9MY5

Structure of the BasE mutant V336A, an NRPS adenylation domain in the acinetobactin biosynthetic pathway bound to 4-methyl salicylic Acid

This is a non-PDB format compatible entry.

Summary for 9MY5

• Entry DOI: 10.2210/pdb9my5/pdb
• Related: 3O82 3O83 3O84 3U16 3U17
• Descriptor: (2,3-dihydroxybenzoyl)adenylate synthase, 2-hydroxy-4-methylbenzoic acid, 1,2-ETHANEDIOL, ... (5 entities in total)
• Functional Keywords: nrps, adenylation domain, nonribosomal peptide siderophore, acinetobactin, ligase, synthetase
• Biological source: Acinetobacter baumannii
• Total number of polymer chains: 2
• Total formula weight: 126485.74

Authors

Ahmed, S.F.,Gulick, A.M. (deposition date: 2025-01-21, release date: 2025-03-26, Last modification date: 2025-04-16)

Primary citation

Ahmed, S.F.,Gulick, A.M.
The structural basis of substrate selectivity of the acinetobactin biosynthetic adenylation domain, BasE.
J.Biol.Chem., 301:108413-108413, 2025

PubMed Abstract: Siderophores are small molecule natural products that are often produced by enzymes called nonribosomal peptide synthetases that many pathogenic bacteria produce to adapt to low iron conditions. Nonribosomal peptide synthetase bioengineering could lead to the production of siderophore analogs with the potential to interrupt this unique bacterial iron uptake system, endowing the molecules with antimicrobial properties. Acinetobacter baumannii produces the catecholate siderophore acinetobactin to scavenge iron, a nutrient essential for several metabolic processes. Previous studies have reported synthetic analogs of acinetobactin that disrupt iron acquisition by A. baumannii, resulting in inhibition of bacterial growth. To foster a long-term goal of using a chemoenzymatic approach to produce additional analogs, we have targeted the adenylation domain BasE for the incorporation of alternate substrates. Here, we report a structure-guided approach to investigate the substrate selectivity of BasE for non-native aryl substrates. Using targeted mutagenesis in the active site of BasE, we generated mutants that catalyze the activation of alternate substrates with catalytic efficiencies comparable to the WT enzyme with its natural substrate 2,3-dihydroxybenzoic acid. We further solved structures of these mutants bound to the non-native substrates that illustrate an expanded binding pocket that support the improved promiscuity of BasE. Motivated to develop an approach to produce analogs of acinetobactin, including molecules that could block iron uptake or be readily conjugated to antibiotic cargo, our work aims to develop a structure-guided approach for using catecholate siderophore pathways to incorporate alternate substrates.

PubMed: 40096888
DOI: 10.1016/j.jbc.2025.108413

Experimental method

X-RAY DIFFRACTION (2.39 Å)