Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Uptake mechanism of iron-phytosiderophore from the soil based on the structure of yellow stripe transporter.
Journal, issue, pages	Nat Commun, Vol. 13, Issue 1, Page 7180, Year 2022
Publish date	Nov 23, 2022
Authors	Atsushi Yamagata / Yoshiko Murata / Kosuke Namba / Tohru Terada / Shuya Fukai / Mikako Shirouzu /
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 ...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.
External links	Nat Commun / PubMed:36424382 / PubMed Central
Methods	EM (single particle)
Resolution	2.7 - 2.9 Å
Structure data	32765 7wsr EMDB-32765, PDB-7wsr: Cryo-EM structure of the barley Yellow stripe 1 transporter Method: EM (single particle) / Resolution: 2.9 Å 32766 7wst EMDB-32766, PDB-7wst: Cryo-EM structure of the barley Yellow stripe 1 transporter in complex with Fe(III)-DMA Method: EM (single particle) / Resolution: 2.7 Å 32767 7wsu EMDB-32767, PDB-7wsu: Cryo-EM structure of the barley Yellow stripe 1 transporter in complex with Fe(III)-PDMA Method: EM (single particle) / Resolution: 2.9 Å
Chemicals	ChemComp-Y01: CHOLESTEROL HEMISUCCINATE ChemComp-FE: Unknown entry / Iron ChemComp-554: (2~{S})-1-[(3~{S})-3-[[(3~{S})-3,4-bis(oxidanyl)-4-oxidanylidene-butyl]amino]-4-oxidanyl-4-oxidanylidene-butyl]azetidine-2-carboxylic acid ChemComp-5ZS: (2~{S})-1-[(3~{S})-3-[[(3~{S})-3,4-bis(oxidanyl)-4-oxidanylidene-butyl]amino]-4-oxidanyl-4-oxidanylidene-butyl]pyrrolidine-2-carboxylic acid
Source	hordeum vulgare (barley)
Keywords	METAL TRANSPORT / iron-phytosiderophore transporter / deoxymugineic acid / proline 2'-deoxymugineic acid