Structural basis of AMPK regulation by adenine nucleotides and glycogen

Abstract

AMP-activated protein kinase (AMPK) is a central cellular energy sensor and regulator of energy homeostasis, and a promising drug target for the treatment of diabetes, obesity, and cancer. Here we present low-resolution crystal structures of the human α1β2γ1 holo-AMPK complex bound to its allosteric modulators AMP and the glycogen-mimic cyclodextrin, both in the phosphorylated (4.05 Å) and non-phosphorylated (4.60 Å) state. In addition, we have solved a 2.95 Å structure of the human kinase domain (KD) bound to the adjacent autoinhibitory domain (AID) and have performed extensive biochemical and mutational studies. Together, these studies illustrate an underlying mechanism of allosteric AMPK modulation by AMP and glycogen, whose binding changes the equilibria between alternate AID (AMP) and carbohydrate-binding module (glycogen) interactions.

AMPK and autophagy in glucose/glycogen metabolism

“…Additional study reported that CBM of β2 subunit binds more tightly to oligosaccharides than β1 subunit (Koay et al, 2010), and this may have physiological implications related to AMPK profile of skeletal muscle, in which β2 subunit is a predominant form. A recent analysis of low-resolution crystal structures of human AMPK bound to glycogen-mimic cyclodextrin further provided a structural basis for understanding the allosteric effect of glycogen on AMPK activity (Li et al, 2015). It was proposed that CBM is a highly dynamic part in the β subunit and closely interacts with the kinase domain of α subunit in the absence of carbohydrate, but addition of glycogen almost abolished this interaction, leading to inhibition of the enzyme activity (Li et al, 2015).…”

“…A recent analysis of low-resolution crystal structures of human AMPK bound to glycogen-mimic cyclodextrin further provided a structural basis for understanding the allosteric effect of glycogen on AMPK activity (Li et al, 2015). It was proposed that CBM is a highly dynamic part in the β subunit and closely interacts with the kinase domain of α subunit in the absence of carbohydrate, but addition of glycogen almost abolished this interaction, leading to inhibition of the enzyme activity (Li et al, 2015). These works are highly intriguing in terms that the allosteric inhibition of AMPK by glycogen may provide some molecular explanations for the above mentioned phenomena, in vivo inhibitory effect of glycogen on AMPK (Derave et al, 2000;Wojtaszewski et al, 2002;Wojtaszewski et al, 2003).…”

Choreography of AMPK activation

“…While some drugs show β-isoform selectivity, others can activate either β1 or β2 isoforms. While previous structures have revealed the drug-binding pocket of β1-containing AMPK [1,2], this report by Li et al [3] represents the first time that the β2 allosteric binding pocket has been visualized. Interestingly, the allosteric binding pockets of the two isoforms superimpose closely, suggesting a shared mechanism.…”

“…However, a physiological role for the glycogen interac-tion has not been conclusively shown. Li et al reveal that the interaction between isolated CBM and KD can be reduced upon glycogen or CD binding to the CBM [3]. Blocking CD/glycogen binding by mutating residue W99 in the CBM partially reversed the reduction in CBM-KD interaction caused by glycogen/CD binding.…”

“…To examine enzyme transitions from the inactive to the active state Li and colleagues have used tags attached at differing N-and/or C-termini throughout the AMPK heterotrimer, which bind to donor and acceptor beads [3]. The AlphaScreen luminescence proximity assay can sense the proximity of one domain to another, and in this way the change in proximity between two domains can be assessed under different nucleotide-binding conditions.…”