Fig. 8: Molecular basis for class-selective histone de-β-hydroxybutyrylation by SIRT3.

a β-staple recognition of H3K9bhb (yellow), H3K4bhb (pink) and H4K16bhb (gray) recognition by SIRT3. All three peptides are depicted as sticks and superimposed for comparison. For clarity, side chains of all peptides are omitted. Backbone dihedral angles (φ/ψ) are illustrated around the −1 to +1 positions of the Kbhb site, with values summarized on the top-left corner. Red arrows denote the Cα position of −1 and +1 residues. Dash lines, hydrogen bonds. b Backbone engagement for H4K16 recognition by HDAC1. Coordinates are taken from PDB entry 5ICN. The H4K16 was replaced by a hydroxamic acid functionality to mimic K16ac. Note that an acidic residue D99 dominates peptide backbone recognition in a non-β manner. c List of peptide sequences used for ITC titration. The Kbhb sites are highlighted red and its flanking glycine residues are highlighted blue. d ITC fitting curves of SIRT3 titrated with wild-type and glycine/alanine-mutant Kbhb peptides around histone sites H3K4 (i), H3K9 (ii), H3K14 (iii), H3K18 (iv), H4K8 (v) and H4K16 (vi). e In vitro deacylation assay results of all wild-type (WT) and mutant histone peptides listed in panel C catalyzed by SIRT3. Error bars represent standard error of mean of three repeats