Structure of a prokaryotic SLC26 transporter

The SLC26 proteins constitute a large family of anion transporters whose malfunctioning in humans is associated with diseases. We determined the first structure of a prokaryotic homolog that defines the common framework for the diverse functional behavior of the family.

HFSP Long-Term Fellow Eric Geertsma and colleagues
authored on Thu, 08 October 2015

The SLC26 family of membrane proteins combines a variety of functions within one conserved molecular scaffold. Its members, besides coupled anion transporters and channels, include the motor protein Prestin (SLC26A5) that resides in cochlear outer hair cells. Small pressure variations from incoming sound waves cause conformational changes in Prestin that lead to rapid alterations in cell length and result in the amplification of sound. Malfunctioning of other human SLC26 transporters is linked to severe diseases, such as growth defects, chronic diarrhea and deafness. Prokaryotic SLC26 proteins transport bicarbonate or dicarboxylic acids in a sodium- or proton-dependent manner. SLC26 transporters have a conserved architecture consisting of a membrane domain and a small cytoplasmic domain. Although structures of isolated cytoplasmic domains have been determined, the structure of a full-length SLC26 transporter has been elusive.

Figure: Structure of a prokaryotic SLC26 transporter from Deinococcus geothermalis.
Upper panel: structure of full-length SLC26Dg. The first repeat of seven transmembrane segments is colored as rainbow gradient; the second repeat is in grey. The soluble cytoplasmic domain is colored purple. Lower panel: individual representation of both repeats. The second repeat is rotated 180 degrees over an axis parallel to the membrane plane. Related helices of both repeats are represented in similar colors. The approximate boundaries of the membrane are indicated by grey lines

We investigated the structural and functional properties of a prokaryotic SLC26 homolog, termed SLC26Dg, from the bacterium Deinococcus geothermalis. This specific homolog was efficiently selected from a set of 92 homologs on the basis of its superior biochemical properties. SLC26Dg is a proton-dependent secondary transporter of the dicarboxylate fumarate. This transport is electrogenic; an inside positive membrane potential stimulates uptake.

We determined the crystal structure of full-length SLC26Dg at 3.2 Ångström. Obtaining crystals of sufficient quality was critically dependent on the use of nanobodies, small crystallization chaperones based on heavy chain only antibodies from camelids. In the structure, the membrane and the cytoplasmic domain of SLC26Dg exhibit only a few interactions. The membrane domain consists of fourteen alpha-helices of variable length, including several short helices that do not span the entire membrane. It is organized in two structurally related halves of seven transmembrane segments each (see figure). These halves are oriented in opposite directions and form an intertwined structure of two inverted repeats. The combination of two inverted repeats is found more often in secondary transporters, but inverted repeats of seven transmembrane segments are rare. This fold has been observed previously only once and suggests a common descent for the SLC26 family and vitamin C symporters of the NCS2 family.

The SLC26Dg structure provides a representative scaffold for the entire SLC26 family. It reveals the location of a potential binding site for a negatively charged substrate at the center of the transporter between two interrupted alpha-helices. The SLC26Dg structure shows an inward-facing conformation with a large aqueous cavity separating the protein into a “core” and “gate” domain. Relative rearrangements between these core and gate domains are currently suspected to underlie transport. The observed architecture suggests that even in family members designated as channels ion-transport may proceed by an alternate-access mechanism. Our structure reveals the architecture of the SLC26 family and provides a platform to study its functional mechanism.

Reference

Structure of a prokaryotic fumarate transporter reveals the architecture of the SLC26 family. Geertsma ER, Chang YN, Shaik FR, Neldner Y, Pardon E, Steyaert J, Dutzler R. Nat Struct Mol Biol. 2015 Sep 14. doi: 10.1038/nsmb.3091.

Pubmed link