coli (38% identity and 50% similarity) and CtpA of B. bacilliformis (53% identity and 69% similarity) as shown in Fig. GSK1120212 molecular weight 1 (Winsor et al., 2009). An S41 peptidase catalytic domain of 167 residues was recognized in PA5134, characteristic for the S41 peptidase family, as well as a 79-residue PDZ domain upstream of the catalytic domain. PDZ domains are involved in protein–protein interactions and in CTPs interacts with the C-terminus of substrates (Beebe et al., 2000). Serine 302 and lysine 327 were predicted to form the catalytic dyad which corresponds to the S41A subfamily of the MEROPS database (Rawlings et al., 2008). PA3257 was annotated as Prc and showed homology to Prc

of E. coli (44% identity and 60% similarity) and CtpA of B. bacilliformis (32% identity and 50% similarity). In analogy Ibrutinib price to PA5134, Prc has a predicted S41 peptidase catalytic domain of 85 residues downstream of a 175-residue PDZ domain. The MEROPS database classifies PA5134 to the subfamily type S41.004, called C-terminal processing peptidases-3

(CTP-3) and Prc to the subfamily S41.001, called C-terminal processing peptidases-1 (CTP-1) E. coli (Rawlings et al., 2008). A 23-amino acid N-terminal signal peptide was predicted by the signalp program in both CTPs, which indicates a possible translocation across the cytoplasmic membrane by the Sec-pathway (Dyrløv Bendtsen et al., 2004). This prediction is supported by an alkaline phosphatase fusion screen, which identified PA5134 and Prc to cross the inner membrane (Lewenza et al., 2005). The calculated molecular weight of PA5134 without the signal peptide is 43.7 kDa and for 75.6 kDa for Prc in comparison to 44.9 kDa, for CtpA of B. bacilliformis and 74.3 kDa of

E. coli. PA5234 and Prc of P. aeruginosa showed homology with 34% identity and 51% similarity. Interestingly, the genome of P. aeruginosa reveals two CTPs. One, PA5734, showed clear similarity to the CTP-3 subfamily with CtpA of B. bacilliformis as a holotype. The other, PA3257 (Prc), showed similarity to Prc of E. coli belonging to the CTP-1 subfamily. Both predicted Carnitine palmitoyltransferase II proteases contain a catalytic peptidase domain downstream of a PDZ domain although the difference in size between both enzymes is about 31.9 kDa. Figure 1 shows the homology between the CTPs of P. aeruginosa and in comparison with other bacteria. Preliminary blast searches reveal that most Gram-negative bacteria have only one CTP. For example, B. bacilliformis, Legionella pneumophila and Neisseria gonorrhoeae have one CTP protease belonging to the CTP-3 subfamily. CTPs can also be found in the bacteria E. coli, Salmonella enterica and Yersinia pestis. These genomes reveal one CTP belonging to the CTP-1 subfamily. Based on the sequence-predicted protein sizes CTPs of the CTP-3 subfamily constitute the same functional domains but are about 30 kDa smaller than proteases of the CTP-1 subfamily.