Structural Basis for a Dual Function ATP Grasp Ligase That Installs Single and Bicyclic ω-Ester Macrocycles in a New Multicore RiPP Natural Product
| Autor: | Carole A. Bewley, Jiadong Sun, Clifton E. Barry, Anastasia N. Nikolskaya, Kira S. Makarova, Dalibor Kosek, Fred Dyda, Brittney Blackburne, Hong-Bing Liu, Gengxiang Zhao, Eugene V. Koonin, Shannon I. Ohlemacher |
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| Rok vydání: | 2021 |
| Předmět: |
Signal peptide
Conformational change Macrocyclic Compounds Stereochemistry Molecular Conformation Peptide 010402 general chemistry 01 natural sciences Biochemistry Article Catalysis Ligases Residue (chemistry) Adenosine Triphosphate Colloid and Surface Chemistry Side chain chemistry.chemical_classification Biological Products DNA ligase Bicyclic molecule Substrate (chemistry) Esters General Chemistry Amides 0104 chemical sciences chemistry Peptides Protein Processing Post-Translational |
| Zdroj: | J Am Chem Soc |
| ISSN: | 1520-5126 0002-7863 |
| DOI: | 10.1021/jacs.1c02316 |
| Popis: | Among the ribosomally synthesized and post-translationally modified peptide (RiPP) natural products, “graspetides” (formerly known as microviridins) contain macrocyclic esters and amides that are formed by ATP-grasp ligase tailoring enzymes using the side chains of Asp/Glu as acceptors and Thr/Ser/Lys as donors. Graspetides exhibit diverse patterns of macrocylization and connectivities exemplified by microviridins, that have a caged tricyclic core, and thuringin and plesiocin that feature a “hairpin topology” with cross-strand ω-ester bonds. Here, we characterize chryseoviridin, a new type of multicore RiPP encoded by Chryseobacterium gregarium DS19109 (Phylum Bacteroidetes) and solve a 2.44 Å resolution crystal structure of a quaternary complex consisting of the ATP-grasp ligase CdnC bound to ADP, a conserved leader peptide and a peptide substrate. HRMS/MS analyses show that chryseoviridin contains four consecutive five- or six-residue macrocycles ending with a microviridin-like core. The crystal structure captures respective subunits of the CdnC homodimer in the apo or substrate-bound state revealing a large conformational change in the B-domain upon substrate binding. A docked model of ATP places the γ-phosphate group within 2.8 Å of the Asp acceptor residue. The orientation of the bound substrate is consistent with a model in which macrocyclization occurs in the N- to C-terminal direction for core peptides containing multiple Thr/Ser-to-Asp macrocycles. Using systematically varied sequences, we validate this model and identify two- or three-amino acid templating elements that flank the macrolactone and are required for enzyme activity in vitro. This work reveals the structural basis for ω-ester bond formation in RiPP biosynthesis. |
| Databáze: | OpenAIRE |
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