Alpha and Omega Classification of β-Lactamase/Transpeptidase-like Superfamily Proteins Based on the Comparison of Their Structural Catalytic Cores.

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

Abstract read

In one paragraph

Article in Molecules (Basel, Switzerland), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

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0cells of the map it votes in

1citing papers in PubMed

–field-weighted citation impact

1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

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3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

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.International journal of molecular sciences · 2026
Article

4 · The record

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PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

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 and 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

β-Lactamase/transpeptidase-like superfamily proteins are serine proteases that use the Ser-Lys catalytic dyad to carry out their biological functions. Here, we investigate the three known families of β-lactamase/transpeptidase-like superfamily proteins, β-lactamase/D-Ala carboxypeptidase, glutaminase, and Dac-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 three zones, the mutual three-dimensional arrangement of which correspondingly determines their belonging to one of seven and twenty-four established groups and subgroups.

Indexed as

beta-LactamasesPeptidyl TransferasesCatalytic DomainModels, MolecularProtein Conformationbeta-LactamasesPeptidyl Transferases3D structurecatalytic coreclassificationDD-carboxypeptidaseglutaminaseβ-lactamase

Identifiers

PMID40363824

DOI10.3390/molecules30092019

PMCPMC12073871

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