7WST

Cryo-EM structure of the barley Yellow stripe 1 transporter in complex with Fe(III)-DMA

Summary for 7WST

• Entry DOI: 10.2210/pdb7wst/pdb
• EMDB information: 32766
• Descriptor: Iron-phytosiderophore transporter, CHOLESTEROL HEMISUCCINATE, FE (III) ION, ... (4 entities in total)
• Functional Keywords: iron-phytosiderophore transporter, deoxymugineic acid, metal transport
• Biological source: Hordeum vulgare
• Total number of polymer chains: 2
• Total formula weight: 154809.15

Authors

Yamagata, A. (deposition date: 2022-02-01, release date: 2022-11-30, Last modification date: 2024-11-06)

Primary citation

Yamagata, A.,Murata, Y.,Namba, K.,Terada, T.,Fukai, S.,Shirouzu, M.
Uptake mechanism of iron-phytosiderophore from the soil based on the structure of yellow stripe transporter.
Nat Commun, 13:7180-7180, 2022

PubMed Abstract: Calcareous soils cover one-third of all land and cause severe growth defects in plants due to the poor water solubility of iron at high pH. Poaceae species use a unique chelation strategy, whereby plants secrete a high-affinity metal chelator, known as phytosiderophores (mugineic acids), and reabsorb the iron-phytosiderophore complex by the yellow stripe 1/yellow stripe 1-like (YS1/YSL) transporter for efficient uptake of iron from the soil. Here, we present three cryo-electron microscopy structures of barley YS1 (HvYS1) in the apo state, in complex with an iron-phytosiderophore complex, Fe(III)-deoxymugineic acid (Fe(III)-DMA), and in complex with the iron-bound synthetic DMA analog (Fe(III)-PDMA). The structures reveal a homodimeric assembly mediated through an anti-parallel β-sheet interaction with cholesterol hemisuccinate. Each protomer adopts an outward open conformation, and Fe(III)-DMA is bound near the extracellular space in the central cavity. Fe(III)-PDMA occupies the same binding site as Fe(III)-DMA, demonstrating that PDMA can function as a potent fertilizer in an essentially identical manner to DMA. Our results provide a structural framework for iron-phytosiderophore recognition and transport by YS1/YSL transporters, which will enable the rational design of new, high-potency fertilizers.

PubMed: 36424382
DOI: 10.1038/s41467-022-34930-1

Experimental method

ELECTRON MICROSCOPY (2.7 Å)