A home run for human NaCT/SLC13A5/INDY: cryo-EM structure and homology model to predict transport mechanisms, inhibitor interactions and mutational defects

Abstract

NaCT (SLC13A5) is a Na+-coupled transporter for citrate, which is expressed in the liver, brain, testes, and bone. It is the mammalian homolog of Drosophila INDY, a cation-independent transporter for citrate, whose partial loss extends lifespan in the organism. In humans, loss-of-function mutations in NaCT cause a disease with severe neurological dysfunction, characterized by neonatal epilepsy and delayed brain development. In contrast with humans, deletion of NaCT in mice results in a beneficial metabolic phenotype with protection against diet-induced obesity and metabolic syndrome; the brain dysfunction is not readily noticeable. The disease-causing mutations are located in different regions of human NaCT protein, suggesting that different mutations might have different mechanisms for the loss of function. The beneficial effects of NaCT loss in the liver versus the detrimental effects of NaCT loss in the brain provide an opportunity to design high-affinity inhibitors for the transporter that do not cross the blood-brain barrier so that only the beneficial effects could be harnessed. To realize these goals, we need a detailed knowledge of the 3D structure of human NaCT. The recent report by Sauer et al. in Nature describing the cryo-EM structure of human NaCT represents such a milestone, paving the way for a better understanding of the structure-function relationship for this interesting and clinically important transporter.

Untargeted Metabolomics of Slc13a5 Deficiency Reveal Critical Liver–Brain Axis for Lipid Homeostasis

“…Citrate is required both as a precursor for de novo fatty acid (FA) synthesis and for the activation of acetyl-CoA carboxylase, the committed step of the pathway [19,20]. SLC13A5 is expressed broadly in the plasma membrane of cells in the brain, testis, kidney, liver, bones, and adrenal gland, with enriched expression in hepatocytes along the sinusoidal membrane [10,19,[21][22][23][24].…”

Role of Sodium dependent SLC13 transporter and its inhibitors in various metabolic disorders

“…The current knowledge for the structural basis of the NaCTs is based upon Vibrio cholerae bacterial dicarboxylate transporter VcINDY. The structure VcINDY greatly differs from the human NaCT but still acts as the best option for the modeling studies [11]. It has a total of 11 transmembrane (TM) helices hairpin loops marked as HP in (hairpin in) and HP out (hairpin out).…”

INDY as a Therapeutic Target for Cardio-Metabolic Disease

“…Although Slc13A5 null mice show some neurological abnormalities, neurological dysfunction does not seem to be present in mice to the same extent [ 18 ]. Based on these different effects of NaCT deficiency in the brain and the periphery, it has been suggested that NaCT inhibitors that do not permeate the blood-brain barrier could have advantages [ 19 ]. It may thus be prudent to avoid complete and sustained NaCT blockade when applying brain-permeable NaCT inhibitors.…”