Structural basis for precursor protein–directed ribosomal peptide macrocyclization

Li, Kunhua; Condurso, H.L.; Li, Gengnan; Ding, Yousong; Bruner, Steven D.

doi:10.1038/nchembio.2200

Cited by 54 publications

(119 citation statements)

References 46 publications

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“…2C). While many RiPP leader peptides have been shown to adopt α-helical conformations in trifluoroethanol, the persistence of this secondary structure upon binding to the tailoring enzyme has only been observed in our structures and the recent structure of MdnC, which binds the leader peptide as a single-turn α-helix but lacks sequence homology to a typical RRE (3,9,11,28).…”

Section: Resultsmentioning

confidence: 81%

Structures of the peptide-modifying radical SAM enzyme SuiB elucidate the basis of substrate recognition

Davis

Schramma

Hansen

et al. 2017

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

131

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Posttranslational modification of ribosomally synthesized peptides provides an elegant means for the production of biologically active molecules known as RiPPs (ribosomally synthesized and posttranslationally modified peptides). Although the leader sequence of the precursor peptide is often required for turnover, the exact mode of recognition by the modifying enzymes remains unclear for many members of this class of natural products. Here, we have used X-ray crystallography and computational modeling to examine the role of the leader peptide in the biosynthesis of a homolog of streptide, a recently identified peptide natural product with an intramolecular lysine-tryptophan cross-link, which is installed by the radical -adenosylmethionine (SAM) enzyme, StrB. We present crystal structures of SuiB, a close ortholog of StrB, in various forms, including apo SuiB, SAM-bound SuiB, and a complex of SuiB with SAM and its peptide substrate, SuiA. Although the N-terminal domain of SuiB adopts a typical RRE (RiPP recognition element) motif, which has been implicated in precursor peptide recognition, we observe binding of the leader peptide in the catalytic barrel rather than the N-terminal domain. Computational simulations support a mechanism in which the leader peptide guides posttranslational modification by positioning the cross-linking residues of the precursor peptide within the active site. Together the results shed light onto binding of the precursor peptide and the associated conformational changes needed for the formation of the unique carbon-carbon cross-link in the streptide family of natural products.

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Section: Resultsmentioning

confidence: 81%

Structures of the peptide-modifying radical SAM enzyme SuiB elucidate the basis of substrate recognition

Davis

Schramma

Hansen

et al. 2017

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

131

View full text Add to dashboard Cite

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“…It has been shown that only a limited region of the leader peptide in many RiPPs is required for efficient modification of the precursor peptide . We investigated which region of the leader peptide is critical for the crosslinking reaction with TgnA‐R1, which was used as a model peptide.…”

Section: Resultsmentioning

confidence: 99%

A Topologically Distinct Modified Peptide with Multiple Bicyclic Core Motifs Expands the Diversity of Microviridin‐Like Peptides

et al. 2019

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Microviridins are ribosomally synthesized and post‐translationally modified peptides (RiPPs) that contain multiple intramolecular ω‐ester or ω‐amide crosslinks between two side chains in peptides. This type of the side‐to‐side macrocyclization may generate diverse structures with distinct topology and ring sizes, but the majority of the microviridin‐like RiPPs present only a single consensus sequence with a tricyclic architecture. Here, we expanded the natural diversity of the microviridin‐like modified peptides by determining the crosslinking connectivity of a new modified peptide, mTgnA and its homologous RiPPs, which we named the thuringinin group. Members of the thuringinin group have core motifs with a distinct consensus sequence, which is transformed to a novel hairpin‐like bicyclic structure by the cognate ATP‐grasp enzyme. We suggest that the microviridin‐like RiPPs naturally have novel sequences and architectures beyond those found in microviridins and comprise a larger RiPP family, termed omega‐ester containing peptides (OEPs).

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“…The sortase class of enzymes, which catalyze transpeptidation by recognizing a C-terminal LXPTG motif 17 , the butelase enzyme, which is an asparagine/aspartate (Asx) peptide ligase 18 , the NRPS thioesterases 19 and the prolyl oligopeptidase (POP) class of enzymes. A further important class of macrocyclases is that of the ATP-grasp superfamily, which as the name suggests rely on ATP hydrolysis to drive macrocycliation 20 . The enzymes that catalyze close to traceless peptide bond formation regardless of the peptide sequence—, i.e., only one residue from the precursor peptide recognition tag is carried over to the final cyclic product—are PatGmac family members, butelase, and POP macrocyclases.…”

Section: Introductionmentioning

confidence: 99%

Characterization of a dual function macrocyclase enables design and use of efficient macrocyclization substrates

et al. 2017

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Peptide macrocycles are promising therapeutic molecules because they are protease resistant, structurally rigid, membrane permeable, and capable of modulating protein–protein interactions. Here, we report the characterization of the dual function macrocyclase-peptidase enzyme involved in the biosynthesis of the highly toxic amanitin toxin family of macrocycles. The enzyme first removes 10 residues from the N-terminus of a 35-residue substrate. Conformational trapping of the 25 amino-acid peptide forces the enzyme to release this intermediate rather than proceed to macrocyclization. The enzyme rebinds the 25 amino-acid peptide in a different conformation and catalyzes macrocyclization of the N-terminal eight residues. Structures of the enzyme bound to both substrates and biophysical analysis characterize the different binding modes rationalizing the mechanism. Using these insights simpler substrates with only five C-terminal residues were designed, allowing the enzyme to be more effectively exploited in biotechnology.

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Structural basis for precursor protein–directed ribosomal peptide macrocyclization

Cited by 54 publications

References 46 publications

Structures of the peptide-modifying radical SAM enzyme SuiB elucidate the basis of substrate recognition

Structures of the peptide-modifying radical SAM enzyme SuiB elucidate the basis of substrate recognition

A Topologically Distinct Modified Peptide with Multiple Bicyclic Core Motifs Expands the Diversity of Microviridin‐Like Peptides

Characterization of a dual function macrocyclase enables design and use of efficient macrocyclization substrates

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