Structural basis of ammonium transport and coordinated regulation of AMT1;1 in Arabidopsis thaliana

Abstract

Efficient ammonium uptake is essential for plant growth and nitrogen-use efficiency, yet the structural basis of ammonium transport and regulation in plant AMTs remains unclear. Here, we determined multiple cryo-electron microscopy structures of the Arabidopsis thaliana ammonium transporter AMT1;1 in apo, ammonium-bound, methylammonium-bound, low-pH and phosphomimetic states. These structures reveal a conserved ammonium conduction pathway comprising an aromatic recruitment vestibule, a Phe-gate/Twin-His-containing pore, and a polar intracellular exit region. We further identified a conserved extracellular N-terminal disulfide bond required for oligomer stability and transport activity, suggesting potential redox-dependent regulation. On the cytoplasmic side, phosphorylation modulates C-terminal interactions with intracellular loops, revealing an allosteric regulatory mechanism. Comparison with the bacterial ammonium-sensing protein Sd -Amt1 uncovers a conserved ammonium-recognition region in At AMT1;1 that contributes to transport activity but lacks the signaling module and ligand-dependent conformational switching observed in Sd -Amt1. Together, these findings provide structural insight into ammonium transport and coordinated regulation in plant AMT transporters.