9BOU

Crystal structure of ATP-grasp ligase PruB from Streptomyces coelicolor A3(2)

9BOU の概要

• エントリーDOI: 10.2210/pdb9bou/pdb
• 分子名称: MvdD-like pre-ATP grasp domain-containing protein, SULFATE ION (3 entities in total)
• 機能のキーワード: atp-grasp ligase, peptide cyclase, ripp biosynthesis, ligase
• 由来する生物種: Streptomyces coelicolor A3(2)
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 72587.56

構造登録者

Patel, K.P.,Bruner, S.D. (登録日: 2024-05-06, 公開日: 2024-12-18, 最終更新日: 2025-01-01)

主引用文献

Rubin, G.M.,Patel, K.P.,Jiang, Y.,Ishee, A.C.,Seabra, G.,Bruner, S.D.,Ding, Y.
Characterization of a Dual Function Peptide Cyclase in Graspetide Biosynthesis.
Acs Chem.Biol., 19:2525-2534, 2024

PubMed Abstract: Graspetides are a diverse family of ribosomally synthesized and post-translationally modified peptides with unique macrocyclic structures formed by ATP-grasp enzymes. Group 11 graspetides, including prunipeptin, feature both macrolactone and macrolactam cross-links. Despite the known involvement of a single ATP-grasp cyclase in the dual macrocyclizations of groups 5, 7, and 11 graspetides, detailed mechanistic insights into these enzymes remain limited. Here, we reconstructed prunipeptin biosynthesis from using recombinant PruA and PruB macrocyclase. PruB exhibited kinetic behavior similar to other characterized graspetide cyclases, with a notably higher , likely due to utilization of an ATP-regeneration system. The X-ray crystal structure of PruB revealed distinct features as compared to groups 1 and 2 enzymes. Site-directed mutagenesis identified critical roles of key residues for the PruB reaction, including the DxR motif conserved in other graspetide cyclases. Additionally, computational modeling of the PruA/PruB cocomplex uncovered substrate interactions and suggested that PruB first catalyzes a macrolactone bond formation on PruA. This study enhances our understanding of ATP-grasp enzyme mechanisms in graspetide biosynthesis and provides insights for engineering these enzymes for future applications.

PubMed: 39630567
DOI: 10.1021/acschembio.4c00626

実験手法

X-RAY DIFFRACTION (2.91 Å)