Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4), and some other non-histone substrates. Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes. Participates in the BCL6 transcriptional repressor activity by deacetylating the H3 'Lys-27' (H3K27) on enhancer elements, antagonizing EP300 acetyltransferase activity and repressing proximal gene expression. Also functions as deacetylase for non-histone targets. In addition to protein deacetylase activity, also acts as protein-lysine deacylase by recognizing other acyl groups: catalyzes removal of (2E)-butenoyl (crotonyl) and 2-hydroxyisobutanoyl (2-hydroxyisobutyryl) acyl groups from lysine residues, leading to protein decrotonylation and de-2-hydroxyisobutyrylation, respectively. H2O + N(6)-acetyl-L-lysyl-[histone] = acetate + L-lysyl-[histone] H2O + N(6)-acetyl-L-lysyl-[protein] = acetate + L-lysyl-[protein] H2O + N(6)-(2E)-butenoyl-L-lysyl-[protein] = (2E)-2-butenoate + L-lysyl-[protein] H2O + N(6)-(2-hydroxyisobutanoyl)-L-lysyl-[protein] = 2-hydroxy-2-methylpropanoate + L-lysyl-[protein] Belongs to the histone deacetylase family. HD type 1 subfamily.