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

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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.

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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.

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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.


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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.

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Correspondence to Jijie Chai.

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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

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