7MGV

Chryseobacterium gregarium RiPP-associated ATP-grasp ligase in complex with ADP, and a leader and core peptide

Summary for 7MGV

• Entry DOI: 10.2210/pdb7mgv/pdb
• Descriptor: CdnC, CdnA3 Leader peptide, CdnA3 Core peptide, ... (6 entities in total)
• Functional Keywords: ribosomally synthesized, post-translationally modified peptide, natural products atp-grasp ligase, precursor peptide, graspetide omega-ester macrocycles macrolactone, ligase
• Biological source: Chryseobacterium gregarium DSM 19109; More
• Total number of polymer chains: 5
• Total formula weight: 88320.25

Authors

Bewley, C.A.,Zhao, G.,Kosek, D.,Dyda, F. (deposition date: 2021-04-13, release date: 2021-06-23, Last modification date: 2023-10-18)

Primary citation

Zhao, G.,Kosek, D.,Liu, H.B.,Ohlemacher, S.I.,Blackburne, B.,Nikolskaya, A.,Makarova, K.S.,Sun, J.,Barry Iii, C.E.,Koonin, E.V.,Dyda, F.,Bewley, C.A.
Structural Basis for a Dual Function ATP Grasp Ligase That Installs Single and Bicyclic omega-Ester Macrocycles in a New Multicore RiPP Natural Product.
J.Am.Chem.Soc., 143:8056-8068, 2021

PubMed Abstract: 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 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.

PubMed: 34028251
DOI: 10.1021/jacs.1c02316

Experimental method

X-RAY DIFFRACTION (2.44 Å)