Theoretical insight into the hydroxylamine oxidoreductase mechanism

The multiheme enzyme hydroxylamine oxidoreductase from the autotrophic bacteria Nitrosomonas europaea catalyzes the conversion of hydroxylamine to nitrite, with a complicate arrangement of heme groups in three subunits. As a distinctive feature, the protein has a covalent linkage between a tyrosyl r...

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Autores principales: Fernández, M.L., Estrin, D.A., Bari, S.E.
Formato: JOUR
Materias:
DFT
Acceso en línea:http://hdl.handle.net/20.500.12110/paper_01620134_v102_n7_p1523_Fernandez
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spelling todo:paper_01620134_v102_n7_p1523_Fernandez2023-10-03T15:01:26Z Theoretical insight into the hydroxylamine oxidoreductase mechanism Fernández, M.L. Estrin, D.A. Bari, S.E. Catalytic activity DFT Hydroxylamine oxidoreductase meso-Substituted heme hydroxylamine hydroxylamine oxidase iron derivative ligand nitrogen tyrosine article catalysis crystal structure density functional theory energy hydrogen bond model Heme Hydrogen Bonding Models, Molecular Models, Theoretical Nitrosomonas Oxidoreductases Nitrosomonas europaea The multiheme enzyme hydroxylamine oxidoreductase from the autotrophic bacteria Nitrosomonas europaea catalyzes the conversion of hydroxylamine to nitrite, with a complicate arrangement of heme groups in three subunits. As a distinctive feature, the protein has a covalent linkage between a tyrosyl residue of one subunit and a meso carbon atom of the heme active site of another. We studied the influence of this bond in the catalysis from a theoretical perspective through electronic structure calculations at the density functional theory level, starting from the crystal structure of the protein. Geometry optimizations of proposed reaction intermediates were used to calculate the dissociation energy of different nitrogen containing ligands, considering the presence and absence of the meso tyrosyl residue. The results indicate that the tyrosine residue enhances the binding of hydroxylamine, and increases the stability of a Fe III NO intermediate, while behaving indifferently in the Fe II NO form. The calculations performed on model systems including neighboring aminoacids revealed the probable formation of a bidentate hydrogen bond between the Fe III H 2 O complex and Asp 257, in a high-spin aquo complex as the resting state. Characterization of non-planar heme distortions showed that the meso-substituent induces significant ruffling in the evaluated intermediates. © 2008 Elsevier Inc. All rights reserved. JOUR info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/2.5/ar http://hdl.handle.net/20.500.12110/paper_01620134_v102_n7_p1523_Fernandez
institution Universidad de Buenos Aires
institution_str I-28
repository_str R-134
collection Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA)
topic Catalytic activity
DFT
Hydroxylamine oxidoreductase
meso-Substituted heme
hydroxylamine
hydroxylamine oxidase
iron derivative
ligand
nitrogen
tyrosine
article
catalysis
crystal structure
density functional theory
energy
hydrogen bond
model
Heme
Hydrogen Bonding
Models, Molecular
Models, Theoretical
Nitrosomonas
Oxidoreductases
Nitrosomonas europaea
spellingShingle Catalytic activity
DFT
Hydroxylamine oxidoreductase
meso-Substituted heme
hydroxylamine
hydroxylamine oxidase
iron derivative
ligand
nitrogen
tyrosine
article
catalysis
crystal structure
density functional theory
energy
hydrogen bond
model
Heme
Hydrogen Bonding
Models, Molecular
Models, Theoretical
Nitrosomonas
Oxidoreductases
Nitrosomonas europaea
Fernández, M.L.
Estrin, D.A.
Bari, S.E.
Theoretical insight into the hydroxylamine oxidoreductase mechanism
topic_facet Catalytic activity
DFT
Hydroxylamine oxidoreductase
meso-Substituted heme
hydroxylamine
hydroxylamine oxidase
iron derivative
ligand
nitrogen
tyrosine
article
catalysis
crystal structure
density functional theory
energy
hydrogen bond
model
Heme
Hydrogen Bonding
Models, Molecular
Models, Theoretical
Nitrosomonas
Oxidoreductases
Nitrosomonas europaea
description The multiheme enzyme hydroxylamine oxidoreductase from the autotrophic bacteria Nitrosomonas europaea catalyzes the conversion of hydroxylamine to nitrite, with a complicate arrangement of heme groups in three subunits. As a distinctive feature, the protein has a covalent linkage between a tyrosyl residue of one subunit and a meso carbon atom of the heme active site of another. We studied the influence of this bond in the catalysis from a theoretical perspective through electronic structure calculations at the density functional theory level, starting from the crystal structure of the protein. Geometry optimizations of proposed reaction intermediates were used to calculate the dissociation energy of different nitrogen containing ligands, considering the presence and absence of the meso tyrosyl residue. The results indicate that the tyrosine residue enhances the binding of hydroxylamine, and increases the stability of a Fe III NO intermediate, while behaving indifferently in the Fe II NO form. The calculations performed on model systems including neighboring aminoacids revealed the probable formation of a bidentate hydrogen bond between the Fe III H 2 O complex and Asp 257, in a high-spin aquo complex as the resting state. Characterization of non-planar heme distortions showed that the meso-substituent induces significant ruffling in the evaluated intermediates. © 2008 Elsevier Inc. All rights reserved.
format JOUR
author Fernández, M.L.
Estrin, D.A.
Bari, S.E.
author_facet Fernández, M.L.
Estrin, D.A.
Bari, S.E.
author_sort Fernández, M.L.
title Theoretical insight into the hydroxylamine oxidoreductase mechanism
title_short Theoretical insight into the hydroxylamine oxidoreductase mechanism
title_full Theoretical insight into the hydroxylamine oxidoreductase mechanism
title_fullStr Theoretical insight into the hydroxylamine oxidoreductase mechanism
title_full_unstemmed Theoretical insight into the hydroxylamine oxidoreductase mechanism
title_sort theoretical insight into the hydroxylamine oxidoreductase mechanism
url http://hdl.handle.net/20.500.12110/paper_01620134_v102_n7_p1523_Fernandez
work_keys_str_mv AT fernandezml theoreticalinsightintothehydroxylamineoxidoreductasemechanism
AT estrinda theoreticalinsightintothehydroxylamineoxidoreductasemechanism
AT barise theoreticalinsightintothehydroxylamineoxidoreductasemechanism
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