Fig. 3: Open and closed active sites of Rpd3 in the two lobes of the Rpd3L complex.
From: Cryo-EM structure of the Saccharomyces cerevisiae Rpd3L histone deacetylase complex
A Left: Rpd3 with an open active site (red dashed lines) in lobe I. Middle: Rpd3 active site occluded by Rxt2 (brown). Right: An HDAC8 mutant (Y306F) bound to an N-epsilon-acetyllysine-bearing peptide substrate (gold; PDB ID: 5D1D)70. B Close-up views of the active sites shown in panel (A). Active site residues and the catalytic Zn2+ ions are labeled in red, while hydrophobic residues forming the mouth of the active site tunnel are labeled in green for all three proteins. The side chain of Leu80 Rxt2 plugs the opening to the active site tunnel (middle), occluding the catalytic site, mimicking the conformation of the N-epsilon-acetyllysine at the backbone and side chain levels (right).
