Catalyzes the deacetylation of N-acetylmuramic acid (MurNAc) residues in peptidoglycan, a modification that confers resistance to lysosyme. Is not able to deacetylate N-acetylglucosamine (GlcNAc) residues in peptidoglycan, but can deacylate chitin oligomers such as GlcNAc4 and GlcNAc5. Is essentially not active toward chitosan (partially deacetylated GlcNAc polymer) and has very low activity toward chitin (GlcNAc polymer). Does not deacetylate GlcNAc. Activated by divalent metal cations; Mn(2+) is the most efficient, followed by Ca(2+) and Mg(2+). In contrast to PgdA from S.pneumoniae, these ions are not absolutely required for deacetylase activity. kcat is 0.32 sec(-1) for the deacetylation of MurNAc residues in peptidoglycan, and 0.24 sec(-1) for the deacetylation of GlcNAc4. Negatively regulated by the two-component system YycFG. Cells lacking this gene show sensitivity to lysosyme, in contrast to wild-type. The product of deacetylated GlcNAc4 by PdaC is GlcNAc-GlcNAc-GlcN-GlcNAc. Derepression of pdaC in cells depleted for yycFG leads to increased resistance of the cell walls to lysozyme digestion. In the N-terminal section; belongs to the RsiV family. In the C-terminal section; belongs to the polysaccharide deacetylase family. Was originally described as a deoxyribonuclease (PubMed:17878218), but it was later shown that PdaC has no DNase activity at all (PubMed:22277649).