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

TL;DR

This paper identifies a structural feature called the Omega subzone that helps classify proteins into two families within the LexA/signal peptidase-like superfamily.

Contribution

The study reveals that the Omega subzone's amino acid composition and 3D structure serve as a marker to distinguish between two protein families.

Findings

The structural catalytic core of LexA/signal peptidase-like proteins includes the NucBaseOmega and Omega subzones.

The Omega subzone varies between the type I signal peptidase and LexA endopeptidase domain-like families.

The Omega subzone's characteristics act as a structural marker for family classification.

Abstract

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.

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