Cleaves the peptide side chain from the N-acetylmuramic acid residues in peptidoglycan. This is a step in the formation of muramic delta-lactam residues in spore cortex. Hydrolyzes the link between N-acetylmuramoyl residues and L-amino acid residues in certain cell-wall glycopeptides. Expression of cwlD takes place in both the mother cell and forespore compartments of sporulating cells. CwlD and PdaA are necessary and sufficient for muramic delta-lactam production in B.subtilis spore peptidoglycan. Belongs to the N-acetylmuramoyl-L-alanine amidase 3 family.