Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). 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. H2O + N(6)-acetyl-L-lysyl-[histone] = acetate + L-lysyl-[histone] Binds 1 zinc ion per subunit. May be due to intron retention. May be due to a competing acceptor splice site. Belongs to the histone deacetylase family. HD type 3 subfamily.