The active site of the SGNH hydrolase-like fold proteins: Nucleophile–oxyanion (Nuc-Oxy) and Acid–Base zones

Denessiouk, Konstantin; Denesyuk, Alexander I.; Permyakov, Sergei E.; Permyakov, Eugene A.; Johnson, Mark S.; Uversky, Vladimir N.

doi:10.1016/j.crstbi.2023.100123

Cited by 2 publications

(1 citation statement)

References 39 publications

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“…Earlier, we have described structural catalytic cores in many serine and cysteine proteases and showed the presence of unique structure/functional environments, "zones", around the catalytic sites in these proteins [1][2][3][4]. Each zone incorporated a segment of the catalytic core, connected to their respective element of protein functional machinery through a network of conserved hydrogen bonds and other interactions.…”

Section: Introductionmentioning

confidence: 99%

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

Denesyuk,

Denessiouk,

Johnson

et al. 2024

Preprint

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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.

show abstract

Section: Introductionmentioning

confidence: 99%

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

Denesyuk,

Denessiouk,

Johnson

et al. 2024

Preprint

View full text Add to dashboard Cite

show abstract

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

Denesyuk,

Denessiouk,

Johnson

et al. 2024

Molecules

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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.

show abstract

The active site of the SGNH hydrolase-like fold proteins: Nucleophile–oxyanion (Nuc-Oxy) and Acid–Base zones

Cited by 2 publications

References 39 publications

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

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

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

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