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

Alexandre Denesyuk; Konstantin Denessiouk; Mark Johnson; Vladimir Uversky

doi:10.3390/molecules30092019

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

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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.

Original language	English
Article number	2019
Number of pages	19
Journal	Molecules
Volume	30
Issue number	9
DOIs	https://doi.org/10.3390/molecules30092019
Publication status	Published - 30 Apr 2025
MoE publication type	A1 Journal article-refereed

Funding

We thank the Biocenter Finland Bioinformatics Network (Jukka Lehtonen) and the CSC IT Center for Science for computational support for the project. The Structural Bioinformatics Laboratory is part of the Solution for Health strategic area of Åbo Akademi University and within the InFLAMES Flagship program on inflammation and infection, Åbo Akademi University and the University of Turku, funded by the Academy of Finland.

Keywords

3D structure; DD-carboxypeptidase; catalytic core; classification; glutaminase; β-lactamase.

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10.3390/molecules30092019

molecules-30-02019-v2Final published version, 2.66 MBLicence: CC BY

https://urn.fi/URN:NBN:fi-fe20251031104377

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AU - Johnson, Mark

AU - Uversky, Vladimir

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AB - 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.

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ER -

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

Abstract

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Keywords

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