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Crystal structure of a bacterial homologue of glucose transporters GLUT1–4

Nature volume 490, pages 361–366 (2012)Cite this article

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Abstract

Glucose transporters are essential for metabolism of glucose in cells of diverse organisms from microbes to humans, exemplified by the disease-related human proteins GLUT1, 2, 3 and 4. Despite rigorous efforts, the structural information for GLUT1–4 or their homologues remains largely unknown. Here we report three related crystal structures of XylE, an Escherichia coli homologue of GLUT1–4, in complex with d-xylose, d-glucose and 6-bromo-6-deoxy-d-glucose, at resolutions of 2.8, 2.9 and 2.6 Å, respectively. The structure consists of a typical major facilitator superfamily fold of 12 transmembrane segments and a unique intracellular four-helix domain. XylE was captured in an outward-facing, partly occluded conformation. Most of the important amino acids responsible for recognition of d-xylose or d-glucose are invariant in GLUT1–4, suggesting functional and mechanistic conservations. Structure-based modelling of GLUT1–4 allows mapping and interpretation of disease-related mutations. The structural and biochemical information reported here constitutes an important framework for mechanistic understanding of glucose transporters and sugar porters in general.

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Figure 1: The structure of XylE bound to d -xylose has an outward-facing, partly occluded conformation.
Figure 2: Recognition of d -xylose by XylE.
Figure 3: Coordination of d -glucose by XylE.
Figure 4: Homology-based modelling of GLUT1 structure.
Figure 5: Functional significance of the conserved SP family signature motifs.

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Accession codes

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Protein Data Bank

Data deposits

The atomic coordinates and structure factors of XylE bound to d-xylose, d-glucose and 6-BrGlc are deposited in the Protein Data Bank with accession codes 4GBY, 4GBZ and 4GC0.

References

  1. Thorens, B. & Mueckler, M. Glucose transporters in the 21st Century. Am. J. Physiol. Endocrinol. Metab. 298, E141–E145 (2010)

    Article  CAS  PubMed  Google Scholar 

  2. Pascual, J. M. et al. GLUT1 deficiency and other glucose transporter diseases. Eur. J. Endocrinol. 150, 627–633 (2004)

    Article  CAS  PubMed  Google Scholar 

  3. Scheepers, A., Joost, H. G. & Schurmann, A. The glucose transporter families SGLT and GLUT: molecular basis of normal and aberrant function. JPEN J. Parenter. Enteral Nutr. 28, 364–371 (2004)

    Article  CAS  PubMed  Google Scholar 

  4. Faham, S. et al. The crystal structure of a sodium galactose transporter reveals mechanistic insights into Na+/sugar symport. Science 321, 810–814 (2008)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  5. Mueckler, M. Facilitative glucose transporters. Eur. J. Biochem. 219, 713–725 (1994)

    Article  CAS  PubMed  Google Scholar 

  6. Mueckler, M. et al. Sequence and structure of a human glucose transporter. Science 229, 941–945 (1985)

    Article  ADS  CAS  PubMed  Google Scholar 

  7. Klepper, J. Glucose transporter deficiency syndrome (GLUT1DS) and the ketogenic diet. Epilepsia 49 (Suppl 8). 46–49 (2008)

    Article  PubMed  Google Scholar 

  8. Brockmann, K. The expanding phenotype of GLUT1-deficiency syndrome. Brain Dev. 31, 545–552 (2009)

    Article  PubMed  Google Scholar 

  9. Scheffer, I. E. GLUT1 deficiency: a glut of epilepsy phenotypes. Neurology 78, 524–525 (2012)

    Article  PubMed  Google Scholar 

  10. Santer, R. et al. Mutations in GLUT2, the gene for the liver-type glucose transporter, in patients with Fanconi–Bickel syndrome. Nature Genet. 17, 324–326 (1997)

    Article  CAS  PubMed  Google Scholar 

  11. Leturque, A., Brot-Laroche, E. & Le Gall, M. GLUT2 mutations, translocation, and receptor function in diet sugar managing. Am. J. Physiol. Endocrinol. Metab. 296, E985–E992 (2009)

    Article  CAS  PubMed  Google Scholar 

  12. Simpson, I. A. et al. The facilitative glucose transporter GLUT3: 20 years of distinction. Am. J. Physiol. Endocrinol. Metab. 295, E242–E253 (2008)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Amann, T. & Hellerbrand, C. GLUT1 as a therapeutic target in hepatocellular carcinoma. Expert Opin. Ther. Targets 13, 1411–1427 (2009)

    Article  CAS  PubMed  Google Scholar 

  14. Macheda, M. L., Rogers, S. & Best, J. D. Molecular and cellular regulation of glucose transporter (GLUT) proteins in cancer. J. Cell. Physiol. 202, 654–662 (2005)

    Article  CAS  PubMed  Google Scholar 

  15. Mueckler, M. The molecular biology of glucose transport: relevance to insulin resistance and non-insulin-dependent diabetes mellitus. J. Diabetes Complications 7, 130–141 (1993)

    Article  CAS  PubMed  Google Scholar 

  16. Leney, S. E. & Tavare, J. M. The molecular basis of insulin-stimulated glucose uptake: signalling, trafficking and potential drug targets. J. Endocrinol. 203, 1–18 (2009)

    Article  CAS  PubMed  Google Scholar 

  17. Nelson, D. L. & Cox, M. M. Lehninger Principles of Biochemistry 1158 (W. H. Freeman, 2008)

    Google Scholar 

  18. Pao, S. S., Paulsen, I. T. & Saier, M. H., Jr Major facilitator superfamily. Microbiol. Mol. Biol. Rev. 62, 1–34 (1998)

    CAS  PubMed  PubMed Central  Google Scholar 

  19. Henderson, P. J. & Maiden, M. C. Homologous sugar transport proteins in Escherichia coli and their relatives in both prokaryotes and eukaryotes. Phil. Trans. R. Soc. Lond. B 326, 391–410 (1990)

    Article  ADS  CAS  Google Scholar 

  20. Ozcan, S. & Johnston, M. Function and regulation of yeast hexose transporters. Microbiol. Mol. Biol. Rev. 63, 554–569 (1999)

    CAS  PubMed  PubMed Central  Google Scholar 

  21. Buttner, M. The monosaccharide transporter(-like) gene family in Arabidopsis. FEBS Lett. 581, 2318–2324 (2007)

    Article  PubMed  Google Scholar 

  22. Li, F. et al. Characterization of sucrose transporter alleles and their association with seed yield-related traits in Brassica napus L. BMC Plant Biol. 11, 168 (2011)

    Article  PubMed  PubMed Central  Google Scholar 

  23. Mueckler, M. & Makepeace, C. Model of the exofacial substrate-binding site and helical folding of the human Glut1 glucose transporter based on scanning mutagenesis. Biochemistry 48, 5934–5942 (2009)

    Article  CAS  PubMed  Google Scholar 

  24. Abramson, J. et al. Structure and mechanism of the lactose permease of Escherichia coli. Science 301, 610–615 (2003)

    Article  ADS  CAS  PubMed  Google Scholar 

  25. Huang, Y., Lemieux, M. J., Song, J., Auer, M. & Wang, D. N. Structure and mechanism of the glycerol-3-phosphate transporter from Escherichia coli. Science 301, 616–620 (2003)

    Article  ADS  CAS  PubMed  Google Scholar 

  26. Yin, Y., He, X., Szewczyk, P., Nguyen, T. & Chang, G. Structure of the multidrug transporter EmrD from Escherichia coli. Science 312, 741–744 (2006)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  27. Dang, S. et al. Structure of a fucose transporter in an outward-open conformation. Nature 467, 734–738 (2010)

    Article  ADS  CAS  PubMed  Google Scholar 

  28. Newstead, S. et al. Crystal structure of a prokaryotic homologue of the mammalian oligopeptide–proton symporters, PepT1 and PepT2. EMBO J. 30, 417–426 (2011)

    Article  CAS  PubMed  Google Scholar 

  29. Lam, V. M., Daruwalla, K. R., Henderson, P. J. & Jones-Mortimer, M. C. Proton-linked d-xylose transport in Escherichia coli. J. Bacteriol. 143, 396–402 (1980)

    CAS  PubMed  PubMed Central  Google Scholar 

  30. Davis, E. O., Jones-Mortimer, M. C. & Henderson, P. J. Location of a structural gene for xylose–H+ symport at 91 min on the linkage map of Escherichia coli K12. J. Biol. Chem. 259, 1520–1525 (1984)

    CAS  PubMed  Google Scholar 

  31. Davis, E. O. & Henderson, P. J. The cloning and DNA sequence of the gene xylE for xylose–proton symport in Escherichia coli K12. J. Biol. Chem. 262, 13928–13932 (1987)

    CAS  PubMed  Google Scholar 

  32. Maiden, M. C., Davis, E. O., Baldwin, S. A., Moore, D. C. & Henderson, P. J. Mammalian and bacterial sugar transport proteins are homologous. Nature 325, 641–643 (1987)

    Article  ADS  CAS  PubMed  Google Scholar 

  33. Henderson, P. J. Proton-linked sugar transport systems in bacteria. J. Bioenerg. Biomembr. 22, 525–569 (1990)

    Article  CAS  PubMed  Google Scholar 

  34. Screpanti, E. & Hunte, C. Discontinuous membrane helices in transport proteins and their correlation with function. J. Struct. Biol. 159, 261–267 (2007)

    Article  CAS  PubMed  Google Scholar 

  35. Snider, C. & White, S. Membrane Proteins of Known 3D Structure (Stephen H. White Lab., Univ. of California Irvine, 2011)

    Google Scholar 

  36. Lu, F. et al. Structure and mechanism of the uracil transporter UraA. Nature 472, 243–246 (2011)

    Article  ADS  CAS  PubMed  Google Scholar 

  37. Ressl, S., Terwisscha van Scheltinga, A. C., Vonrhein, C., Ott, V. & Ziegler, C. Molecular basis of transport and regulation in the Na+/betaine symporter BetP. Nature 458, 47–52 (2009)

    Article  ADS  CAS  PubMed  Google Scholar 

  38. Gao, X. et al. Structure and mechanism of an amino acid antiporter. Science 324, 1565–1568 (2009)

    Article  ADS  CAS  PubMed  Google Scholar 

  39. Fang, Y. et al. Structure of a prokaryotic virtual proton pump at 3.2 Å resolution. Nature 460, 1040–1043 (2009)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  40. Gao, X. et al. Mechanism of substrate recognition and transport by an amino acid antiporter. Nature 463, 828–832 (2010)

    Article  ADS  CAS  PubMed  Google Scholar 

  41. Desai, T. A. & Rao, C. V. Regulation of arabinose and xylose metabolism in Escherichia coli. Appl. Environ. Microbiol. 76, 1524–1532 (2010)

    Article  CAS  PubMed  Google Scholar 

  42. Xiang, Z., Steinbach, P. J., Jacobson, M. P., Friesner, R. A. & Honig, B. Prediction of side-chain conformations on protein surfaces. Proteins 66, 814–823 (2007)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Wang, D. et al. Glut-1 deficiency syndrome: clinical, genetic, and therapeutic aspects. Ann. Neurol. 57, 111–118 (2005)

    Article  CAS  PubMed  Google Scholar 

  44. Cunningham, P., Afzal-Ahmed, I. & Naftalin, R. J. Docking studies show that d-glucose and quercetin slide through the transporter GLUT1. J. Biol. Chem. 281, 5797–5803 (2006)

    Article  CAS  PubMed  Google Scholar 

  45. Brockmann, K. et al. Autosomal dominant Glut-1 deficiency syndrome and familial epilepsy. Ann. Neurol. 50, 476–485 (2001)

    Article  CAS  PubMed  Google Scholar 

  46. Ho, Y. Y. et al. Glucose transporter type 1 deficiency syndrome (Glut1DS): methylxanthines potentiate GLUT1 haploinsufficiency in vitro. Pediatr. Res. 50, 254–260 (2001)

    Article  CAS  PubMed  Google Scholar 

  47. Franco, P. J. & Brooker, R. J. Functional roles of Glu-269 and Glu-325 within the lactose permease of Escherichia coli. J. Biol. Chem. 269, 7379–7386 (1994)

    CAS  PubMed  Google Scholar 

  48. Guan, L. & Kaback, H. R. Lessons from lactose permease. Annu. Rev. Biophys. Biomol. Struct. 35, 67–91 (2006)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Schneider, T. R. & Sheldrick, G. M. Substructure solution with SHELXD. Acta Crystallogr. D 58, 1772–1779 (2002)

    Article  PubMed  Google Scholar 

  50. DeLano, W. L. The PyMOL Molecular Graphics System. http://www.pymol.org (2002)

  51. Saier, M. H., Jr, Yen, M. R., Noto, K., Tamang, D. G. & Elkan, C. The Transporter Classification Database: recent advances. Nucleic Acids Res. 37, D274–D278 (2009)

    Article  CAS  PubMed  Google Scholar 

  52. Saier, M. H., Jr, Tran, C. V. & Barabote, R. D. TCDB: the Transporter Classification Database for membrane transport protein analyses and information. Nucleic Acids Res. 34, D181–D186 (2006)

    Article  CAS  PubMed  Google Scholar 

  53. Thompson, J. D., Higgins, D. G. & Gibson, T. J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673–4680 (1994)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Felsenstein, J. PHYLIP—Phylogeny Inference Package (version 3.2). Cladistics 5, 164–166 (1989)

    Google Scholar 

  55. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997)

    Article  CAS  PubMed  Google Scholar 

  56. Collaborative Computational Project Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D 50, 760–763 (1994)

  57. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004)

    Article  PubMed  Google Scholar 

  58. McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Cryst. 40, 658–674 (2007)

    Article  CAS  Google Scholar 

  59. Cowtan, K. dm: an automated procedure for phase improvement by density modification. Joint CCP4 ESF-EACBM Newsl. Prot. Crystallogr. 31, 34–38 (1994)

    Google Scholar 

  60. Adams, P. D. et al. PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr. D 58, 1948–1954 (2002)

    Article  PubMed  Google Scholar 

  61. Veenhoff, L. M. & Poolman, B. Substrate recognition at the cytoplasmic and extracellular binding site of the lactose transport protein of Streptococcus thermophilus. J. Biol. Chem. 274, 33244–33250 (1999)

    Article  CAS  PubMed  Google Scholar 

  62. Scheich, C., Kummel, D., Soumailakakis, D., Heinemann, U. & Bussow, K. Vectors for co-expression of an unrestricted number of proteins. Nucleic Acids Res. 35, e43 (2007)

    Article  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

We thank J. He, L. Tang, F. Yu and S. Huang at Shanghai Synchrotron Radiation Facility, and K. Hasegawa and T. Kumasaka at the SPring-8 beamline BL41XU, for on-site assistance. This work was supported by funds from the Ministry of Science and Technology (grant numbers 2009CB918802 and 2011CB910501), projects 31125009 and 91017011 of the National Natural Science Foundation of China, and funds from Tsinghua University.

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  1. Linfeng Sun and Xin Zeng: These authors contributed equally to this work.

Authors and Affiliations

  1. State Key Laboratory of Bio-membrane and Membrane Biotechnology, Center for Structural Biology, Tsinghua University, Beijing, 100084, China

    Linfeng Sun, Xin Zeng, Chuangye Yan, Xinqi Gong & Nieng Yan

  2. School of Life Sciences and School of Medicine, Tsinghua University, Beijing, 100084, China

    Linfeng Sun, Xin Zeng, Chuangye Yan, Xiuyun Sun, Xinqi Gong, Yu Rao & Nieng Yan

  3. Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China

    Linfeng Sun, Xin Zeng, Chuangye Yan, Xinqi Gong & Nieng Yan

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Contributions

L.S., X.Z. and N.Y. designed all experiments. L.S., X.Z., C.Y., X.G. and N.Y. performed the experiments for structural determination, homology-based structure modelling and biochemical analysis. X.S. and Y.R. synthesized 6-BrGlc. All authors analysed the data and contributed to manuscript preparation. N.Y. wrote the manuscript.

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Correspondence to Nieng Yan.

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Sun, L., Zeng, X., Yan, C. et al. Crystal structure of a bacterial homologue of glucose transporters GLUT1–4. Nature 490, 361–366 (2012). https://doi.org/10.1038/nature11524

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