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

Alexander I. Denesyuk; Konstantin Denessiouk; Mark S. Johnson; Vladimir N. Uversky

doi:10.20944/preprints202406.1599.v1

Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

Version 1 : Received: 21 June 2024 / Approved: 22 June 2024 / Online: 24 June 2024 (11:25:52 CEST)

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 packs all conserved substructure elements around the catalytic machinery, and which can be found in all enzymes of the Acid proteases superfamily. The SCC is a dimer of several structural blocks, such as the DD-link, the D-loop and the G-loop, around two catalytic aspartates in each protease subunit or within an individual chain. The dimer of two D-loop/DD-link substructures makes a DD-zone, and the dimer of two D-loop/G-loop substructures makes a psi-loop. These structural markers are useful for protein comparison, structure identification, protein family separation and protein engineering.

Pepsin; Retropepsin; Ddi1; Lpg0085; Acid protease; three-dimensional structure; active site; catalytic aspartate

Biology and Life Sciences, Life Sciences

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

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