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

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14310%2F08%3A00025615" target="_blank" >RIV/00216224:14310/08:00025615 - isvavai.cz</a>

Alternative codes found

RIV/61989592:15310/08:00005477

Result on the web

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DOI - Digital Object Identifier

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Result language

angličtina

Original language name

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

Original language description

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, QMcalculations 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

Czech name

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

Czech description

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

Type

J_x - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)

CEP classification

CE - Biochemistry

OECD FORD branch

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Project

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)<br>Z - Vyzkumny zamer (s odkazem do CEZ)

Publication year

2008

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Proteins: Structure, Function, and Bioinformatics

ISSN

0887-3585

e-ISSN

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Volume of the periodical

70

Issue of the periodical within the volume

000

Country of publishing house

US - UNITED STATES

Number of pages

11

Pages from-to

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UT code for WoS article

000252836300009

EID of the result in the Scopus database

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