Determinants of substrate and cation transport in the human Na+/dicarboxylate cotransporter, NaDC3 [Computational Biology]

May 7th, 2014 by Schlessinger, A., Sun, N. N., Colas, C., Pajor, A. M.

Metabolic intermediates, such as succinate and citrate, regulate important processes ranging from energy metabolism to fatty acid synthesis. Cytosolic concentrations of these metabolites are controlled in part by members of the SLC13 gene family. The molecular mechanism underlying Na+-coupled di- and tricarboxylate transport by this family is poorly understood. The human Na+/dicarboxylate cotransporter, NaDC3 (SLC13A3), is found in various tissues including the kidney, liver, and brain. In addition to citric acid cycle intermediates, such as α-ketoglutarate and succinate, NaDC3 transports other compounds into cells including N-acetylaspartate, mercaptosuccinate and glutathione, in keeping with its dual roles in cell nutrition and detoxification. In the present study, we construct a homology structural model of NaDC3 based on the structure of the Vibrio cholerae homolog, vcINDY. Our computations are followed by experimental testing of the predicted NaDC3 structure and mode of interaction with various substrates. The results of this study show that the substrate and cation binding domains of NaDC3 are composed of residues in the opposing hairpin loops and unwound portions of adjacent helices. Furthermore, these results provide a possible explanation for the differential substrate specificity among dicarboxylate transporters that underpin their diverse biological roles in metabolism and detoxification. The structural model of NaDC3 provides a framework for understanding substrate selectivity and the Na+-coupled anion transport mechanism by the human SLC13 family and other key solute carrier transporters.