Oligopeptidase B (OpdB) is a serine peptidase broadly distributed among unicellular eukaryotes, gramnegative bacteria, and spirochetes which has emerged as an important virulence factor and potential therapeutic target in infectious diseases. We report here the cloning and expression of the opdB homologue from Salmonella enterica serovar Typhimurium and demonstrate that it exhibits amidolytic activity exclusively against substrates with basic residues in P 1 . While similar to its eukaryotic homologues in terms of substrate specificity, Salmonella OpdB differs significantly in catalytic power and inhibition and activation properties. In addition to oligopeptide substrates, restricted proteolysis of histone proteins was observed, although no cleavage was seen at or near residues that had been posttranslationally modified or at defined secondary structures. This supports the idea that the catalytic site of OpdB may be accessible only to unstructured oligopeptides, similar to the closely related prolyl oligopeptidase (POP). Salmonella OpdB was employed as a model enzyme to define determinants of substrate specificity that distinguish OpdB from POP, which hydrolyzes substrates exclusively at proline residues. Using site-directed mutagenesis, nine acidic residues that are conserved in OpdBs but absent from POPs were converted to their corresponding residues in POP. In this manner, we identified a pair of glutamic acid residues, Glu 576 and Glu 578 , that define P 1 specificity and direct OpdB cleavage C terminal to basic residues. We have also identified a second pair of residues, Asp 460 and Asp 462 , that may be involved in defining P 2 specificity and thus direct preferential cleavage by OpdB after pairs of basic residues.The oligopeptidase B (OpdB; EC 3.4.21.83) subfamily of serine peptidases represents one of two branches of the prolyl oligopeptidase family of serine peptidases (the S9 family, in the nomenclature of Barrett and Rawlings [2]). The archetypical member of this family, prolyl oligopeptidase (POP; EC 3.4.21.26), exclusively hydrolyzes peptide bonds C terminal to proline residues in peptides (31). It has been implicated in the pathophysiology of depression (20) and has attracted pharmaceutical attention, since POP inhibitors have shown potential in the treatment of amnesia (39) and Alzheimer's disease (36). Prolyl oligopeptidase has also served as a model for structural studies of serine oligopeptidases. A 1.4-Å crystal structure analysis of POP recently revealed that an N-terminal regulatory domain, consisting of a seven-bladed -propeller, regulates substrate access to the C-terminal catalytic domain (7) by a gating filter mechanism (8).In contrast to the POPs, the OpdB branch of the POP family has received much less attention. These enzymes demonstrate a trypsin-like substrate specificity, hydrolyzing peptide bonds on the C-terminal side of basic amino acid residues of lowmolecular-mass (Ͻ3 kDa) peptides (17,30,37,41). Of great importance for potential therapeutic applications, OpdB is only found i...