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Structural insight into the autoinhibition mechanism of AMP-activated protein kinase


The AMP-activated protein kinase (AMPK) is characterized by its ability to bind to AMP, which enables it to adjust enzymatic activity by sensing the cellular energy status and maintain the balance between ATP production and consumption in eukaryotic cells1,2. It also has important roles in the regulation of cell growth and proliferation, and in the establishment and maintenance of cell polarity3. These important functions have rendered AMPK an important drug target for obesity, type 2 diabetes and cancer treatments4. However, the regulatory mechanism of AMPK activity by AMP binding remains unsolved. Here we report the crystal structures of an unphosphorylated fragment of the AMPK α-subunit (KD-AID) from Schizosaccharomyces pombe that contains both the catalytic kinase domain and an autoinhibitory domain (AID), and of a phosphorylated kinase domain from Saccharomyces cerevisiae (Snf1-pKD). The AID binds, from the ‘backside’, to the hinge region of its kinase domain, forming contacts with both amino-terminal and carboxy-terminal lobes. Structural analyses indicate that AID binding might constrain the mobility of helix αC, hence resulting in an autoinhibited KD-AID with much lower kinase activity than that of the kinase domain alone. AMP activates AMPK both allosterically and by inhibiting dephosphorylation5,6. Further in vitro kinetic studies demonstrate that disruption of the KD-AID interface reverses the autoinhibition and these AMPK heterotrimeric mutants no longer respond to the change in AMP concentration. The structural and biochemical data have shown the primary mechanism of AMPK autoinhibition and suggest a conformational switch model for AMPK activation by AMP.

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Figure 1: Structure and activity of the AMPK kinase domain and KD-AID.
Figure 2: The AID immobilizes the open conformation of kinase domain.
Figure 3: Disruption of KD-AID interface abolishes AID inhibition.
Figure 4: Effect of KD-AID interface mutants on AMP-regulation of AMPK holoenzyme.

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Primary accessions

Protein Data Bank

Data deposits

The structural and atomic coordinates have been deposited in the Protein Data Bank under accession codes 3H4J for S. pombe KD-AID and 3DAE for S. cerevisiae Snf1-pKD.


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We thank Y. Shi and S. C. Lin for critical discussions and reading of the manuscript; J. Chai and Y. Dong for help with data collection and processing; L. Gu and J. Wang for advice on structure determination. This work is supported in part by MOST grants 2006CB503900 and 2007CB914400, and by NSFC grants 30425005 and 30770476.

Author Contributions L.C., Z.-H.J. and L.-S.Z. designed, performed and analysed most of the experiments. Y.-Y.Z. and S.-T.X. provided technical assistance. Z.-X.W. contributed to discussions. J.-W.W. led the team and wrote the paper.

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Correspondence to Jia-Wei Wu.

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Chen, L., Jiao, ZH., Zheng, LS. et al. Structural insight into the autoinhibition mechanism of AMP-activated protein kinase. Nature 459, 1146–1149 (2009).

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