Structure and mechanism of the uracil transporter UraA

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The nucleobase/ascorbate transporter (NAT) proteins, also known as nucleobase/cation symporter 2 (NCS2) proteins, are responsible for the uptake of nucleobases in all kingdoms of life and for the transport of vitamin C in mammals1,2. Despite functional characterization of the NAT family members in bacteria, fungi and mammals, detailed structural information remains unavailable. Here we report the crystal structure of a representative NAT protein, the Escherichia coli uracil/H+ symporter UraA, in complex with uracil at a resolution of 2.8 Å. UraA has a novel structural fold, with 14 transmembrane segments (TMs) divided into two inverted repeats. A pair of antiparallel β-strands is located between TM3 and TM10 and has an important role in structural organization and substrate recognition. The structure is spatially arranged into a core domain and a gate domain. Uracil, located at the interface between the two domains, is coordinated mainly by residues from the core domain. Structural analysis suggests that alternating access of the substrate may be achieved through conformational changes of the gate domain.

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Figure 1: The structure of UraA reveals a novel fold.
Figure 2: Domain organization of UraA.
Figure 3: Uracil coordination by UraA.
Figure 4: Working model for the transport mechanism of UraA.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Theatomic coordinates of UraAhave been deposited in the Protein Data Bank under accession code 3QE7.

Change history

  • 14 April 2011

    In the Fig. 4b legend, Glu245 was corrected to Glu290.


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We thank N. Shimizu at the Spring-8 beamline BL41XU, and J. He and S. Huang at the Shanghai Synchrotron Radiation Facility for on-site assistance. We thank Y. Shi and Y. Yan for critical discussions. This work was supported by funds from the Ministry of Science and Technology (grant numbers 2009CB918802 and 2011CB910501), Tsinghua University 985 Phase II funds and Project 91017011 supported by the National Natural Science Foundation of China. N.Y. acknowledges support from the Yuyuan Foundation and the Li Foundation.

Author information

F.L., S.L., Y.J., J.J., H.F., G.L. and N.Y. designed all experiments. F.L., S.L., Y.J., J.J., H.F., G.L., D.D., S.D. and X.Z. performed the experiments. All authors analysed the data. F.L., J.W. and N.Y. contributed to manuscript preparation. N.Y. wrote the manuscript.

Correspondence to Nieng Yan.

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Lu, F., Li, S., Jiang, Y. et al. Structure and mechanism of the uracil transporter UraA. Nature 472, 243–246 (2011) doi:10.1038/nature09885

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