Crystal structure of the heterotrimer core of Saccharomyces cerevisiae AMPK homologue SNF1

AMP-activated protein kinase ( AMPK) is a central regulator of energy homeostasis in mammals and is an attractive target for drug discovery against diabetes, obesity and other diseases(1-5). The AMPK homologue in Saccharomyces cerevisiae, known as SNF1, is essential for responses to glucose starvation as well as for other cellular processes, although SNF1 seems to be activated by a ligand other than AMP(1,6-8). Here we report the crystal structure at 2.6 angstrom resolution of the heterotrimer core of SNF1. The ligand-binding site in the gamma-subunit (Snf4) has clear structural differences from that of the Schizosaccharomyces pombe enzyme(9), although our crystallographic data indicate that AMP can also bind to Snf4. The glycogen-binding domain in the beta-subunit (Sip2) interacts with Snf4 in the heterotrimer but should still be able to bind carbohydrates(10-13). Our structure is supported by a large body of biochemical and genetic data on this complex(1,6-8,14-18). Most significantly, the structure reveals that part of the regulatory sequence in the alpha-subunit (Snf1)(15,16,18,19) is sequestered by Snf4, demonstrating a direct interaction between the alpha- and gamma-subunits and indicating that our structure may represent the heterotrimer core of SNF1 in its activated state.