Urea transporter: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
Wayne Decatur (talk | contribs)
Editor, widgeteditor
7,596 edits
mNo edit summary
Michal Harel (talk | contribs)
31,761 edits
No edit summary
 
(19 intermediate revisions by 5 users not shown)
Line 1: Line 1:
[[Image:3k3f.png|left|200px]]
<StructureSection load='' size='350' side='right' caption='Urea transporter ([[3me1]]' scene='Urea_transporter/3k3fdefault/1' pspeed='8'>


<!--
===Crystal Structure of the Urea Transporter from Desulfovibrio Vulgaris===
The line below this paragraph, containing "STRUCTURE_3k3f", creates the "Structure Box" on the page.
You may change the PDB parameter (which sets the PDB file loaded into the applet)
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
or leave the SCENE parameter empty for the default display.
-->


===Crystal Structure of the Urea Transporter from Desulfovibrio Vulgaris===
<!--
The line below this paragraph, {{ABSTRACT_PUBMED_19865084}}, adds the Publication Abstract to the page
(as it appears on PubMed at http://www.pubmed.gov), where 19865084 is the PubMed ID number.
-->
{{ABSTRACT_PUBMED_19865084}}
{{ABSTRACT_PUBMED_19865084}}


==About this Structure==
==About this Structure==
{{Structure
|PDB= 3k3f  |SIZE=400|SCENE=Urea_transporter/3k3fdefault/1 |CAPTION= urea transporter ([[3k3f]]), resolution 2.30&Aring; (<scene name='Urea_transporter/3k3fdefault/1'>initial scene</scene>)
|SITE=
|LIGAND=
|ACTIVITY=
|GENE=
|DOMAIN=
|RELATEDENTRY=
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3k3f  FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k3f  OCA], [http://www.ebi.ac.uk/pdbsum/3k3f  PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=3k3f  RCSB]</span>
}}
The structure revealed <scene name='Urea_transporter/3k3fdefault/1a> monomer of the urea transporter</scene> in the asymmetric unit.


However, the urea transporter crystallized as <scene name='Urea_transporter/3k3f_trimer/1'>a homotrimer that corresponds to its functional biological state</scene>, 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='Urea_transporter/Opm_3k3f/3'>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.
To help give a better idea of how the '''urea transporter''' is oriented in the membrane lipid bilayer, <scene name='Urea_transporter/Opm_3k3f/3'>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]]-->
[[Image:Opm_periplasmic_topology.gif]] <!--I got this from Eric Martz's [[Mechanosensitive channels: opening and closing]]-->


==PDB entry==
</StructureSection>
[[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].
==3D structures of '''urea transporter''' or  '''solute carrier family 14'''==
 
Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
 
[[8blp]] – hUT 1 + cholesterol derivative – human<br />
[[6qd5]] – hUT 1 (mutant) + cholesterol derivative <br />
[[8blo]] – hUT 2 + choline derivative <br />
[[4ezc]] – bUT + ceramide - bovine<br />
[[4ezd]] – bUT + ceramide + selenourea<br />
[[3k3f]], [[3me1]] – DvUT – ''Desulfovibrio vulgaris''<br />
[[3m6e]] – DvUT (mutant)<br />
[[3k3g]] – DvUT + dimethylurea<br />
[[7s6e]] – UT + urea – ''synechococcus''<br />


==Reference for the structure==
==Reference for the structure==
Line 40: Line 30:


==See Also==
==See Also==
* <ref group="xtra">PMID:20010678</ref><references group="xtra"/>
<ref group="xtra">PMID:20010678</ref><references group="xtra"/>
* For Additional Information, See [[Membrane Channels & Pumps]]


==Reference==
==Reference==
Line 60: Line 51:


''Page started with original page on [[3k3f]] seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jan 28 14:58:46 2010''
''Page started with original page on [[3k3f]] seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jan 28 14:58:46 2010''
[[Category:Topic Page]]

Latest revision as of 12:23, 13 March 2024


Crystal Structure of the Urea Transporter from Desulfovibrio Vulgaris

Publication Abstract from PubMed

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 Structure

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.


Urea transporter (3me1

Drag the structure with the mouse to rotate

3D structures of urea transporter or solute carrier family 143D structures of urea transporter or solute carrier family 14

Updated on 13-March-2024

8blp – hUT 1 + cholesterol derivative – human
6qd5 – hUT 1 (mutant) + cholesterol derivative
8blo – hUT 2 + choline derivative
4ezc – bUT + ceramide - bovine
4ezd – bUT + ceramide + selenourea
3k3f, 3me1 – DvUT – Desulfovibrio vulgaris
3m6e – DvUT (mutant)
3k3g – DvUT + dimethylurea
7s6e – UT + urea – synechococcus

Reference for the structureReference for the structure

[xtra 1]

  1. ↑ 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

See AlsoSee Also

[xtra 1]

  1. ↑ Knepper MA, Mindell JA. Structural biology: Molecular coin slots for urea. Nature. 2009 Dec 10;462(7274):733-4. PMID:20010678 doi:10.1038/462733a

ReferenceReference

Page started with original page on 3k3f seeded by OCA on Thu Jan 28 14:58:46 2010

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Wayne Decatur, Jaime Prilusky, David Canner, Michal Harel, Joel L. Sussman
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=Urea_transporter&oldid=4085616"