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Enzymes that can catalyze the macrocyclization of linear peptide substrates have long been sought for the production of libraries of structurally diverse scaffolds via combinatorial gene assembly as well as to afford rapid in vivo screening methods. Orbitides are plant ribosomally synthesized and posttranslationally modified peptides (RiPPs) of various sizes and topologies, several of which are shown to be biologically active. The diversity in size and sequence of orbitides suggests that the corresponding macrocyclases may be ideal catalysts for production of cyclic peptides. Here we present the biochemical characterization and crystal structures of the plant enzyme PCY1 involved in orbitide macrocyclization. These studies demonstrate how the PCY1 S9A protease fold has been adapted for transamidation, rather than hydrolysis, of acyl-enzyme intermediates to yield cyclic products. Notably, PCY1 uses an unusual strategy in which the cleaved C-terminal follower peptide from the substrate stabilizes the enzyme in a productive conformation to facilitate macrocyclization of the N-terminal fragment. The broad substrate tolerance of PCY1 can be exploited as a biotechnological tool to generate structurally diverse arrays of macrocycles, including those with nonproteinogenic elements.RiPP | biosynthesis | peptide | plant | orbitide

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Section: Resultsmentioning

confidence: 88%

Characterization of the macrocyclase involved in the biosynthesis of RiPP cyclic peptides in plants

Chekan

Estrada

Covello

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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“…Amino acid substitutions in the conserved regions within the leader peptide have shown that the composition of these common motifs is important for the maturation of the core peptide, while a vast majority of the leader peptide does not have any amino acid sequence specificity (19,20,26,27). Solution nuclear magnetic resonance studies have shown that the leader peptide sequence lacks secondary structure (28), while the cocrystal structure of NisB in complex with the substrate peptide NisA shows an antiparallel ␤ strand (29). It is likely that the leader peptide remains unstructured until it binds to the PTM enzymes.…”

mentioning

confidence: 99%

Biosynthesis and Transport of the Lantibiotic Mutacin 1140 Produced by Streptococcus mutans

et al. 2015

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Lantibiotics are ribosomally synthesized peptide antibiotics composed of an N-terminal leader peptide that is cleaved to yield the active antibacterial peptide. Significant advancements in molecular tools that promote the study of lantibiotic biosynthesis can be used in Streptococcus mutans. Herein, we further our understanding of leader peptide sequence and core peptide structural requirements for the biosynthesis and transport of the lantibiotic mutacin 1140. Our study on mutacin 1140 biosynthesis shows a dedicated secondary cleavage site within the leader peptide and the dependency of transport on core peptide posttranslational modifications (PTMs). The secondary cleavage site on the leader peptide is found at the ؊9 position, and secondary cleavage occurs before the core peptide is transported out of the cell. The coordinated cleavage at the ؊9 position was absent in a lanT deletion strain, suggesting that the core peptide interaction with the LanT transporter enables uniform cleavage at the ؊9 position. Following transport, the LanP protease was found to be tolerant to a wide variety of amino acid substitutions at the primary leader peptide cleavage site, with the exception of arginine at the ؊1 position. Several leader and core peptide mutations produced core peptide variants that had intermediate stages of PTM enzyme modifications, supporting the concept that PTM enzyme modifications, secondary cleavage, and transport are occurring in a highly coordinated fashion. IMPORTANCEMutacin 1140 belongs to the class I lantibiotic family of ribosomally synthesized and posttranslationally modified peptides (RiPPs). The biosynthesis of mutacin 1140 is a highly efficient process which does not lead to a discernible level of production of partially modified core peptide variants. The products isolated from an extensive mutagenesis study on the leader and core peptides of mutacin 1140 show that the posttranslational modifications (PTMs) on the core peptide occur under a highly coordinated dynamic process. PTMs are dictated by the distance of the core peptide modifiable residues from PTM enzyme active sites. The formation of lanthionine rings aids in the formation of successive PTMs, as was observed in a peptide variant lacking a Cterminal decarboxylation. Lantibiotics are a class of ribosomally synthesized peptide antibiotics produced by Gram-positive bacteria, such as Lactococcus lactis and Streptococcus mutans (1, 2). Lantibiotics are characterized by the presence of posttranslational modifications (PTMs), such as dehydrated residues and lanthionine rings. The modified residues 2,3-didehydroalanine (Dha) and 2,3-didehydrobutyrine (Dhb) are formed from dehydration of serines and threonines, respectively. The cyclization between a cysteine and either a Dha or a Dhb forms a lanthionine or a methyllanthionine ring, respectively. The biosynthetic gene cluster contains all the genes necessary to produce a lantibiotic. The lan operon for class I lantibiotics contains genes encoding the lantibiotic peptide (lanA); the...

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“…Strengthening these findings, crystal structures of several RRE domains found in RiPP pathways are available. Examples of the available structures are NisB (PDB code 4WD9) and LynD (nisin biosynthesis, PDB code 4V1T), both of which have been co-crystallized with their respective peptides (46,47). Significantly, the RRE domains of NisB and LynD are structurally homologous to PqqD, and they allow us to visualize a possible binding mode for the interaction of PqqA with PqqD (Fig.…”

Section: Minireview: Free Radical Enzymology Of Peptidesmentioning

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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Structure and mechanism of the tRNA-dependent lantibiotic dehydratase NisB

Cited by 274 publications

References 49 publications

Characterization of the macrocyclase involved in the biosynthesis of RiPP cyclic peptides in plants

Characterization of the macrocyclase involved in the biosynthesis of RiPP cyclic peptides in plants

Biosynthesis and Transport of the Lantibiotic Mutacin 1140 Produced by Streptococcus mutans

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

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