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

Konstantin Denessiouk; Alexander Denesyuk; Sergei E. Permyakov; Eugene A. Permyakov; Mark Johnson; 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

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

^*Corresponding author for this work

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

5 Citations (Scopus)

237 Downloads (Pure)

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

Funding

We thank the Biocenter Finland Bioinformatics Network (Dr. Jukka Lehtonen) and 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 . The project was supported by the Sigrid Jusélius Foundation (A.I.D. and M.S.J). The project was supported by the Sigrid Jusélius Foundation (A.I.D. and M.S.J).We thank the Biocenter Finland Bioinformatics Network (Dr. Jukka Lehtonen) and 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

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

Cite this

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

year = "2024",

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

language = "English",

volume = "7",

journal = "Current Research in Structural Biology",

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AU - Denessiouk, Konstantin

AU - Denesyuk, Alexander

AU - Permyakov, Sergei E.

AU - Permyakov, Eugene A.

AU - Johnson, Mark

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

Funding

Keywords

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