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

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 associa...

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Autores principales: Pecsi, Ildiko, Leveles, Ibolya, Harmat, Veronika, Vertessy, Beata G., Toth, Judit
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2978360/
https://www.ncbi.nlm.nih.gov/pubmed/20601405
http://dx.doi.org/10.1093/nar/gkq584
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author Pecsi, Ildiko
Leveles, Ibolya
Harmat, Veronika
Vertessy, Beata G.
Toth, Judit
author_facet Pecsi, Ildiko
Leveles, Ibolya
Harmat, Veronika
Vertessy, Beata G.
Toth, Judit
author_sort Pecsi, Ildiko
collection PubMed
description 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 π–π 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.
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spelling pubmed-29783602010-11-12 Aromatic stacking between nucleobase and enzyme promotes phosphate ester hydrolysis in dUTPase Pecsi, Ildiko Leveles, Ibolya Harmat, Veronika Vertessy, Beata G. Toth, Judit Nucleic Acids Res Nucleic Acid Enzymes 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 π–π 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. Oxford University Press 2010-11 2010-07-02 /pmc/articles/PMC2978360/ /pubmed/20601405 http://dx.doi.org/10.1093/nar/gkq584 Text en © The Author(s) 2010. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.5 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Nucleic Acid Enzymes
Pecsi, Ildiko
Leveles, Ibolya
Harmat, Veronika
Vertessy, Beata G.
Toth, Judit
Aromatic stacking between nucleobase and enzyme promotes phosphate ester hydrolysis in dUTPase
title Aromatic stacking between nucleobase and enzyme promotes phosphate ester hydrolysis in dUTPase
title_full Aromatic stacking between nucleobase and enzyme promotes phosphate ester hydrolysis in dUTPase
title_fullStr Aromatic stacking between nucleobase and enzyme promotes phosphate ester hydrolysis in dUTPase
title_full_unstemmed Aromatic stacking between nucleobase and enzyme promotes phosphate ester hydrolysis in dUTPase
title_short Aromatic stacking between nucleobase and enzyme promotes phosphate ester hydrolysis in dUTPase
title_sort aromatic stacking between nucleobase and enzyme promotes phosphate ester hydrolysis in dutpase
topic Nucleic Acid Enzymes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2978360/
https://www.ncbi.nlm.nih.gov/pubmed/20601405
http://dx.doi.org/10.1093/nar/gkq584
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