Aromatic stacking between nucleobase and enzyme promotes phosphate ester hydrolysis in dUTPase

Ildiko Pecsi, Ibolya Leveles, V. Harmat, B. Vértessy, J. Tóth

Research output: Contribution to journalArticle

38 Citations (Scopus)

Abstract

Aromatic interactions are well-known players in molecular recognition but their catalytic role in biological systems is less documented. Here, we report that a conserved aromatic stacking interaction between dUTPase and its nucleotide substrate largely contributes to the stabilization of the associative type transition state of the nucleotide hydrolysis reaction. The effect of the aromatic stacking on catalysis is peculiar in that uracil, the aromatic moiety influenced by the aromatic interaction is relatively distant from the site of hydrolysis at the alpha-phosphate group. Using crystallographic, kinetics, optical spectroscopy and thermodynamics calculation approaches we delineate a possible mechanism by which rate acceleration is achieved through the remote n-n interaction. The abundance of similarly positioned aromatic interactions in various nucleotide hydrolyzing enzymes (e.g. most families of ATPases) raises the possibility of the reported phenomenon being a general component of the enzymatic catalysis of phosphate ester hydrolysis.

Original languageEnglish
Pages (from-to)7179-7186
Number of pages8
JournalNucleic Acids Research
Volume38
Issue number20
DOIs
Publication statusPublished - Nov 2010

Fingerprint

Esters
Hydrolysis
Nucleotides
Phosphates
Catalysis
Enzymes
Uracil
Thermodynamics
Adenosine Triphosphatases
Spectrum Analysis
dUTP pyrophosphatase

ASJC Scopus subject areas

  • Genetics

Cite this

Aromatic stacking between nucleobase and enzyme promotes phosphate ester hydrolysis in dUTPase. / Pecsi, Ildiko; Leveles, Ibolya; Harmat, V.; Vértessy, B.; Tóth, J.

In: Nucleic Acids Research, Vol. 38, No. 20, 11.2010, p. 7179-7186.

Research output: Contribution to journalArticle

@article{064bc5d8f0e342ccbae03ca1dd882f93,
title = "Aromatic stacking between nucleobase and enzyme promotes phosphate ester hydrolysis in dUTPase",
abstract = "Aromatic interactions are well-known players in molecular recognition but their catalytic role in biological systems is less documented. Here, we report that a conserved aromatic stacking interaction between dUTPase and its nucleotide substrate largely contributes to the stabilization of the associative type transition state of the nucleotide hydrolysis reaction. The effect of the aromatic stacking on catalysis is peculiar in that uracil, the aromatic moiety influenced by the aromatic interaction is relatively distant from the site of hydrolysis at the alpha-phosphate group. Using crystallographic, kinetics, optical spectroscopy and thermodynamics calculation approaches we delineate a possible mechanism by which rate acceleration is achieved through the remote n-n interaction. The abundance of similarly positioned aromatic interactions in various nucleotide hydrolyzing enzymes (e.g. most families of ATPases) raises the possibility of the reported phenomenon being a general component of the enzymatic catalysis of phosphate ester hydrolysis.",
author = "Ildiko Pecsi and Ibolya Leveles and V. Harmat and B. V{\'e}rtessy and J. T{\'o}th",
year = "2010",
month = "11",
doi = "10.1093/nar/gkq584",
language = "English",
volume = "38",
pages = "7179--7186",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "20",

}

TY - JOUR

T1 - Aromatic stacking between nucleobase and enzyme promotes phosphate ester hydrolysis in dUTPase

AU - Pecsi, Ildiko

AU - Leveles, Ibolya

AU - Harmat, V.

AU - Vértessy, B.

AU - Tóth, J.

PY - 2010/11

Y1 - 2010/11

N2 - Aromatic interactions are well-known players in molecular recognition but their catalytic role in biological systems is less documented. Here, we report that a conserved aromatic stacking interaction between dUTPase and its nucleotide substrate largely contributes to the stabilization of the associative type transition state of the nucleotide hydrolysis reaction. The effect of the aromatic stacking on catalysis is peculiar in that uracil, the aromatic moiety influenced by the aromatic interaction is relatively distant from the site of hydrolysis at the alpha-phosphate group. Using crystallographic, kinetics, optical spectroscopy and thermodynamics calculation approaches we delineate a possible mechanism by which rate acceleration is achieved through the remote n-n interaction. The abundance of similarly positioned aromatic interactions in various nucleotide hydrolyzing enzymes (e.g. most families of ATPases) raises the possibility of the reported phenomenon being a general component of the enzymatic catalysis of phosphate ester hydrolysis.

AB - Aromatic interactions are well-known players in molecular recognition but their catalytic role in biological systems is less documented. Here, we report that a conserved aromatic stacking interaction between dUTPase and its nucleotide substrate largely contributes to the stabilization of the associative type transition state of the nucleotide hydrolysis reaction. The effect of the aromatic stacking on catalysis is peculiar in that uracil, the aromatic moiety influenced by the aromatic interaction is relatively distant from the site of hydrolysis at the alpha-phosphate group. Using crystallographic, kinetics, optical spectroscopy and thermodynamics calculation approaches we delineate a possible mechanism by which rate acceleration is achieved through the remote n-n interaction. The abundance of similarly positioned aromatic interactions in various nucleotide hydrolyzing enzymes (e.g. most families of ATPases) raises the possibility of the reported phenomenon being a general component of the enzymatic catalysis of phosphate ester hydrolysis.

UR - http://www.scopus.com/inward/record.url?scp=78651277475&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=78651277475&partnerID=8YFLogxK

U2 - 10.1093/nar/gkq584

DO - 10.1093/nar/gkq584

M3 - Article

C2 - 20601405

AN - SCOPUS:78651277475

VL - 38

SP - 7179

EP - 7186

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - 20

ER -