Zoocin A is a streptococcolytic peptidoglycan hydrolase with an unknown site of action that is produced by Streptococcus equi subsp. zooepidemicus 4881. Zoocin A has now been determined to be a D-alanyl-L-alanine endopeptidase by digesting susceptible peptidoglycan with a combination of mutanolysin and zoocin A, separating the resulting muropeptides by reverse-phase high-pressure liquid chromatography, and analyzing them by mass spectrometry (MS) in both the positive-and negative-ion modes to determine their compositions. In order to distinguish among possible structures for these muropeptides, they were N-terminally labeled with 4-sulfophenyl isothiocyanate (SPITC) and analyzed by tandem MS in the negative-ion mode. This novel application of SPITC labeling and MS/MS analysis can be used to analyze the structure of peptidoglycans and to determine the sites of action of other peptidoglycan hydrolases.Streptococcal peptidoglycans (16) have a repeating backbone of the amino sugars N-acetylglucosamine (GlcNAc) and N-acetylmuramic acid (MurNAc). Connected to the lactyl group of MurNAc is a tetrapeptide (stem peptide) composed of L-alanine, D-isoglutamine (or D-isoglutamate), L-lysine, and D-alanine. The stem peptides are connected by peptide cross bridges that typically contain two or three L-alanine residues ( Fig. 1). During peptidoglycan synthesis, the stem peptides contain an additional C-terminal D-alanine ( Fig. 1) that is removed during cross-bridge formation by a transpeptidase (11). In some cases, the cross bridges are not formed and the terminal D-alanine may or may not be removed by a carboxypeptidase (11).Zoocin A is a streptococcolytic enzyme produced by Streptococcus equi subsp. zooepidemicus 4881. The genes for zoocin A and for the zoocin A immunity factor (zif) are adjacent on the chromosome and are divergently transcribed (1). Zoocin A hydrolyzes the cell walls of some closely related streptococci, including S. pyogenes and S. mutans, the main causative agents of group A streptococcal sore throat and dental caries, respectively (20). Zoocin A is presumed to target peptidoglycan cross bridges based on three lines of evidence. First, the catalytic domain of zoocin A has a high degree of similarity to the catalytic domains of several bacteriolytic endopeptidases (lysostaphin [21], ALE-1 [22], LytM [23], and millericin B [3]). Second, the introduction of the gene for lysostaphin resistance into a zoocin A-sensitive streptococcus resulted in the insertion of serines into its peptidoglycan cross bridges and a decrease in sensitivity to zoocin A (6). Third, zoocin A covalently binds penicillin and slowly hydrolyzes a chromogenic cephalosporin, both of which are D-alanyl-D-alanine analogs. These three lines of evidence suggest that zoocin A hydrolyzes the bond between the terminal D-alanine of the stem peptide and the first Lalanine of the cross bridge (8).If zoocin A is an endopeptidase, determination of its site of action on streptococcal peptidoglycans only by the mass of the products is not possible beca...