Many type I signal peptidases from eubacterial cells appear to contain a serine/lysine catalytic dyad. In contrast, our data show that the signal peptidase complex from the endoplasmic reticulum lacks an apparent catalytic lysine. Instead, a serine, histidine, and two aspartic acids are important for signal peptidase activity by the Sec11p subunit of the yeast signal peptidase complex. Amino acids critical to the eubacterial signal peptidases and Sec11p are, however, positioned similarly along their primary sequences, suggesting the presence of a common structural element(s) near the catalytic sites of these enzymes.Cleavable signal sequences, which are usually located at the N termini of precursor proteins, function in the delivery of their protein cargo to specific destinations within both eukaryotic and eubacterial cells. A large number of signal sequences possess a common motif consisting of an n-region that is often positively charged and a hydrophobic core (the h-region) followed by a polar c-region containing the cleavage site (1). Small uncharged amino acids are usually present at the Ϫ1 and Ϫ3 positions from the cleavage site. Signals exhibiting this motif are recognized and cleaved by type I signal peptidases. Type I signal peptidases are found within the endoplasmic reticulum (ER) 1 membrane, the mitochondrial inner membrane, and the cytoplasmic membrane of eubacterial cells (reviewed in Ref. 2). There is a strong functional conservation of the signal sequence cleavage reaction, revealed by the fact that signal sequences of proteins targeted normally to the ER can be cleaved by eubacterial signal peptidase (3), and eubacterial signal sequences can be cleaved by ER signal peptidase (4).Site-directed mutagenesis studies suggest that many eubacterial signal peptidases contain a serine/lysine dyad with which to catalyze the cleavage reaction (5-9). A similar catalytic dyad is thought to be present in the LexA and UmuD proteins of Escherichia coli (10, 11) and in both catalytic subunits of mitochondrial signal peptidase (12). Recent x-ray crystallographic analysis confirms the role of serine as a nucleophile and is consistent with a lysine acting as a general base in catalysis by E. coli leader peptidase (13).At least one eubacterial signal peptidase, SipW of Bacillus subtilus, may exhibit a catalytic site more like that of Sec11p of the ER signal peptidase. B. subtilus contains five distinct chromosomally encoded signal peptidases, SipW being the only one like Sec11p (14, 15). As shown in Fig. 1, Sec11p contains a serine residue that aligns to the catalytic serine of leader peptidase; however, within the limited regions of homology that exist between Sec11p and leader peptidase, Sec11p contains a histidine that has been aligned to the catalytic lysine of leader peptidase (16,17). From this, the type I signal peptidase family may contain a subgroup, represented by Sec11p and SipW, that uses a distinct catalytic mechanism (14). It has been noted previously, however, that an alignment of Sec11p to the E. col...