Second Step of Hydrolytic Dehalogenation in Haloalkane
Dehalogenase Investigated by QM/MM Methods

J 2008

Second Step of Hydrolytic Dehalogenation in Haloalkane Dehalogenase Investigated by QM/MM Methods

OTYEPKA, Michal, Pavel BANÁŠ, A. MAGISTRATO, P. CARLONI, Jiří DAMBORSKÝ et. al.

Basic information

Original name

Second Step of Hydrolytic Dehalogenation in Haloalkane Dehalogenase Investigated by QM/MM Methods

Name in Czech

Druhý krok hydrolytické dehalogenace v haloalkan dehalogenáze prováděný metodou QM/MM

Authors

OTYEPKA, Michal (203 Czech Republic), Pavel BANÁŠ (203 Czech Republic), A. MAGISTRATO (380 Italy), P. CARLONI (380 Italy) and Jiří DAMBORSKÝ (203 Czech Republic, guarantor)

Edition

Proteins: Structure, Function, and Bioinformatics, 2008, 0887-3585

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10600 1.6 Biological sciences

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 3.419

RIV identification code

RIV/00216224:14310/08:00025615

Organization unit

Faculty of Science

UT WoS

000252836300009

Keywords in English

dehalogenase; LinB; Sphingomonas paucimobilis UT26; quantum-mechanical/molecular mechanics (QM/MM) simulations

Abstract

ORIG CZ

V originále

We investigate mechanism and energetics of the hydrolytic dehalogenation catalyzed by haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26 by Car-Parrinello (CP) and ONIOM hybrid quantum-mechanical/molecular mechanics (QM/MM) simulations, QM calculations and classical molecular dynamics. We focus on the second reaction step of the catalytic cycle, which comprises a general base-catalyzed hydrolysis of an ester intermediate to alcohol and free enzyme. In this step, 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 ester intermediate. 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 is caused by strong stabilization of the reaction intermediate and transition state by local electrostatic field of the enzyme, while its intrinsic dynamics plays a minor role. In the formation of the products, the protonated aspartic acid (Asp108) can easily adopt conformation of the relaxed state found in the free enzyme.

In Czech

V článku jsou popisovány výpočty mechanismů a energii při hydrolytické dehalogenaci katalyyované pomocí haloalkan dehalogenázou LinB z bakterie Sphingomonas paucimobilis UT26

Links

LC06010, research and development project

Name: Centrum biokatalýzy a biotransformací

Investor: Ministry of Education, Youth and Sports of the CR, Center of Biocatalysis and Biotransformation

MSM0021622413, plan (intention)

Name: Proteiny v metabolismu a při interakci organismů s prostředím

Investor: Ministry of Education, Youth and Sports of the CR, Proteins in metabolism and interaction of organisms with the environment

Citovat

OTYEPKA, Michal, Pavel BANÁŠ, A. MAGISTRATO, P. CARLONI and Jiří DAMBORSKÝ. Second Step of Hydrolytic Dehalogenation in Haloalkane Dehalogenase Investigated by QM/MM Methods. Proteins: Structure, Function, and Bioinformatics. 2008, vol. 70, No 000, p. 707-717. ISSN 0887-3585.

@article{721204,
   author = {Otyepka, Michal and Banáš, Pavel and Magistrato, A. and Carloni, P. and Damborský, Jiří},
   article_number = {000},
   keywords = {dehalogenase; LinB; Sphingomonas paucimobilis UT26; quantum-mechanical/molecular mechanics (QM/MM) simulations},
   language = {eng},
   issn = {0887-3585},
   journal = {Proteins: Structure, Function, and Bioinformatics},
   title = {Second Step of Hydrolytic Dehalogenation in Haloalkane Dehalogenase Investigated by QM/MM Methods},
   url = {http://loschmidt.chemi.muni.cz/peg/abstracts/prot07b.html},
   volume = {70},
   year = {2008}
}

TY  - JOUR
ID  - 721204
AU  - Otyepka, Michal - Banáš, Pavel - Magistrato, A. - Carloni, P. - Damborský, Jiří
PY  - 2008
TI  - Second Step of Hydrolytic Dehalogenation in Haloalkane Dehalogenase Investigated by QM/MM Methods
JF  - Proteins: Structure, Function, and Bioinformatics
VL  - 70
IS  - 000
SP  - 707-717
EP  - 707-717
SN  - 08873585
KW  - dehalogenase
KW  - LinB
KW  - Sphingomonas paucimobilis UT26
KW  - quantum-mechanical/molecular mechanics (QM/MM) simulations
UR  - http://loschmidt.chemi.muni.cz/peg/abstracts/prot07b.html
N2  - We investigate mechanism and energetics of the hydrolytic dehalogenation catalyzed by haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26 by Car-Parrinello (CP) and ONIOM hybrid quantum-mechanical/molecular mechanics (QM/MM) simulations, QM calculations and classical molecular dynamics. We focus on the second reaction step of the catalytic cycle, which comprises a general base-catalyzed hydrolysis of an ester intermediate to alcohol and free enzyme. In this step, 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 ester intermediate. 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 is caused by strong stabilization of the reaction intermediate and transition state by local electrostatic field of the enzyme, while its intrinsic dynamics plays a minor role. In the formation of the products, the protonated aspartic acid (Asp108) can easily adopt conformation of the relaxed state found in the free enzyme.
ER  -

OTYEPKA, Michal, Pavel BANÁŠ, A. MAGISTRATO, P. CARLONI and Jiří DAMBORSKÝ. Second Step of Hydrolytic Dehalogenation in Haloalkane Dehalogenase Investigated by QM/MM Methods. \textit{Proteins: Structure, Function, and Bioinformatics}. 2008, vol.~70, No~000, p.~707-717. ISSN~0887-3585.

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