Histone deacetylase that catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4) (PubMed:10454532). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events (PubMed:10454532). Histone deacetylases act via the formation of large multiprotein complexes (By similarity). Also functions as deacetylase for non-histone proteins. In addition to protein deacetylase activity, also has protein-lysine deacylase activity: acts as a protein decrotonylase by mediating decrotonylation ((2E)-butenoyl) of histones (By similarity). 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] Found in a large complex with RBBP4 and MI-2. Belongs to the histone deacetylase family. HD type 1 subfamily.