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Research Themes Protein-protein interactions

Urea transporter

PSI-SGKB [doi:10.1038/fa_psisgkb.2010.02]
Featured Article - February 2010
Short description: The X-ray crystal structure of a bacterial homolog of the mammalian urea transporter reveals a highly specific, channel-like transport mechanism.

Fold and oligomeric structure of dvUT. a, Cartoon representation of the dvUT protomer. The two-fold pseudo-symmetry axis, marked as a black oval, is normal to the plane of the figure. b, Cartoon representation of the full dvUT trimer. The crystallographic three-fold symmetry axis is marked as a black triangle.

Mammals use urea to get rid of excess nitrogen. It is the end product of protein breakdown and is highly concentrated in the kidney, where it helps the body to re-absorb water. Although urea is uncharged it is highly polar and extremely water-soluble, making its unaided transport across the hydrophobic cell membrane far too slow to be practicable.

Specialized membrane transport proteins have evolved to move it rapidly across the lipid bilayer, and now Ming Zhou and colleagues reveal the molecular details of this operation. They suggest that urea enters through small 'slots' in the protein and travels in single file through the transporter's internal channel.

They investigated the urea transporter from the bacterium Desulfovibrio vulgaris (dvUT). It was initially cloned and screened for expression by PSI NYCOMPS.

dvUT is a bacterial protein with sequence similarity to mammalian kidney cell urea channels, but to be sure that conclusions from dvUT would be broadly relevant, Zhou and his team tested whether dvUT transports urea. They confirmed that it does, and also found that the mammalian channel blocker phloretin works on the bacterial protein, suggesting that the two proteins use a similar mechanism.

The overall structure of dvUT is reminiscent of other channel proteins, such as aquaporin and amtB, that move small neutral molecules across the membrane. It is a homotrimer and each subunit forms a membrane-spanning pore; each subunit is composed of two homologous motifs, so both halves of the molecule have similar amino-acid sequences but point in opposite directions. The continuous pathway through the membrane is typical of a channel protein, and large conformational changes do not seem to be needed for transport.

To probe the transport mechanism further, the team used the urea analog dimethylurea, because urea cannot be seen within the structure. Two dimethylurea molecules could be clearly seen bound to two sites within the channel, each molecule forming bonds with the oxygen atoms that line the inside of the pore, dubbed an 'oxygen ladder' by the authors.

At the entrance to the pore, two phenylalanine residues form a flat hydrophobic 'slot' by alignment of their planar aromatic residues. This constriction acts as a filter, allowing the small, planar urea molecule to pass through, while preventing larger molecules from entering.

From this information, Zhou and colleagues were able to propose that urea enters the channel through the slots in each pore, which orient the substrate so that it can bind to the row of oxygens forming the ladder, guiding the substrate into the channel. Urea molecules pass through the channel one by one, each maintaining its orientation throughout by the effects of carefully spaced hydrophobic residues that allow optimal hydrogen bonding.

The structure explains the specificity and efficiency of the urea transporter and will pave the way for studying other urea channel families.

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References

  1. E. J. Levin, M. Quick and M. Zhou Crystal structure of a bacterial homologue of the kidney urea transporter.
    Nature 462, 757-761 (2009). doi:10.1038/nature08558

Structural Biology Knowledgebase ISSN: 1758-1338
Funded by a grant from the National Institute of General Medical Sciences of the National Institutes of Health