The AMP-activated Protein Kinaes (AMPK/SNF1) Project

The AMP-activated Protein Kinase (AMPK/SNF1) Project

AMP-activated protein kinase (AMPK) is a master metabolic regulator. AMPK activation leads to the down regulation of energy-demanding, anabolic processes (fatty acid and cholesterol biosynthesis, gluconeogenesis, glycogen synthesis and others) and the stimulation of energy-producing, catabolic processes (fatty acid oxidation, glucose uptake, glycolysis and others). AMPK is a dual inhibitor of ACC1 and ACC2, by phosphorylating them near the N terminus.

AMPKs are hetero-trimeric enzymes, with a catalytic alpha subunit and two regulatory (beta and gamma) subunits. The alpha subunit contains the protein kinase domain, and the beta subunit a glycogen binding domain. The gamma subunit contains 4 repeats of the cystathionine-beta-synthase (CBS) motif. Each CBS tandem pair is also known as the Bateman domain. AMP is believed to regulate AMPK by binding to the gamma subunit.

AMPK is an attractive target for drug discovery. Metformin is believed to function through indirect activation of this kinase.

Major findings from this project

The structure of the heterotrimer core of yeast AMPK homolog SNF1 has been determined at 2.6 A resolution.

The regulatory segment (RS) in the alpha subunit (Snf1) is sequestered by the gamma subunit (Snf4) in the structure.

The glycogen binding domain (GBD) is located near Snf4 in the structure.

The structure of the catalytic domain of the alpha subunit of yeast AMPK (Snf1) has been determined at 2.2 A resolution.

A dimer of the kinase domain was observed in the crystal. The biological relevance of this dimer remains to be determined.

The structure of the second Bateman domain of yeast Snf4 (the gamma subunit) has been determined at 1.9 A resolution.

The Bateman2 domain alone forms a dimer with an extensive interface, with a prominent pocket in the center of the dimer.

Publications from this project

M.J. Rudolph, G.A. Amodeo, Y. Bai & L. Tong. (2005). Crystal structure of the protein kinase domain of yeast AMP-activated protein kinase Snf1. Biochem. Biophys. Res. Commun. 337, 1224-1228. Reprint(PDF)
M.J. Rudolph, G.A. Amodeo, S.H. Iram, S.-P. Hong, G. Pirino, M. Carlson & L. Tong. (2007). Crystal structure of the Bateman2 domain of yeast Snf4: dimeric association and relevance for AMP binding. Structure, 15, 65-74. Reprint(PDF)
G.A. Amodeo, M.J. Rudolph & L. Tong. (2007). Crystal structure of the heterotrimer core of Saccharomyces cerevisiae AMPK homolog SNF1. Nature, 449, 492-495. Reprint(PDF)
G.A. Amodeo, M. Momcilovic, M. Carlson & L. Tong. (2010). Biochemical and functional studies on the regulation of the Saccharomyces cerevisiae AMPK homolog SNF1. Biochem. Biophys. Res. Commun., 397, 197-201. Reprint(PDF)
M.J. Rudolph, G.A. Amodeo & L. Tong. (2010). An inhibited conformation for the protein kinase domain of the Saccharomyces cerevisiae AMPK homolog Snf1. Acta Cryst., F66, 999-1002. Reprint(PDF)

Funding for this project

NIH R01 DK67238