The Role of the Omega Subzone in Determining the Membership of a Protein in One of the Two Families of the LexA/Signal Peptidase-like Superfamily

LexA/signal peptidase-like superfamily proteins are serine proteases that use the Ser-Lys catalytic dyad to carry out their biological functions. Here, we investigate the two known families of LexA/signal peptidase-like superfamily proteins, the type I signal peptidase and LexA endopeptidase domain-like, and describe the structural catalytic cores that govern the catalytic residues in these proteins. We show that the structural catalytic core of these proteins is a combination of two subzones, the NucBaseOmega and Omega. While the NucBaseOmega subzone is a pattern observed in all proteins of the studied superfamily, the Omega subzone in the type I signal peptidase family differs from that of the LexA endopeptidase domain-like family. Thus, the amino acids and 3D characteristics of the Omega subzone are a structural marker of the proteins belonging to a specific family.