Structural analysis of leader peptide binding enables leader-free cyanobactin processing

Koehnke, Jesko; Mann, Greg; Bent, Andrew F.; Ludewig, Hannes; Shirran, Sally L.; Botting, Catherine H.; Lébl, Tomáš; Houssen, Wael E.; Jaspars, Marcel; Naismith, James H.

doi:10.1038/nchembio.1841

Cited by 165 publications

(297 citation statements)

References 43 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%

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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%

“…The role of the leader/follower peptide in stabilizing active conformations of biosynthetic enzymes is an emerging theme in RiPP biosynthesis. For example, during cyanobactin biosynthesis, binding of the PatE′ leader peptide to the LynD cyclodehydratase stabilizes the enzyme in a catalytically competent form (47).…”

Section: Resultsmentioning

confidence: 99%

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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“…Only one other sequence displaying this unusual combination of truncated ThiF-like and FDTH domains has been deposited in the NCBI nonredundant protein sequence database; this hypothetical protein is uncharacterized and no information on the context of this gene is available. 26 The ThiF family is similar to the E1-like proteins that have been implicated in the specific binding of peptide substrates in ribosomal peptide natural product biosynthesis, 27,28 and it is possible that the Cterminal domain serves a similar function here. (PrnA Trp Halogenase, red) that were identified using HHpred.…”

Section: Bioinformatic Analysis Of Krmimentioning

confidence: 99%

An Unusual Flavin-Dependent Halogenase from the Metagenome of the Marine Sponge Theonella swinhoei WA

et al. 2017

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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.

show abstract

Structural analysis of leader peptide binding enables leader-free cyanobactin processing

Cited by 165 publications

References 43 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

An Unusual Flavin-Dependent Halogenase from the Metagenome of the Marine Sponge Theonella swinhoei WA

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

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