Second step of hydrolytic dehalogenation in haloalkane dehalogenase investigated by QM/MM methods

Autor: Jiří Damborský, Pavel Banáš, Michal Otyepka, Paolo Carloni, Alessandra Magistrato
Rok vydání: 2008
Předmět:
Models
Molecular
ONIOM
Reaction mechanism
Halogenation
ester hydrolysis
Hydrolases
Protein Conformation
INITIO MOLECULAR-DYNAMICS
QUANTUM MECHANICS/MOLECULAR MECHANICS
Reaction intermediate
010402 general chemistry
Photochemistry
Sphingomonas
01 natural sciences
Biochemistry
Catalysis
QM/MM
Bacterial Proteins
Structural Biology
Computational chemistry
Tetrahedral carbonyl addition compound
0103 physical sciences
Molecular Biology
SPHINGOMONAS-PAUCIMOBILIS UT26
Settore CHIM/03 - Chimica Generale e Inorganica
Binding Sites
ENZYME CATALYSIS
010304 chemical physics
tetrahedral intermediate
Reaction step
Chemistry
Hydrolysis
catalytic triad
enzyme dynamics
reaction mechanism
0104 chemical sciences
Kinetics
Catalytic cycle
Quantum Theory
Thermodynamics
NUCLEOPHILIC-SUBSTITUTION REACTION
Haloalkane dehalogenase
Zdroj: Proteins
70 (2008): 707–717. doi:10.1002/prot.21523
info:cnr-pdr/source/autori:Otyepka, M; Banas, P; Magistrato, A; Carloni, P; Damborsky, J/titolo:Second step of hydrolytic dehalogenation in haloalkane dehalogenase investigated by QM%2FMM methods/doi:10.1002%2Fprot.21523/rivista:Proteins (Print)/anno:2008/pagina_da:707/pagina_a:717/intervallo_pagine:707–717/volume:70
ISSN: 1097-0134
0887-3585
DOI: 10.1002/prot.21523
Popis: Mechanistic studies on the hydrolytic dehalogenation catalyzed by haloalkane dehalogenases are of importance for environmental and industrial applications. Here, Car-Parrinello (CP) and ONIOM hybrid quantum-mechanical/molecular mechanics (QM/MM) are used investigate the second reaction step of the catalytic cycle, which comprises a general base-catalyzed hydrolysis of an ester intermediate (EI) to alcohol and free enzyme. We focus on the enzyme LinB from Sphingo-monas paucimobilis UT26, for which the X-ray structure at atomic resolution is available. In agreement with previous proposals, our calculations suggest that a histidine residue (His272), polarized by glutamate (Glu132), acts as a base, accepting a proton from the catalytic water molecule and transferring it to an alcoholate ion. The reaction proceeds through a metastable tetrahedral intermediate, which shows an easily reversed reaction to the EI In the formation of the products, the protonated aspartic acid (Asp 108) can easily adopt conformation of the relaxed state found in the free enzyme. The overall free energy barrier of the reaction calculated by potential of the mean force integration using CP-QM/MM calculations is equal to 19.5 +/- 2 kcal . mol(-1). The lowering of the energy barrier of catalyzed reaction with respect to the water reaction is caused by strong stabilization of the reaction intermediate and transition state and their preorganization by electrostatic field of the enzyme.
Databáze: OpenAIRE
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