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.

Alexander I Denesyuk, Konstantin Denessiouk, Mark S Johnson, Vladimir N Uversky

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Article in International journal of molecular sciences, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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4 authors.

Alexander I DenesyukStructural Bioinformatics Laboratory, Biochemistry, InFLAMES Research Flagship Center, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland.

Konstantin DenessioukStructural Bioinformatics Laboratory, Biochemistry, InFLAMES Research Flagship Center, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland.

Mark S JohnsonStructural Bioinformatics Laboratory, Biochemistry, InFLAMES Research Flagship Center, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland.ORCID 0000-0002-0496-358X

Vladimir N UverskyDepartment of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.ORCID 0000-0002-4037-5857

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

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.

Indexed as

Bacterial ProteinsMembrane ProteinsSerine EndopeptidasesAmino Acid SequenceCatalytic DomainLexA Repressor ProteinModels, MolecularProtein ConformationBacterial ProteinsLexA Repressor ProteinMembrane ProteinsSerine Endopeptidasestype I signal peptidase3D structurecatalytic coreLexA endopeptidaseOmega subzoneprotein familysignal peptidasestructural marker

Identifiers

PMID41828355

DOI10.3390/ijms27052127

PMCPMC12984324

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