The catalytic mechanism of fluoroacetate dehalogenase

a computational exploration of biological dehalogenation

Takashi Kamachi, Tomonori Nakayama, Osamu Shitamichi, Keiji Jitsumori, Tatsuo Kurihara, Nobuyoshi Esaki, Kazunari Yoshizawa

Research output: Contribution to journalArticle

21 Citations (Scopus)

Abstract

The biological dehalogenation of fluoroacetate carried out by fluoroacetate dehalogenase is discussed by using quantum mechanical/molecular mechanical (QM/MM) calculations for a whole-enzyme model of 10800 atoms. Substrate fluoroacetate is anchored by a hydrogen-bonding network with water molecules and the surrounding amino acid residues of Arg105, Arg108, His149, Trp150, and Tyr212 in the active site in a similar way to haloalkane dehalogenase. Asp104 is likely to act as a nucleophile to attack the a-carbon of fluoroacetate, resulting in the formation of an ester intermediate, which is subsequently hydrolyzed by the nucleophilic attack of a water molecule to the carbonyl carbon atom. The cleavage of the strong C-F bond is greatly facilitated by the hydrogen-bonding interactions between the leaving fluorine atom and the three amino acid residues of Hisl49, Trp150, and Tyr212. The hydrolysis of the ester intermediate is initiated by a proton transfer from the water molecule to His271 and by the simultaneous nucleophilic attack of the water molecule. The transition state and produced tetrahedral intermediate are stabilized by Asp128 and the oxyanion hole composed of Phe34 and Arg105.

Original languageEnglish
Pages (from-to)7394-7403
Number of pages10
JournalChemistry - A European Journal
Volume15
Issue number30
DOIs
Publication statusPublished - Jul 27 2009

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haloacetate dehalogenase
Dehalogenation
Fluoroacetates
haloalkane dehalogenase
Molecules
Water
Atoms
Amino acids
Esters
Hydrogen bonds
Carbon
Amino Acids
Nucleophiles
Proton transfer
Fluorine
Hydrolysis
Enzymes
Substrates

All Science Journal Classification (ASJC) codes

  • Chemistry(all)

Cite this

The catalytic mechanism of fluoroacetate dehalogenase : a computational exploration of biological dehalogenation. / Kamachi, Takashi; Nakayama, Tomonori; Shitamichi, Osamu; Jitsumori, Keiji; Kurihara, Tatsuo; Esaki, Nobuyoshi; Yoshizawa, Kazunari.

In: Chemistry - A European Journal, Vol. 15, No. 30, 27.07.2009, p. 7394-7403.

Research output: Contribution to journalArticle

Kamachi, Takashi ; Nakayama, Tomonori ; Shitamichi, Osamu ; Jitsumori, Keiji ; Kurihara, Tatsuo ; Esaki, Nobuyoshi ; Yoshizawa, Kazunari. / The catalytic mechanism of fluoroacetate dehalogenase : a computational exploration of biological dehalogenation. In: Chemistry - A European Journal. 2009 ; Vol. 15, No. 30. pp. 7394-7403.
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