Structural Catalytic Core of the Members of the Superfamily of Acid Proteases

The superfamily of acid proteases has two catalytic aspartates for proteolysis of their peptide substrates. Here, we show a minimal structural scaffold, the structural catalytic core (SCC), which is conserved within each family of acid proteases, but varies between families, and thus can serve as a...

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Bibliographic Details
Published in:Molecules (Basel, Switzerland) Switzerland), 2024-08, Vol.29 (15), p.3451
Main Authors: Denesyuk, Alexander I, Denessiouk, Konstantin, Johnson, Mark S, Uversky, Vladimir N
Format: Article
Language:English
Subjects:
acid protease
Amino Acid Sequence
Amino acids
Analysis
Catalytic Domain
Ddi1
Family
Hydrogen bonds
Ligands
Lpg0085
Models, Molecular
pepsin
Peptide Hydrolases - chemistry
Peptide Hydrolases - metabolism
Proteases
Protein Conformation
Proteins
Proteolysis
retropepsin
Software
three-dimensional structure
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Description
Summary:The superfamily of acid proteases has two catalytic aspartates for proteolysis of their peptide substrates. Here, we show a minimal structural scaffold, the structural catalytic core (SCC), which is conserved within each family of acid proteases, but varies between families, and thus can serve as a structural marker of four individual protease families. The SCC is a dimer of several structural blocks, such as the DD-link, D-loop, and G-loop, around two catalytic aspartates in each protease subunit or an individual chain. A dimer made of two (D-loop + DD-link) structural elements makes a DD-zone, and the D-loop + G-loop combination makes a psi-loop. These structural markers are useful for protein comparison, structure identification, protein family separation, and protein engineering.
ISSN:1420-3049
1420-3049
DOI:10.3390/molecules29153451