Letter | Published:

Structure and mechanism of a bacterial sodium-dependent dicarboxylate transporter

Nature volume 491, pages 622626 (22 November 2012) | Download Citation

Abstract

In human cells, cytosolic citrate is a chief precursor for the synthesis of fatty acids, triacylglycerols, cholesterol and low-density lipoprotein. Cytosolic citrate further regulates the energy balance of the cell by activating the fatty-acid-synthesis pathway while downregulating both the glycolysis and fatty-acid β-oxidation pathways1,2,3,4. The rate of fatty-acid synthesis in liver and adipose cells, the two main tissue types for such synthesis, correlates directly with the concentration of citrate in the cytosol2,3,4,5, with the cytosolic citrate concentration partially depending on direct import across the plasma membrane through the Na+-dependent citrate transporter (NaCT)6,7. Mutations of the homologous fly gene (Indy; I’m not dead yet) result in reduced fat storage through calorie restriction8. More recently, Nact (also known as Slc13a5)-knockout mice have been found to have increased hepatic mitochondrial biogenesis, higher lipid oxidation and energy expenditure, and reduced lipogenesis, which taken together protect the mice from obesity and insulin resistance9. To understand the transport mechanism of NaCT and INDY proteins, here we report the 3.2 Å crystal structure of a bacterial INDY homologue. One citrate molecule and one sodium ion are bound per protein, and their binding sites are defined by conserved amino acid motifs, forming the structural basis for understanding the specificity of the transporter. Comparison of the structures of the two symmetrical halves of the transporter suggests conformational changes that propel substrate translocation.

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Accessions

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Protein Data Bank

Data deposits

The atomic coordinates and structure factors have been deposited in the Protein Data Bank under accession code 4F35.

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Acknowledgements

We are grateful to M. Punta and B. Rost for bioinformatics analysis of membrane transporters, to J. Love and B. Kloss for assistance in cloning, and to the staff at beamlines X4, X25 and X29 of the National Synchrotron Light Source in the Brookhaven National Laboratory and at the 23ID at the Advanced Photon Source at the Argonne National Laboratory for assistance in X-ray diffraction experiments, and to J. Llodra for help with artwork. We thank B. K. Czyzewski, W. A. Hendrickson, N. K. Karpowich, F. Mancia and J. J. Marden for discussions and for participating in synchrotron trips. This work was financially supported by National Institutes of Health grants U54-GM075026, R01-DK073973, R01-GM093825 and R01-MH083840.

Author information

Affiliations

  1. The Helen L. and Martin S. Kimmel Center for Biology and Medicine at the Skirball Institute of Biomolecular Medicine, New York University School of Medicine, 540 First Avenue, New York, New York 10016, USA

    • Romina Mancusso
    • , G. Glenn Gregorio
    •  & Da-Neng Wang
  2. Molecular Biophysics Graduate Program, New York University School of Medicine, 540 First Avenue, New York, New York 10016, USA

    • Romina Mancusso
  3. New York Structural Biology Center, NSLS X4, Brookhaven National Laboratory, Upton, New York 11973, USA

    • Qun Liu
  4. Department of Cell Biology, New York University School of Medicine, 540 First Avenue, New York, New York 10016, USA

    • Da-Neng Wang

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Contributions

R.M. and D.-N.W. designed the project. R.M. did all the experiments, with assistance from G.G.G. in diffraction data processing, phasing and structure refinement, and from Q.L. in phasing. R.M. and D.-N.W. wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Da-Neng Wang.

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    Supplementary Information

    This file contains a Supplementary Discussion, Supplementary References, Supplementary Tables 1-3 and Supplementary Figures 1-17.

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https://doi.org/10.1038/nature11542

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