Crystal structure of a bacterial homologue of the kidney urea transporter

Abstract

Urea is highly concentrated in the mammalian kidney to produce the osmotic gradient necessary for water re-absorption. Free diffusion of urea across cell membranes is slow owing to its high polarity, and specialized urea transporters have evolved to achieve rapid and selective urea permeation. Here we present the 2.3 Å structure of a functional urea transporter from the bacterium Desulfovibrio vulgaris. The transporter is a homotrimer, and each subunit contains a continuous membrane-spanning pore formed by the two homologous halves of the protein. The pore contains a constricted selectivity filter that can accommodate several dehydrated urea molecules in single file. Backbone and side-chain oxygen atoms provide continuous coordination of urea as it progresses through the filter, and well-placed α-helix dipoles provide further compensation for dehydration energy. These results establish that the urea transporter operates by a channel-like mechanism and reveal the physical and chemical basis of urea selectivity.

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Figure 1: dvUT mediated urea flux and binding.
Figure 2: Fold and oligomeric structure of dvUT.
Figure 3: Structure of the dvUT pore and DMU-binding sites.
Figure 4: Schematic view of the selectivity filter.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Atomic coordinates and structure factors have been deposited with the Protein Data Bank under accession 3K3F and 3K3G.

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Acknowledgements

We thank R. MacKinnon for advice and support throughout the project, C. Miller and E. Gouaux for comments on the manuscript, J. Love and NYCOMPS for cloning and the initial screen of protein expression levels, Y. Pan for messenger RNA preparation and oocyte injection, and J. Weng and Y. Cao for crystal screening and data collection at the synchrotrons. Data for this study were measured at beamlines X4A, X4C, X25 and X29 of the NSLS and the NE-CAT 24ID-E at the Advanced Photon Source. This work was supported by the US National Institutes of Health (HL086392 to M.Z. and T32HL087745 to E.J.L.), the NYCOMPS that is supported by the NIH Protein Structure Initiatives PSI-II (GM075026 to W. A. Hendrickson), and the American Heart Association (0630148N to M.Z.). M.Z. is a Pew Scholar in Biomedical Sciences.

Author Contributions E.J.L. and M.Z. conceived and designed the experiments. E.J.L. purified and crystallized the protein; M.Q. performed and analysed the radiotracer flux and SPA binding assays; E.J.L. and M.Z. collected and processed the X-ray data, solved the structure, and wrote the paper.

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Correspondence to Ming Zhou.

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Levin, E., Quick, M. & Zhou, M. Crystal structure of a bacterial homologue of the kidney urea transporter . Nature 462, 757–761 (2009). https://doi.org/10.1038/nature08558

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