Urea is one of the most predominant nitrogen fertilizers in agricultural production and a key nitrogen metabolite in plants, playing an essential role in modern agriculture. In plant cells, DUR3 is a plasma membrane-localized, proton-driven, high-affinity urea transporter and a member of the sodium/solute symporter (SSS) family. It mediates both the uptake of external urea at low concentrations as a nutrient and the retrieval of urea from senescing leaves, facilitating nitrogen redistribution within the plant. Although DUR3 is crucial for efficient nitrogen utilization, the molecular mechanism underlying its high-affinity urea transport has remained elusive.

Dr. Jun Zhao from the Microstructure Research Platform at the Peking University Institute of Advanced Agricultural Sciences, in collaboration with Profs. Kai Zhang and Yan Zhao from the Institute of Biophysics, Chinese Academy of Sciences (CAS), has reported in Nature Communications the cryo-EM structures of Arabidopsis thaliana DUR3 in two distinct conformational states — an inward-open apo state and an occluded urea-bound state (Fig. 1B, C). The study, entitled "Structural basis of urea transport by Arabidopsis thaliana DUR3", provides a structural framework for understanding the mechanism of proton-coupled, high-affinity urea transport by plant DUR3.

 

Fig. 1. DUR3 adopts different conformational states and the proposed substrate transport mechanism.

 

DUR3 forms a homodimer with two parallel protomers, each containing 15 transmembrane helices adopting a canonical LeuT-like fold (Fig. 1A). Comparative analysis of the two structures revealed a spherical density within the central cavity — specifically in a pocket formed by TM1, TM2, TM6, TM7, and TM10 — that perfectly matches the size and shape of a urea molecule, identifying it as the substrate-binding site.

 

Functional complementation assays in a urea uptake-deficient yeast strain (YNVW1) identified several residues critical for substrate recognition. Aromatic side chains, particularly the conserved "tryptophan dyad" (W95 on TM1 and W338 on TM7), were found to be indispensable for urea binding. In the urea-bound structure, two titratable acidic residues were identified lining the transport cavity; mutation of either significantly impaired urea transport activity in yeast. Integrating structural and functional data, the authors propose a model for proton-coupled urea transport by DUR3 (Fig. 1D).

 

This work elucidates the molecular basis of high-affinity urea transport by plant DUR3, advances the understanding of proton-driven substrate transport within the SSS family, and provides structural insights that could contribute to improving urea-use efficiency in crops.

 

Profs. Kai Zhang and Yan Zhao (Institute of Biophysics, CAS) and Dr. Jun Zhao are co-corresponding authors. Visiting student Weidong An (now an assistant researcher at the Microstructure Research Platform), PhD student Yiwei Gao (Institute of Biophysics, CAS), and Prof. Laihua Liu (China Agricultural University) are co-first authors. PhD student Qinru Bai (Institute of Biophysics, CAS) also made important contributions. The Peking University Institute of Advanced Agricultural Sciences / Shandong Laboratory of Advanced Agriculture Sciences in Weifang is the first affiliation.

 

Original Article:

https://www.nature.com/articles/s41467-025-56943-2