Structural basis for nicotinamide inhibition and base exchange in Sir2 enzymes.
The Sir2 family of proteins consists of broadly conserved NAD(+)-dependent deacetylases that are implicated in diverse biological processes, including DNA regulation, metabolism, and longevity. Sir2 proteins are regulated in part by the cellular concentrations of a noncompetitive inhibitor, nicotinamide, that reacts with a Sir2 reaction intermediate via a base-exchange reaction to reform NAD(+) at the expense of deacetylation. To gain a mechanistic understanding of nicotinamide inhibition in Sir2 enzymes, we captured the structure of nicotinamide bound to a Sir2 homolog, yeast Hst2, in complex with its acetyl-lysine 16 histone H4 substrate and a reaction intermediate analog, ADP-HPD. Together with related biochemical studies and structures, we identify a nicotinamide inhibition and base-exchange site that is distinct from the so-called "C pocket" binding site for the nicotinamide group of NAD(+). These results provide insights into the Sir2 mechanism of nicotinamide inhibition and have important implications for the development of Sir2-specific effectors.
Sanders
Brandi D
BD
The Wistar Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
Zhao
Kehao
K
Slama
James T
JT
Marmorstein
Ronen
R
D000107:Acetylation; D001665:Binding Sites; D005656:Fungal Proteins / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000648:ultrastructure; D006657:Histones / Q000737:chemistry / Q000378:metabolism / Q000648:ultrastructure; D007700:Kinetics; D008239:Lysine / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D009536:Niacinamide / Q000737:chemistry* / Q000378:metabolism / Q000502:physiology; D017434:Protein Structure, Tertiary; D037761:Sirtuins / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000648:ultrastructure
D005656:Fungal Proteins; D006657:Histones; D009536:Niacinamide; D037761:Sirtuins; D008239:Lysine