Structure and inhibition mechanism of the human citrate transporter NaCT

• Published in: Nature (London) Vol. 591; no. 7848; pp. 157 - 161
• Main Authors: Sauer, David B., Song, Jinmei, Wang, Bing, Hilton, Jacob K., Karpowich, Nathan K., Mindell, Joseph A., Rice, William J., Wang, Da-Neng
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 04-03-2021; Nature Publishing Group
• Subjects: 101/28; 631/535/1258/1259; 631/57/2283; 82/80; 82/83; Binding Sites; Brain - metabolism; Carrier Proteins - antagonists & inhibitors; Carrier Proteins - chemistry; Carrier Proteins - genetics; Carrier Proteins - ultrastructure; Citric acid; Citric Acid - chemistry; Citric Acid - metabolism; Cryoelectron Microscopy; Dicarboxylic Acid Transporters - chemistry; Dicarboxylic Acid Transporters - metabolism; Electron microscopy; Energy metabolism; Enzymes; Epilepsy; Epilepsy - genetics; Epilepsy - metabolism; Fatty acids; Hepatocytes; Homology; Humanities and Social Sciences; Humans; Hydrogen bonds; Liver diseases; Malates - chemistry; Malates - pharmacology; Metabolism; Metabolites; Microscopy; Models, Molecular; multidisciplinary; Mutation; Neonates; Obesity; Phenylbutyrates - chemistry; Phenylbutyrates - pharmacology; Protein Multimerization; Proteins; Science; Science (multidisciplinary); Selectivity; Sodium - metabolism; Substrate Specificity - drug effects; Substrate Specificity - genetics; Symporters - antagonists & inhibitors; Symporters - chemistry; Symporters - genetics; Symporters - ultrastructure; Tricarboxylic acid cycle
• ISSN: 0028-0836; 1476-4687
• DOI: 10.1038/s41586-021-03230-x

Citrate is best known as an intermediate in the tricarboxylic acid cycle of the cell. In addition to this essential role in energy metabolism, the tricarboxylate anion also acts as both a precursor and a regulator of fatty acid synthesis
1
–
3
. Thus, the rate of fatty acid synthesis correlates directly with the cytosolic concentration of citrate
4
,
5
. Liver cells import citrate through the sodium-dependent citrate transporter NaCT (encoded by
SLC13A5
) and, as a consequence, this protein is a potential target for anti-obesity drugs. Here, to understand the structural basis of its inhibition mechanism, we determined cryo-electron microscopy structures of human NaCT in complexes with citrate or a small-molecule inhibitor. These structures reveal how the inhibitor—which binds to the same site as citrate—arrests the transport cycle of NaCT. The NaCT–inhibitor structure also explains why the compound selectively inhibits NaCT over two homologous human dicarboxylate transporters, and suggests ways to further improve the affinity and selectivity. Finally, the NaCT structures provide a framework for understanding how various mutations abolish the transport activity of NaCT in the brain and thereby cause epilepsy associated with mutations in
SLC13A5
in newborns (which is known as SLC13A5-epilepsy)
6
–
8
.
Structures of the human sodium-dependent citrate transporter NaCT in complexes with citrate or a small-molecule inhibitor reveal how the inhibitor—which binds to the same site as citrate—arrests the transport cycle of NaCT.