9WI0

cryo-EM structure of E.coli ArnA

Summary for 9WI0

• Entry DOI: 10.2210/pdb9wi0/pdb
• EMDB information: 65981
• Descriptor: Bifunctional polymyxin resistance protein ArnA (1 entity in total)
• Functional Keywords: bifunctional polymyxin resistance protein arna, antibiotic
• Biological source: Escherichia coli BW25113
• Total number of polymer chains: 6
• Total formula weight: 446314.64

Authors

Liu, X.,Li, J. (deposition date: 2025-08-27, release date: 2025-11-26, Last modification date: 2025-12-17)

Primary citation

Liu, X.,Yang, R.,Ren, L.,Li, T.,Li, Y.,Yan, Z.,Gao, Y.,Yang, M.,Li, J.
Structural Basis for Targeting the Bifunctional Enzyme ArnA.
Biomolecules, 15:-, 2025

PubMed Abstract: Polymyxin antibiotics are often the last line of defense against multidrug-resistant Gram-negative pathogens. A key resistance mechanism involves the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) to lipid A, mediated by the bifunctional enzyme ArnA. However, the evolutionary rationale and structural basis for ArnA's domain fusion, hexameric assembly, and catalytic coordination remain mechanistically unresolved. Here, we integrate evolutionary genomics, high-resolution cryo-electron microscopy (cryo-EM), and computational protein design to provide a comprehensive mechanistic analysis of ArnA. Our evolutionary analysis reveals that the dehydrogenase (DH) and formyltransferase (TF) domains evolved independently and were selectively fused in Gammaproteobacteria, suggesting an adaptive advantage. A 2.89 Å cryo-EM structure of apo-ArnA resolves the flexible interdomain linker and reveals a DH-driven hexameric architecture essential for enzymatic activity. 3D variability analysis captures intrinsic conformational dynamics, indicating a molecular switch that may coordinate sequential catalysis and substrate channeling. Structure-based peptide inhibitors targeting the hexamerization and predicted ArnA-ArnB interaction interfaces were computationally designed, offering a novel strategy for disrupting L-Ara4N biosynthesis. These findings illuminate a previously uncharacterized structural mechanism of antimicrobial resistance and lay the groundwork for therapeutic intervention.

PubMed: 41301511
DOI: 10.3390/biom15111594

Experimental method

ELECTRON MICROSCOPY (2.89 Å)