Identification of 2H phosphoesterase superfamily proteins with 2′-CPDase activity

Shuhei Mitsutomi, Nobuyoshi Akimitsu, Kazuhisa Sekimizu, Chikara Kaito

Research output: Contribution to journalArticle

Abstract

The 2H phosphoesterase superfamily (2H family) proteins are widely conserved among organisms. The 2H family is classified into several subgroups, including YjcG-like proteins whose enzymatic activity has not been reported. In the present study, we found that two YjcG-like proteins (Staphylococcus aureus SA0873 and Bacillus subtilis YjcG) have 2′-CPDase activity that hydrolyzes a 2′,3′-cyclic nucleotide, thereby producing a nucleotide with a 3′-phosphate. The SA0873 protein selectively hydrolyzes a 2′,3′-cyclic nucleotide with a purine base. Four SA0873 mutant proteins (H34A, T36A, H115A, and T117A), in which alanine was substituted for amino acid residues in the HxT/Sx motifs that are conserved in the 2H family, abolished the 2′-CPDase activity. Comparison of three-dimensional structures between the YjcG-like proteins with 2′-CPDase activity and another 2H family subgroup, LigT/2′-5′ RNA ligase-like proteins with 3′-CPDase activity, revealed that the orientation of the substrate binding pocket is reversed between the two groups. Our findings revealed that YjcG-like proteins not only have a substrate-binding pocket different from that of LigT/2′-5′ RNA ligase-like proteins, but they also have 2′-CPDase activity.

Original languageEnglish
Pages (from-to)235-244
Number of pages10
JournalBiochimie
Volume165
DOIs
Publication statusPublished - Oct 2019

Fingerprint

Proteins
Cyclic Nucleotides
Ligases
RNA
Bacilli
Mutant Proteins
Substrates
Bacillus subtilis
Alanine
Staphylococcus aureus
Nucleotides
Phosphates
Amino Acids

Keywords

  • 2H phosphoesterase superfamily
  • 2′,3′-cyclic nucleotide
  • Cyclic phosphodiesterase
  • LigT/2′-5′ RNA ligase-like proteins
  • YjcG-like protein

ASJC Scopus subject areas

  • Biochemistry

Cite this

Identification of 2H phosphoesterase superfamily proteins with 2′-CPDase activity. / Mitsutomi, Shuhei; Akimitsu, Nobuyoshi; Sekimizu, Kazuhisa; Kaito, Chikara.

In: Biochimie, Vol. 165, 10.2019, p. 235-244.

Research output: Contribution to journalArticle

Mitsutomi, Shuhei ; Akimitsu, Nobuyoshi ; Sekimizu, Kazuhisa ; Kaito, Chikara. / Identification of 2H phosphoesterase superfamily proteins with 2′-CPDase activity. In: Biochimie. 2019 ; Vol. 165. pp. 235-244.
@article{718e7fa3df544216af02890f249453aa,
title = "Identification of 2H phosphoesterase superfamily proteins with 2′-CPDase activity",
abstract = "The 2H phosphoesterase superfamily (2H family) proteins are widely conserved among organisms. The 2H family is classified into several subgroups, including YjcG-like proteins whose enzymatic activity has not been reported. In the present study, we found that two YjcG-like proteins (Staphylococcus aureus SA0873 and Bacillus subtilis YjcG) have 2′-CPDase activity that hydrolyzes a 2′,3′-cyclic nucleotide, thereby producing a nucleotide with a 3′-phosphate. The SA0873 protein selectively hydrolyzes a 2′,3′-cyclic nucleotide with a purine base. Four SA0873 mutant proteins (H34A, T36A, H115A, and T117A), in which alanine was substituted for amino acid residues in the HxT/Sx motifs that are conserved in the 2H family, abolished the 2′-CPDase activity. Comparison of three-dimensional structures between the YjcG-like proteins with 2′-CPDase activity and another 2H family subgroup, LigT/2′-5′ RNA ligase-like proteins with 3′-CPDase activity, revealed that the orientation of the substrate binding pocket is reversed between the two groups. Our findings revealed that YjcG-like proteins not only have a substrate-binding pocket different from that of LigT/2′-5′ RNA ligase-like proteins, but they also have 2′-CPDase activity.",
keywords = "2H phosphoesterase superfamily, 2′,3′-cyclic nucleotide, Cyclic phosphodiesterase, LigT/2′-5′ RNA ligase-like proteins, YjcG-like protein",
author = "Shuhei Mitsutomi and Nobuyoshi Akimitsu and Kazuhisa Sekimizu and Chikara Kaito",
year = "2019",
month = "10",
doi = "10.1016/j.biochi.2019.08.008",
language = "English",
volume = "165",
pages = "235--244",
journal = "Biochimie",
issn = "0300-9084",
publisher = "Elsevier",

}

TY - JOUR

T1 - Identification of 2H phosphoesterase superfamily proteins with 2′-CPDase activity

AU - Mitsutomi, Shuhei

AU - Akimitsu, Nobuyoshi

AU - Sekimizu, Kazuhisa

AU - Kaito, Chikara

PY - 2019/10

Y1 - 2019/10

N2 - The 2H phosphoesterase superfamily (2H family) proteins are widely conserved among organisms. The 2H family is classified into several subgroups, including YjcG-like proteins whose enzymatic activity has not been reported. In the present study, we found that two YjcG-like proteins (Staphylococcus aureus SA0873 and Bacillus subtilis YjcG) have 2′-CPDase activity that hydrolyzes a 2′,3′-cyclic nucleotide, thereby producing a nucleotide with a 3′-phosphate. The SA0873 protein selectively hydrolyzes a 2′,3′-cyclic nucleotide with a purine base. Four SA0873 mutant proteins (H34A, T36A, H115A, and T117A), in which alanine was substituted for amino acid residues in the HxT/Sx motifs that are conserved in the 2H family, abolished the 2′-CPDase activity. Comparison of three-dimensional structures between the YjcG-like proteins with 2′-CPDase activity and another 2H family subgroup, LigT/2′-5′ RNA ligase-like proteins with 3′-CPDase activity, revealed that the orientation of the substrate binding pocket is reversed between the two groups. Our findings revealed that YjcG-like proteins not only have a substrate-binding pocket different from that of LigT/2′-5′ RNA ligase-like proteins, but they also have 2′-CPDase activity.

AB - The 2H phosphoesterase superfamily (2H family) proteins are widely conserved among organisms. The 2H family is classified into several subgroups, including YjcG-like proteins whose enzymatic activity has not been reported. In the present study, we found that two YjcG-like proteins (Staphylococcus aureus SA0873 and Bacillus subtilis YjcG) have 2′-CPDase activity that hydrolyzes a 2′,3′-cyclic nucleotide, thereby producing a nucleotide with a 3′-phosphate. The SA0873 protein selectively hydrolyzes a 2′,3′-cyclic nucleotide with a purine base. Four SA0873 mutant proteins (H34A, T36A, H115A, and T117A), in which alanine was substituted for amino acid residues in the HxT/Sx motifs that are conserved in the 2H family, abolished the 2′-CPDase activity. Comparison of three-dimensional structures between the YjcG-like proteins with 2′-CPDase activity and another 2H family subgroup, LigT/2′-5′ RNA ligase-like proteins with 3′-CPDase activity, revealed that the orientation of the substrate binding pocket is reversed between the two groups. Our findings revealed that YjcG-like proteins not only have a substrate-binding pocket different from that of LigT/2′-5′ RNA ligase-like proteins, but they also have 2′-CPDase activity.

KW - 2H phosphoesterase superfamily

KW - 2′,3′-cyclic nucleotide

KW - Cyclic phosphodiesterase

KW - LigT/2′-5′ RNA ligase-like proteins

KW - YjcG-like protein

UR - http://www.scopus.com/inward/record.url?scp=85070896727&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85070896727&partnerID=8YFLogxK

U2 - 10.1016/j.biochi.2019.08.008

DO - 10.1016/j.biochi.2019.08.008

M3 - Article

C2 - 31422053

AN - SCOPUS:85070896727

VL - 165

SP - 235

EP - 244

JO - Biochimie

JF - Biochimie

SN - 0300-9084

ER -