Reaction Mechanism of Fluoroacetate Dehalogenase from Moraxella sp. B

劉, 吉泉; Kurihara, Tatsuo; Ichiyama, Susumu; Miyagi, Masaru; Tsunasawa, Susumu; Kawasaki, Haruhiko; Soda, Kenji; Esaki, Nobuyoshi

doi:10.1074/jbc.273.47.30897

Cited by 74 publications

(78 citation statements)

References 33 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To clarify the enzymatic defluorination mechanism, we investigated the reaction mechanism of FAc-DEX H1 by sitedirected mutagenesis and mass spectrometric analysis and revealed that the reaction proceeds in two steps (23). In the first step, the carboxylate group of Asp105 nucleophilically attacks the ␣-carbon atom of fluoroacetate to displace the fluorine atom, leading to the formation of an ester intermediate.…”

mentioning

confidence: 99%

X-Ray Crystallographic and Mutational Studies of Fluoroacetate Dehalogenase from Burkholderia sp. Strain FA1

et al. 2009

Self Cite

View full text Add to dashboard Cite

Fluoroacetate dehalogenase catalyzes the hydrolytic defluorination of fluoroacetate to produce glycolate. The enzyme is unique in that it catalyzes the cleavage of a carbon-fluorine bond of an aliphatic compound: the bond energy of the carbon-fluorine bond is among the highest found in natural products. The enzyme also acts on chloroacetate, although much less efficiently. We here determined the X-ray crystal structure of the enzyme from Burkholderia sp. strain FA1 as the first experimentally determined three-dimensional structure of fluoroacetate dehalogenase. The enzyme belongs to the ␣/␤ hydrolase superfamily and exists as a homodimer. Each subunit consists of core and cap domains. The catalytic triad, Asp104-His271-Asp128, of which Asp104 serves as the catalytic nucleophile, was found in the core domain at the domain interface. The active site was composed of Phe34, Asp104, Arg105, Arg108, Asp128, His271, and Phe272 of the core domain and Tyr147, His149, Trp150, and Tyr212 of the cap domain. An electron density peak corresponding to a chloride ion was found in the vicinity of the N 1 atom of Trp150 and the N 2 atom of His149, suggesting that these are the halide ion acceptors. Site-directed replacement of each of the active-site residues, except for Trp150, by Ala caused the total loss of the activity toward fluoroacetate and chloroacetate, whereas the replacement of Trp150 caused the loss of the activity only toward fluoroacetate. An interaction between Trp150 and the fluorine atom is probably an absolute requirement for the reduction of the activation energy for the cleavage of the carbon-fluorine bond.Fluoroacetate is a naturally occurring organofluorine compound. An actinomycete, "Streptomyces cattleya" (30), and some plants in Australia and Africa (2) produce this highly toxic compound. Fluoroacetate has a carbon-fluorine bond, whose dissociation energy is among the highest found in nature (8). Despite this fact, fluoroacetate dehalogenases (FAcDEXs) from Burkholderia sp. strain FA1 (FAc-DEX FA1) (20) and Delftia acidovorans strain B (formerly Moraxella sp. strain B; FAc-DEX H1) (16) catalyze the hydrolytic defluorination of fluoroacetate to produce glycolate. These enzymes are unique in that they catalyze the cleavage of the carbon-fluorine bond, which is much stronger than other carbon-halogen bonds.FAc-DEXs show weak but significant sequence similarity to proteins that belong to the ␣/␤ hydrolase superfamily, such as epoxide hydrolases from Agrobacterium radiobacter AD1 (37) and humans and haloalkane dehalogenases from Sphingobium japonicum UT26 (formerly Sphingomonas paucimobilis UT26) (32) and Xanthobacter autotrophicus GJ10 (17). Although haloalkane dehalogenases of this superfamily catalyze the hydrolytic cleavage of carbon-halogen bonds, none of them catalyzes the cleavage of a carbon-fluorine bond. Dehalogenases that belong to other families, such as L-2-haloacid dehalogenase (22), DL-2-haloacid dehalogenase (28), and haloalcohol dehalogenase (42), also do not catalyze the cleavage of a carbon-...

show abstract

mentioning

confidence: 99%

X-Ray Crystallographic and Mutational Studies of Fluoroacetate Dehalogenase from Burkholderia sp. Strain FA1

et al. 2009

Self Cite

View full text Add to dashboard Cite

show abstract

“…Many different enzymes generally referred to as dehalogenases catalyze this reaction; for example, different classes include hydrolytic, oxygenolytic, and reductive enzymes (21, 22). Dehalogenation of ␣-halocarboxylic acids such as the herbicide Dalapon (2,2-dichloropropionic acid) is catalyzed by one of the classes of hydrolytic dehalogenases that is best characterized, in that protein structures and mechanisms have been reported (31,32,36,37) for the two distinct evolutionary families of these enzymes, the group I and group II deh products (17). There is preliminary evidence to suggest that other families of halocarboxylic acid dehalogenases exist (17, 23).…”

mentioning

confidence: 99%

Transposition of DEH , a Broad-Host-Range Transposon Flanked by IS Ppu12 , in Pseudomonas putida Is Associated with Genomic Rearrangements and Dehalogenase Gene Silencing

et al. 2002

View full text Add to dashboard Cite

Pseudomonas putida strain PP3 produces two hydrolytic dehalogenases encoded by dehI and dehII, which are members of different deh gene families. The 9.74-kb DEH transposon containing dehI and its cognate regulatory gene, dehR I , was isolated from strain PP3 by using the TOL plasmid pWW0. DEH was fully sequenced and shown to have a composite transposon structure, within which dehI and dehR I were divergently transcribed and were flanked on either side by 3.73-kb identical direct repeats. The flanking repeat unit, designated ISPpu12, had the structure of an insertion sequence in that it was bordered by 24-bp near-perfect inverted repeats and contained four open reading frames (ORFs), one of which was identified as tnpA, putatively encoding an ISL3 family transposase. A putative lipoprotein signal peptidase was encoded by an adjacent ORF, lspA, and the others, ISPpu12 orf1 and orf2, were tentatively identified as a truncated cation efflux transporter gene and a PbrR family regulator gene, respectively. The orf1-orf2 intergenic region contained an exact match with a previously described active, outward-orientated promoter, Pout. Transposition of DEH-ISPpu12 was investigated by cloning the whole transposon into a suicide plasmid donor, pAWT34, and transferring the construct to various recipients. In this way DEH-ISPpu12 was shown to transpose in a broad range of Proteobacteria. Transposition of ISPpu12 independently from DEH, and inverse transposition, whereby the vector DNA and ISPpu12 inserted into the target genome without the deh genes, were also observed to occur at high frequencies in P. putida PaW340. Transposition of a second DEH-ISPpu12 derivative introduced exogenously into P. putida PP3 via the suicide donor pAWT50 resulted in silencing of resident dehI and dehII genes in about 10% of transposition transconjugants and provided a genetic link between transposition of ISPpu12 and dehalogenase gene silencing. Database searches identified ISPpu12-related sequences in several bacterial species, predominantly associated with plasmids and xenobiotic degradative genes. The potential role of ISPpu12 in gene silencing and activation, as well as the adaptation of bacteria to degrade xenobiotic compounds, is discussed.A key step in the biodegradation of halo-organic compounds is cleavage of the carbon-halogen bond. Many different enzymes generally referred to as dehalogenases catalyze this reaction; for example, different classes include hydrolytic, oxygenolytic, and reductive enzymes (21, 22). Dehalogenation of ␣-halocarboxylic acids such as the herbicide Dalapon (2,2-dichloropropionic acid) is catalyzed by one of the classes of hydrolytic dehalogenases that is best characterized, in that protein structures and mechanisms have been reported (31,32,36,37) for the two distinct evolutionary families of these enzymes, the group I and group II deh products (17). There is preliminary evidence to suggest that other families of halocarboxylic acid dehalogenases exist (17, 23).The dehalogenase system of Pseudomonas putida st...

show abstract

“…42) Site-directed mutagenesis and mass spectrometric analysis were carried out to elucidate the reaction mechanism of fluoroacetate dehalogenase from D. acidovorans strain B (FAc-DEX H1). 29,43,44) The studies revealed that Asp105 serves as a nucleophile to attack the -carbon atom of the substrate to displace the fluorine atom, leading to the formation of an ester intermediate (Fig. 4).…”

Section: )mentioning

confidence: 99%

“…[27][28][29] DL-2-Haloacid dehalogenase is unique in that a water molecule attacks the substrate directly to displace the halogen atom without the formation of an ester intermediate. Considering the sequence similarity between DL-2-haloacid dehalogenase and D-2-haloacid dehalogenase, the reaction catalyzed by D-2-haloacid dehalogenase probably proceeds through the same mechanism as that of DL-2-haloacid dehalogenase.…”

Section: )mentioning

confidence: 99%

A Mechanistic Analysis of Enzymatic Degradation of Organohalogen Compounds

Kurihara¹

2011

Bioscience, Biotechnology, and Biochemistry

Self Cite

View full text Add to dashboard Cite

Abbreviations: HAD, haloacid dehalogenase; L-DEX YL, L-2-haloacid dehalogenase from Pseudomonas sp. YL; DL-DEX 113, DL-2-haloacid dehalogenase from Pseudomonas sp. 113; DehI, DL-2-haloacid dehalogenase from Pseudomonas putida strain PP3; FAc-DEX H1, fluoroacetate dehalogenase from Delftia acidovorans strain B; FAc-DEX FA1, fluoroacetate dehalogenase from Burkholderia sp. FA1; QM/MM, quantum mechanical/molecular mechanical; 2-CAA, 2-chloroacrylate; PAGE, polyacrylamide gel electrophoresis

show abstract

Reaction Mechanism of Fluoroacetate Dehalogenase from Moraxella sp. B

Cited by 74 publications

References 33 publications

X-Ray Crystallographic and Mutational Studies of Fluoroacetate Dehalogenase from Burkholderia sp. Strain FA1

X-Ray Crystallographic and Mutational Studies of Fluoroacetate Dehalogenase from Burkholderia sp. Strain FA1

Transposition of DEH , a Broad-Host-Range Transposon Flanked by IS Ppu12 , in Pseudomonas putida Is Associated with Genomic Rearrangements and Dehalogenase Gene Silencing

A Mechanistic Analysis of Enzymatic Degradation of Organohalogen Compounds

Contact Info

Product

Resources

About