The present invention provides amidases, polynucleotides encoding the amidases, methods of making and using these polynucleotides and polypeptides. In one aspect, the invention provides enzymes having secondary
amidase activity, e.g., having activity in the
hydrolysis of amides, including enzymes having peptidase,
protease and / or hydantoinase activity. In alternative aspects, the enzymes of the invention can be used to used to increase
flavor in food (e.g.,
enzyme ripened cheese), promote bacterial and fungal killing, modify and de-protect
fine chemical intermediates, synthesize
peptide bonds, carry out chiral resolutions, hydrolyze
Cephalosporin C. The enzymes of the invention can be used to generate 7-aminocephalosporanic acid (7-ACA) and semi-synthetic
cephalosporin antibiotics, including caphalothin, cephaloridine and
cefuroxime. The enzymes of the invention can be used as
antimicrobial agents, e.g., as
cell wall hydrolytic agents. The invention also provides a fluorescent
amidase substrate comprising 7-(epsilon-D-2-aminoadipoyladipoylamido)-4-methylcoumarin.