Urea transporter: Difference between revisions
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{{Structure | {{Structure | ||
|PDB= 3k3f |SIZE=400|SCENE= |CAPTION= urea transporter (3k3f), resolution 2.30Å (<scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Default3kg2/1'>initial scene</scene>) | |PDB= 3k3f |SIZE=400|SCENE= |CAPTION= urea transporter ([[3k3f]]), resolution 2.30Å (<scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Default3kg2/1'>initial scene</scene>) | ||
|SITE= | |SITE= | ||
|LIGAND= | |LIGAND= | ||
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==About this Structure== | ==About this Structure== | ||
3K3F is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris_str._hildenborough Desulfovibrio vulgaris str. hildenborough]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K3F OCA]. | The structure revealed a monomer of the urea transporter in the asymmetric unit. | ||
However, the urea transporter crystallized as a homotrimer that corresponds to its functional biological state, and this is seen when considering the crystallographic three-fold symmetry axis. | |||
To help give a better idea of how the urea transporter is oriented in the membrane lipid bilayer,<scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/3kg2opm_mem/10'>a slab representative of hydrophobic core of the lipid bilayer</scene> as calculated by the [http://opm.phar.umich.edu/protein.php?pdbid=3kg2 Orientations of Proteins in Membranes database](University of Michigan, USA) is shown with the red patch of spheres indicating the boundary of the hydrophobic core closet to the outside of the cell and the dark blue patch of spheres indicating the boundary closest to the inside of the cell. | |||
[[Image:Opm_periplasmic_topology.gif]] <!--I got this from Eric Martz's [[Mechanosensitive channels: opening and closing]]--> | |||
==PDB entry== | |||
[[3K3F]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris_str._hildenborough Desulfovibrio vulgaris str. hildenborough]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K3F OCA]. | |||
==Reference for the structure== | |||
<ref group="xtra">PMID:19865084</ref><references group="xtra"/> | |||
==Reference== | ==Reference== | ||
<ref group="xtra">PMID:19865084</ref><references group="xtra"/> | {{Reflist}}<ref group="xtra">PMID:19865084</ref><references group="xtra"/> | ||
[[Category: Desulfovibrio vulgaris str. hildenborough]] | [[Category: Desulfovibrio vulgaris str. hildenborough]] | ||
[[Category: Levin, E J.]] | [[Category: Levin, E J.]] | ||
Revision as of 05:56, 4 July 2010
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| urea transporter (3k3f), resolution 2.30Å () | |||||||
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal Structure of the Urea Transporter from Desulfovibrio VulgarisCrystal Structure of the Urea Transporter from Desulfovibrio Vulgaris
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 A 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 alpha-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.
Crystal structure of a bacterial homologue of the kidney urea transporter., Levin EJ, Quick M, Zhou M, Nature. 2009 Dec 10;462(7274):757-61. Epub . PMID:19865084
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
About this StructureAbout this Structure
The structure revealed a monomer of the urea transporter in the asymmetric unit.
However, the urea transporter crystallized as a homotrimer that corresponds to its functional biological state, and this is seen when considering the crystallographic three-fold symmetry axis.
To help give a better idea of how the urea transporter is oriented in the membrane lipid bilayer, as calculated by the Orientations of Proteins in Membranes database(University of Michigan, USA) is shown with the red patch of spheres indicating the boundary of the hydrophobic core closet to the outside of the cell and the dark blue patch of spheres indicating the boundary closest to the inside of the cell.
PDB entryPDB entry
3K3F is a 1 chain structure with sequence from Desulfovibrio vulgaris str. hildenborough. Full crystallographic information is available from OCA.
Reference for the structureReference for the structure
- ↑ Levin EJ, Quick M, Zhou M. Crystal structure of a bacterial homologue of the kidney urea transporter. Nature. 2009 Dec 10;462(7274):757-61. Epub . PMID:19865084 doi:10.1038/nature08558
ReferenceReference
- ↑ Levin EJ, Quick M, Zhou M. Crystal structure of a bacterial homologue of the kidney urea transporter. Nature. 2009 Dec 10;462(7274):757-61. Epub . PMID:19865084 doi:10.1038/nature08558
Page started with original page on 3k3f seeded by OCA on Thu Jan 28 14:58:46 2010