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TitleStructural Basis for Targeting the Bifunctional Enzyme ArnA.
Journal, issue, pagesBiomolecules, Vol. 15, Issue 11, Year 2025
Publish dateNov 13, 2025
AuthorsXinyu Liu / Ruochen Yang / Libang Ren / Tong Li / Yanrong Li / Zhihua Yan / Yanrong Gao / Mingqi Yang / Jiazhi Li /
PubMed AbstractPolymyxin 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) ...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.
External linksBiomolecules / PubMed:41301511 / PubMed Central
MethodsEM (single particle)
Resolution2.89 Å
Structure data

65981

9wi0

EMDB-65981, PDB-9wi0:
cryo-EM structure of E.coli ArnA
Method: EM (single particle) / Resolution: 2.89 Å

Source
  • escherichia coli bw25113 (bacteria)
KeywordsANTIBIOTIC / Bifunctional polymyxin resistance protein ArnA

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