8K5T

The structure of EntE with2-methyl-3-chloro-benzoic acid sulfamoyl adenosine

Summary for 8K5T

• Entry DOI: 10.2210/pdb8k5t/pdb
• Descriptor: Enterobactin synthase component E, [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-(3-chloranyl-2-methyl-phenyl)carbonylsulfamate (3 entities in total)
• Functional Keywords: adenylation, atp binding, nonribosomal peptide synthetase, biosynthesis, ligase
• Biological source: Escherichia coli
• Total number of polymer chains: 2
• Total formula weight: 123664.25

Authors

Miyanaga, A.,Ishikawa, F. (deposition date: 2023-07-24, release date: 2024-07-31, Last modification date: 2025-01-01)

Primary citation

Ishikawa, F.,Nohara, M.,Miyanaga, A.,Kuramoto, S.,Miyano, N.,Asamizu, S.,Kudo, F.,Onaka, H.,Eguchi, T.,Tanabe, G.
Biosynthetic Incorporation of Non-native Aryl Acid Building Blocks into Peptide Products Using Engineered Adenylation Domains.
Acs Chem.Biol., 19:2569-2579, 2024

PubMed Abstract: Nonribosomal peptides (NRPs), one of the most widespread secondary metabolites in nature, with therapeutically significant activities, are biosynthesized by modular nonribosomal peptide synthetases (NRPSs). Aryl acids contribute to the structural diversity of NRPs as well as nonproteinogenic amino acids and keto acids. We previously confirmed that a single Asn-to-Gly substitution in the 2,3-dihydroxybenzoic acid-activating adenylation (A) domain EntE involved in enterobactin biosynthesis accepts monosubstituted benzoic acid derivatives with nitro, cyano, bromo, and iodo functionalities at the 2 or 3 positions. Here, we showed that the mutant EntE (N235G) accommodates various disubstituted benzoic acid derivatives with halogen, methyl, methoxy, nitro, and cyano functionalities at the 2 and 3 positions and monosubstituted benzoic acid with an alkyne at the 3 position. Structural analysis of the mutant EntE (N235G) with nonhydrolyzable aryl-AMP analogues using 3-chloro-2-methylbenzoic acid and 3-prop-2-ynoxybenzoic acid revealed how bulky 3-chloro-2-methylbenzoic acid and clickable 3-prop-2-ynoxybenzoic acid are recognized by enlarging the substrate-binding pocket of the enzyme. When engineered EntE mutants were coupled with enterobactin and vibriobactin biosynthetic enzymes, 3-hydroxybenzoic acid-, salicylic acid-, and 3-bromo-2-fluorobenzoic acid-containing peptides were produced as early stage intermediates, highlighting the potential of NRP biosynthetic pathway engineering for constructing diverse aryl acid-containing metabolites.

PubMed: 39620357
DOI: 10.1021/acschembio.4c00663

Experimental method

X-RAY DIFFRACTION (2.8 Å)