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mTOR kinase structure, mechanism and regulation

Nature volume 497, pages 217223 (09 May 2013) | Download Citation

Abstract

The mammalian target of rapamycin (mTOR), a phosphoinositide 3-kinase-related protein kinase, controls cell growth in response to nutrients and growth factors and is frequently deregulated in cancer. Here we report co-crystal structures of a complex of truncated mTOR and mammalian lethal with SEC13 protein 8 (mLST8) with an ATP transition state mimic and with ATP-site inhibitors. The structures reveal an intrinsically active kinase conformation, with catalytic residues and a catalytic mechanism remarkably similar to canonical protein kinases. The active site is highly recessed owing to the FKBP12–rapamycin-binding (FRB) domain and an inhibitory helix protruding from the catalytic cleft. mTOR-activating mutations map to the structural framework that holds these elements in place, indicating that the kinase is controlled by restricted access. In vitro biochemistry shows that the FRB domain acts as a gatekeeper, with its rapamycin-binding site interacting with substrates to grant them access to the restricted active site. Rapamycin–FKBP12 inhibits the kinase by directly blocking substrate recruitment and by further restricting active-site access. The structures also reveal active-site residues and conformational changes that underlie inhibitor potency and specificity.

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Accessions

Data deposits

The coordinates and structure factors have been deposited in the Protein Data Bank under the accession numbers 4JSN (native structure), 4JSP (ATPcS-Mgcomplex), 4JSV (ADP-Mg-F complex), 4JSX (Torin2complex), 4JT5 (PP242 complex) and 4JT6 (PI-103 complex).

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Acknowledgements

We thank D. King for mass spectroscopic analysis, H. Erdjument-Bromage for N-terminal sequencing, the staff of the Advanced Photon Source ID24 beamlines for help with data collection and D. Tzvetkova-Robev for help with protein expression in HEK293 cells. This work was supported by the Howard Hughes Medical Institute.

Author information

Affiliations

  1. Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA

    • Haijuan Yang
    • , Derek G. Rudge
    • , Joseph D. Koos
    • , Bhamini Vaidialingam
    • , Hyo J. Yang
    •  & Nikola P. Pavletich
  2. Howard Hughes Medical Institute, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA

    • Nikola P. Pavletich

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Contributions

H.Y. and N.P.P. designed the experiments, solved the structures and wrote the manuscript. H.Y., D.G.R., J.D.K., B.M. and H.J.Y. carried out protein production, crystallization and biochemical experiments. H.Y. performed all other experiments.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Nikola P. Pavletich.

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    Supplementary Information

    This file contains Supplementary Tables 1-3, Supplementary Figures 1-13 and Supplementary References.

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https://doi.org/10.1038/nature12122

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