PDBsum entry 3k3f

Transport protein

PDB id: 3k3f

Contents

Protein chain

332 a.a. *

Metals

_AU ×9

Waters ×55

* Residue conservation analysis

PDB id:

3k3f

Name:

Transport protein

Title:

Crystal structure of the urea transporter from desulfovibrio vulgaris

Structure:

Urea transporter. Chain: a. Engineered: yes

Source:

Desulfovibrio vulgaris. Organism_taxid: 882. Strain: hildenborough. Gene: dvu_1160. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.30Å R-factor: 0.180 R-free: 0.204

Authors:

E.J.Levin,M.Zhou,New York Consortium On Membrane Protein Structure (Nycomps)

Key ref:

E.J.Levin et al. (2009). Crystal structure of a bacterial homologue of the kidney urea transporter. Nature, 462, 757-761. PubMed id: 19865084 DOI: 10.1038/nature08558

Date:

02-Oct-09 Release date: 17-Nov-09

Protein chain

Q72CX3  (UT_DESVH) -  Urea transporter DVU1160 from Desulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough)

Seq: 337 a.a.

Struc: 332 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1038/nature08558

Nature 462:757-761 (2009)

PubMed id: 19865084

Crystal structure of a bacterial homologue of the kidney urea transporter.

E.J.Levin, M.Quick, M.Zhou.

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 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.

Selected figure(s)

Figure 2.
Figure 2: 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. Colour of helices matches that in the topology diagram (Supplementary Fig. 1b). b, Cartoon representation of the full dvUT trimer. The crystallographic three-fold symmetry axis is marked as a black triangle.

Figure 4.
Figure 4: Schematic view of the selectivity filter. The selectivity filter is shown from two angles. The predicted locations of three urea molecules and their hydrogen-bonding partners are on the left. In the perpendicular direction, the filter is compressed by phenylalanine and leucine side chains lining the walls of the pore (right). Helices contributing residues to the selectivity filter are represented as grey cylinders.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2009, 462, 757-761) copyright 2009.

Figures were selected by the author.