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

Alexandre Denesyuk; Konstantin Denessiouk; Mark Johnson; Sergei E. Permyakov; Eugene A. Permyakov; Vladimir N. Uversky

doi:10.1016/j.crstbi.2023.100123

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

Alexandre Denesyuk^*, Konstantin Denessiouk, Mark Johnson, Sergei E. Permyakov, Eugene A. Permyakov, Vladimir N. Uversky^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › Scientific › peer-review

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Abstract

SGNH hydrolase-like fold proteins are serine proteases with the default Asp-His-Ser catalytic triad. Here, we show that these proteins share two unique conserved structural organizations around the active site: (1) the Nuc-Oxy Zone around the catalytic nucleophile and the oxyanion hole, and (2) the Acid-Base Zone around the catalytic acid and base. The Nuc-Oxy Zone consists of 14 amino acids cross-linked with eight conserved intra- and inter-block hydrogen bonds. The Acid–Base Zone is constructed from a single fragment of the polypeptide chain, which incorporates both the catalytic acid and base, and whose N- and C-terminal residues are linked together by a conserved hydrogen bond. The Nuc-Oxy and Acid-Base Zones are connected by an SHLink, a two-bond conserved interaction from amino acids, adjacent to the catalytic nucleophile and base

Original language	English
Article number	100123
Number of pages	9
Journal	Current Research in Structural Biology
Volume	7
DOIs	https://doi.org/10.1016/j.crstbi.2023.100123
Publication status	Published - Jan 2024
MoE publication type	A1 Journal article-refereed

Keywords

SGNH-Hydrolases
Catalytic triad

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10.1016/j.crstbi.2023.100123Licence: CC BY-NC-ND

1-s2.0-S2665928X23000296-mainFinal published version, 2.88 MBLicence: CC BY-NC-ND

https://urn.fi/URN:NBN:fi-fe2024040113794

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

abstract = "SGNH hydrolase-like fold proteins are serine proteases with the default Asp-His-Ser catalytic triad. Here, we show that these proteins share two unique conserved structural organizations around the active site: (1) the Nuc-Oxy Zone around the catalytic nucleophile and the oxyanion hole, and (2) the Acid-Base Zone around the catalytic acid and base. The Nuc-Oxy Zone consists of 14 amino acids cross-linked with eight conserved intra- and inter-block hydrogen bonds. The Acid–Base Zone is constructed from a single fragment of the polypeptide chain, which incorporates both the catalytic acid and base, and whose N- and C-terminal residues are linked together by a conserved hydrogen bond. The Nuc-Oxy and Acid-Base Zones are connected by an SHLink, a two-bond conserved interaction from amino acids, adjacent to the catalytic nucleophile and base",

keywords = "SGNH-Hydrolases, Catalytic triad",

author = "Alexandre Denesyuk and Konstantin Denessiouk and Mark Johnson and Permyakov, {Sergei E.} and Permyakov, {Eugene A.} and Uversky, {Vladimir N.}",

year = "2024",

month = jan,

doi = "10.1016/j.crstbi.2023.100123",

language = "English",

volume = "7",

journal = "Current Research in Structural Biology",

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T1 - The active site of the SGNH hydrolase-like fold proteins: Nucleophile–oxyanion (Nuc- Oxy) and Acid–Base zones

AU - Denesyuk, Alexandre

AU - Denessiouk, Konstantin

AU - Johnson, Mark

AU - Permyakov, Sergei E.

AU - Permyakov, Eugene A.

AU - Uversky, Vladimir N.

PY - 2024/1

Y1 - 2024/1

N2 - SGNH hydrolase-like fold proteins are serine proteases with the default Asp-His-Ser catalytic triad. Here, we show that these proteins share two unique conserved structural organizations around the active site: (1) the Nuc-Oxy Zone around the catalytic nucleophile and the oxyanion hole, and (2) the Acid-Base Zone around the catalytic acid and base. The Nuc-Oxy Zone consists of 14 amino acids cross-linked with eight conserved intra- and inter-block hydrogen bonds. The Acid–Base Zone is constructed from a single fragment of the polypeptide chain, which incorporates both the catalytic acid and base, and whose N- and C-terminal residues are linked together by a conserved hydrogen bond. The Nuc-Oxy and Acid-Base Zones are connected by an SHLink, a two-bond conserved interaction from amino acids, adjacent to the catalytic nucleophile and base

AB - SGNH hydrolase-like fold proteins are serine proteases with the default Asp-His-Ser catalytic triad. Here, we show that these proteins share two unique conserved structural organizations around the active site: (1) the Nuc-Oxy Zone around the catalytic nucleophile and the oxyanion hole, and (2) the Acid-Base Zone around the catalytic acid and base. The Nuc-Oxy Zone consists of 14 amino acids cross-linked with eight conserved intra- and inter-block hydrogen bonds. The Acid–Base Zone is constructed from a single fragment of the polypeptide chain, which incorporates both the catalytic acid and base, and whose N- and C-terminal residues are linked together by a conserved hydrogen bond. The Nuc-Oxy and Acid-Base Zones are connected by an SHLink, a two-bond conserved interaction from amino acids, adjacent to the catalytic nucleophile and base

KW - SGNH-Hydrolases

KW - Catalytic triad

U2 - 10.1016/j.crstbi.2023.100123

DO - 10.1016/j.crstbi.2023.100123

M3 - Article

SN - 2665-928X

VL - 7

JO - Current Research in Structural Biology

JF - Current Research in Structural Biology

M1 - 100123

ER -

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

Abstract

Keywords

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