Crystal structure of the FTO protein reveals basis for its substrate specificity

Article metrics

Abstract

Recent studies1,2,3,4,5 have unequivocally associated the fat mass and obesity-associated (FTO) gene with the risk of obesity. In vitro FTO protein is an AlkB-like DNA/RNA demethylase with a strong preference for 3-methylthymidine (3-meT) in single-stranded DNA or 3-methyluracil (3-meU) in single-stranded RNA6,7,8. Here we report the crystal structure of FTO in complex with the mononucleotide 3-meT. FTO comprises an amino-terminal AlkB-like domain and a carboxy-terminal domain with a novel fold. Biochemical assays show that these two domains interact with each other, which is required for FTO catalytic activity. In contrast with the structures of other AlkB members, FTO possesses an extra loop covering one side of the conserved jelly-roll motif. Structural comparison shows that this loop selectively competes with the unmethylated strand of the DNA duplex for binding to FTO, suggesting that it has an important role in FTO selection against double-stranded nucleic acids. The ability of FTO to distinguish 3-meT or 3-meU from other nucleotides is conferred by its hydrogen-bonding interaction with the two carbonyl oxygen atoms in 3-meT or 3-meU. Taken together, these results provide a structural basis for understanding FTO substrate-specificity, and serve as a foundation for the rational design of FTO inhibitors.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Figure 1: FTO contains two well-defined domains.
Figure 2: Interaction between the NTD and CTD of FTO.
Figure 3: An extra loop of FTO is probably important for its selection against dsDNA.
Figure 4: Specific recognition of 3-meT by FTO.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

The atomic coordinates and structure factors of the FTOΔ31–3-meT complex have been deposited in the Protein Data Bank under accession code 3LFM.

References

  1. 1

    Frayling, T. M. et al. A common variant in the FTO gene is associated with body mass index and predisposes to childhood and adult obesity. Science 316, 889–894 (2007)

  2. 2

    Dina, C. et al. Variation in FTO contributes to childhood obesity and severe adult obesity. Nature Genet. 39, 724–726 (2007)

  3. 3

    Fischer, J. et al. Inactivation of the Fto gene protects from obesity. Nature 458, 894–898 (2009)

  4. 4

    Church, C. et al. A mouse model for the metabolic effects of the human fat mass and obesity associated FTO gene. PLoS Genet. 5, e1000599 (2009)

  5. 5

    Speakman, J. R., Rance, K. A. & Johnstone, A. M. Polymorphisms of the FTO gene are associated with variation in energy intake, but not energy expenditure. Obesity 16, 1961–1965 (2008)

  6. 6

    Gerken, T. et al. The obesity-associated FTO gene encodes a 2-oxoglutarate-dependent nucleic acid demethylase. Science 318, 1469–1472 (2007)

  7. 7

    Sanchez-Pulido, L. & Andrade-Navarro, M. A. The FTO (fat mass and obesity associated) gene codes for a novel member of the non-heme dioxygenase superfamily. BMC Biochem. 8, 23 (2007)

  8. 8

    Jia, G. et al. Oxidative demethylation of 3-methylthymine and 3-methyluracil in single-stranded DNA and RNA by mouse and human FTO. FEBS Lett. 582, 3313–3319 (2008)

  9. 9

    Trewick, S. C., Henshaw, T. F., Hausinger, R. P., Lindahl, T. & Sedgwick, B. Oxidative demethylation by Escherichia coli AlkB directly reverts DNA base damage. Nature 419, 174–178 (2002)

  10. 10

    Falnes, P. Ø., Johansen, R. F. & Seeberg, E. AlkB-mediated oxidative demethylation reverses DNA damage in Escherichia coli. Nature 419, 178–182 (2002)

  11. 11

    Westbye, M. P. et al. Human AlkB homolog 1 is a mitochondrial protein that demethylates 3-methylcytosine in DNA and RNA. J. Biol. Chem. 283, 25046–25056 (2008)

  12. 12

    Aas, P. A. et al. Human and bacterial oxidative demethylases repair alkylation damage in both RNA and DNA. Nature 421, 859–863 (2003)

  13. 13

    Duncan, T. et al. Reversal of DNA alkylation damage by two human dioxygenases. Proc. Natl Acad. Sci. USA 99, 16660–16665 (2002)

  14. 14

    Falnes, P. Ø. Repair of 3-methylthymine and 1-methylguanine lesions by bacterial and human AlkB proteins. Nucleic Acids Res. 32, 6260–6267 (2004)

  15. 15

    Ougland, R. et al. AlkB restores the biological function of mRNA and tRNA inactivated by chemical methylation. Mol. Cell 16, 107–116 (2004)

  16. 16

    Yu, B. et al. Crystal structures of catalytic complexes of the oxidative DNA/RNA repair enzyme AlkB. Nature 439, 879–884 (2006)

  17. 17

    Sundheim, O. et al. Human ABH3 structure and key residues for oxidative demethylation to reverse DNA/RNA damage. EMBO J. 25, 3389–3397 (2006)

  18. 18

    Yang, C. G. et al. Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA. Nature 452, 961–965 (2008)

  19. 19

    Yu, B. & Hunt, J. F. Enzymological and structural studies of the mechanism of promiscuous substrate recognition by the oxidative DNA repair enzyme AlkB. Proc. Natl Acad. Sci. USA 106, 14315–14320 (2009)

  20. 20

    Koivisto, P., Duncan, T., Lindahl, T. & Sedgwick, B. Minimal methylated substrate and extended substrate range of Escherichia coli AlkB protein, a 1-methyladenine-DNA dioxygenase. J. Biol. Chem. 278, 44348–44354 (2003)

  21. 21

    Meyre, D. et al. Prevalence of loss-of-function FTO mutations in lean and obese individuals. Diabetes 59, 311–318 (2010)

  22. 22

    Boissel, S. et al. Loss-of-function mutation in the dioxygenase-encoding FTO gene causes severe growth retardation and multiple malformations. Am. J. Hum. Genet. 85, 106–111 (2009)

  23. 23

    Costas, M., Mehn, M. P., Jensen, M. P. & Que, L. Dioxygen activation at mononuclear nonheme iron active sites: enzymes, models, and intermediates. Chem. Rev. 104, 939–986 (2004)

  24. 24

    Sundheim, O., Talstad, V. A., Vagbo, C. B., Slupphaug, G. & Krokan, H. E. AlkB demethylases flip out in different ways. DNA Repair 7, 1916–1923 (2008)

  25. 25

    Mol, C. D. et al. Crystal structure and mutational analysis of human uracil-DNA glycosylase: structural basis for specificity and catalysis. Cell 80, 869–878 (1995)

  26. 26

    Slupphaug, G. et al. A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA. Nature 384, 87–92 (1996)

  27. 27

    Nègre, D., Weitzmann, C. & Ofengand, J. In vitro methylation of Escherichia coli 16S ribosomal RNA and 30S ribosomes. Proc. Natl Acad. Sci. USA 86, 4902–4906 (1989)

  28. 28

    Micura, R. et al. Methylation of the nucleobases in RNA oligonucleotides mediates duplex-hairpin conversion. Nucleic Acids Res. 29, 3997–4005 (2001)

  29. 29

    Fan, J., Schnare, M. N. & Lee, R. W. Characterization of fragmented mitochondrial ribosomal RNAs of the colorless green alga Polytomella parva. Nucleic Acids Res. 31, 769–778 (2003)

  30. 30

    Klagsbrun, M. Differences in the methylation of transfer ribonucleic acid in vitro by the mitochondrial and cytoplasmic transfer ribonucleic acid methylases of HeLa cells. J. Biol. Chem. 248, 2606–2611 (1973)

Download references

Acknowledgements

We thank Y. Yamada at Photon Factory of Japan for assistance with data collection. This research was funded by Chinese Ministry of Science and Technology ‘863’ grant no. 2008AA022305 and ‘973’ grant no. 2006CB806704 to J. Chai, ‘863’ grant no. 2008AA022317 to X.L. and the National Outstanding Young Scholar Science Foundation of National Natural Science Foundation of China grant no. 30825043 to J. Chang.

Author Contributions Z.H., T.N. and J. Chai designed the experiments. Experiments were performed by Z.H., T.N, J.B.C., X.L., M.Z., Q.W., W.C., J.W. and Y.F. Data were analysed by Z.H., T.N., X.L., J. Chai and J. Chang. J. Chai wrote the paper and Z.H. and X.L. contributed to editing the manuscript.

Author information

Correspondence to Jijie Chai.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Table 1 and Supplementary Figures 1-9 with legends. (PDF 821 kb)

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Han, Z., Niu, T., Chang, J. et al. Crystal structure of the FTO protein reveals basis for its substrate specificity. Nature 464, 1205–1209 (2010) doi:10.1038/nature08921

Download citation

Further reading

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.