Biodegradation of chlorinated aliphatic compounds

Leisinger, Thomas

doi:10.1016/s0958-1669(96)80033-4

Cited by 39 publications

(16 citation statements)

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“…Haloalkane dehalogenases have been identified in organisms growing on 1-chloro-n-alkanes, 1-bromo-n-alkanes, or ␣,-dihalo-n-alkanes (13) and are not considered to be generally present in uncontaminated environments, since they were isolated above all from bacteria colonizing contaminated environments (8,9,13,15).…”

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Dehalogenation of Haloalkanes byMycobacterium tuberculosisH37Rv and Other Mycobacteria

Jesenská¹,

Sedláček²,

Damborský

2000

Appl Environ Microbiol

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Haloalkane dehalogenases convert haloalkanes to their corresponding alcohols by a hydrolytic mechanism. To date, various haloalkane dehalogenases have been isolated from bacteria colonizing environments that are contaminated with halogenated compounds. A search of current databases with the sequences of these known haloalkane dehalogenases revealed the presence of three different genes encoding putative haloalkane dehalogenases in the genome of the human parasite Mycobacterium tuberculosis H37Rv. The ability of M. tuberculosis and several other mycobacterial strains to dehalogenate haloaliphatic compounds was therefore studied. Intact cells of M. tuberculosis H37Rv were found to dehalogenate 1-chlorobutane, 1-chlorodecane, 1-bromobutane, and 1,2-dibromoethane. Nine isolates of mycobacteria from clinical material and four strains from a collection of microorganisms were found to be capable of dehalogenating 1,2-dibromoethane. Crude extracts prepared from two of these strains, Mycobacterium avium MU1 and Mycobacterium smegmatis CCM 4622, showed broad substrate specificity toward a number of halogenated substrates. Dehalogenase activity in the absence of oxygen and the identification of primary alcohols as the products of the reaction suggest a hydrolytic dehalogenation mechanism. The presence of dehalogenases in bacterial isolates from clinical material, including the species colonizing both animal tissues and free environment, indicates a possible role of parasitic microorganisms in the distribution of degradation genes in the environment.Hydrolytic dehalogenation by haloalkane dehalogenases is commonly observed as the first step in the aerobic degradation of synthetic haloalkanes that occur as soil pollutants (16). Haloalkane dehalogenases have been identified in organisms growing on 1-chloro-n-alkanes, 1-bromo-n-alkanes, or ␣,-dihalo-n-alkanes (13) and are not considered to be generally present in uncontaminated environments, since they were isolated above all from bacteria colonizing contaminated environments (8, 9, 13, 15).The amino acid sequence of haloalkane dehalogenase is known for at least three bacteria: Xanthobacter autotrophicus GJ10 (dehalogenase DhlA) (12), Sphingomonas paucimobilis UT26 (dehalogenase LinB) (19,20), and Rhodococcus rhodochrous NCIMB 13064 (dehalogenase DhaA) (14). These three sequences were compared with the sequences deposited in the genetic databases. This comparison revealed the presence of three different genes encoding for putative haloalkane dehalogenases on the chromosome of Mycobacterium tuberculosis H37Rv, whose complete genome has been sequenced recently (3).The objectives of this study were to confirm activity of M. tuberculosis H37Rv toward halogenated aliphatic substrates and to study if other representatives of the genus Mycobacterium also show the ability to dehalogenate haloalkanes. MATERIALS AND METHODSHomology search, sequence alignment, solvent accessibility, and secondary structure prediction. The BLAST program (1) was used to screen protein and DNA databases for...

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confidence: 99%

Dehalogenation of Haloalkanes byMycobacterium tuberculosisH37Rv and Other Mycobacteria

Jesenská¹,

Sedláček²,

Damborský

2000

Appl Environ Microbiol

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“…Dehalogenation enzymes have attracted considerable attention owning to the potential of applying these enzymes to the treatment of halogenated hydrocarbon-contaminated soil and water supplies (9)(10)(11). Haloalkane dehalogenase is of particular interest because it catalyzes hydrolysis of alkyl halides without requiring any cofactors or metal ions (8).…”

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Non-enzymatic and enzymatic hydrolysis of alkyl halides: A haloalkane dehalogenation enzyme evolved to stabilize the gas-phase transition state of an S _N 2 displacement reaction

Lightstone

Zheng

Maulitz

et al. 1997

Proc. Natl. Acad. Sci. U.S.A.

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The semiempirical PM3 method, calibrated against ab initio HF͞6-31؉G(d) theory, has been used to elucidate the reaction of 1,2-dichloroethane (DCE) with the carboxylate of Asp-124 at the active site of haloalkane dehalogenase of Xanthobacter autothropicus. Asp-124 and 13 other amino acid side chains that make up the active site cavity (Glu-56, Trp-125, Phe-128, Phe-172, Trp-175, Leu-179, Val-219, Phe-222, Pro-223, Val-226, Leu-262, Leu-263, and His-289) were included in the calculations. The three most significant observations of the present study are that: (i) the DCE substrate and Asp-124 carboxylate, in the reactive ES complex, are present as an ion-molecule complex with a structure similar to that seen in the gas-phase reaction of AcO ؊ with DCE; (ii) the structures of the transition states in the gasphase and enzymatic reaction are much the same where the structure formed at the active site is somewhat exploded; and (iii) the enthalpies in going from ground states to transition states in the enzymatic and gas-phase reactions differ by only a couple kcal͞mol. The dehalogenase derives its catalytic power from: (i) bringing the electrophile and nucleophile together in a low-dielectric environment in an orientation that allows the reaction to occur without much structural reorganization; (ii) desolvation; and (iii) stabilizing the leaving chloride anion by Trp-125 and Trp-175 through hydrogen bonding.

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“…The highest reactivity was observed with 1,2-dichloroethane (DCE) (1), and the dehalogenation proceeds via the formation of the corresponding alcohol (ROH). This observation has stimulated much interest because it offers an elegant way to decontaminate water and soil that have been spoiled by man-made haloalkanes (2,3). The generally accepted mechanism for the haloalkane dehalogenase enzyme is a two-step process (4)(5)(6)(7).…”

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Nonenzymatic and enzymatic hydrolysis of alkyl halides: A theoretical study of the S_N2 reactions of acetate and hydroxide ions with alkyl chlorides

Maulitz

Lightstone

Zheng

et al. 1997

Proc. Natl. Acad. Sci. U.S.A.

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The S N 2 displacements of chloride ion from CH 3 Cl, C 2 H 5 Cl, and C 2 H 4 Cl 2 by acetate and hydroxide ions have been investigated, using ab initio molecular orbital theory at the HF͞6 -31؉G(d), MP2͞6 -31؉G(d), and MP4͞6 -31؉G(d) levels of theory. The central barriers (calculated from the initial ion-molecule complex) of the reactions, the differences of the overall reaction energies, and the geometries of the transition states are compared. Essential stereochemical changes before and after the displacement reactions are described for selected cases. The gas phase reactions of hydroxide with CH 3 Cl, C 2 H 5 Cl, and C 2 H 4 Cl 2 have no overall barrier, but there is a small overall barrier for the reactions of acetate with CH 3 Cl, C 2 H 5 Cl, and C 2 H 4 Cl 2 . A self-consistent reaction field solvation model was used to examine the S N 2 reactions between methyl chloride and hydroxide ion and between 1,2-dichloroethane and acetate in solution. As expected, the reactions in polar solvent have a large barrier. However, the transition state structures determined by ab initio calculations change only slightly in the presence of a highly polar solvent as compared with the gas phase. We also calibrated the PM3 method for future study of an enzymatic S N 2 displacement of halogen.Haloalkanes are widely used as herbicides, pesticides, refrigerants, or solvents. The haloalkane dehalogenase enzyme from Xanthobacter autothropicus GJ10 catalyzes the dehalogenation of n-RX compounds, where R is a C(1) to C(4) chain and X ϭ Cl, Br, and I. The highest reactivity was observed with 1,2-dichloroethane (DCE) (1), and the dehalogenation proceeds via the formation of the corresponding alcohol (ROH). This observation has stimulated much interest because it offers an elegant way to decontaminate water and soil that have been spoiled by man-made haloalkanes (2, 3). The generally accepted mechanism for the haloalkane dehalogenase enzyme is a two-step process (4-7). First, the carboxylate of Asp-124 performs a nucleophilic attack on the halosubstituted carbon atom of the substrate, displacing the halogen ion and forming an alkyl-enzyme ester intermediate which is subsequently hydrolyzed by a water (4). In this hydrolysis step, the imidazole of His-289 serves as a general base catalyst (7). Ultimately, we wish to understand the catalytic mechanism of the Asp-124-CO 2 Ϫ S N 2 displacement on alkyl chlorides in the enzymatic reaction. We begin with the present theoretical investigation of the reactions of CH 3 CO 2 Ϫ with a number of alkyl chlorides. Experimental energetic data concerning halogenated compounds are scarce. Empirical rules have been devised to estimate the free energy of formation of chlorinated aliphatic compounds (8). Although this empirical approach could provide reasonable estimates for reaction energy, it is unable to provide useful information regarding the reaction barrier.Knowledge of the nonenzymatic dehalogenation reactions are critical for the understanding of the catalytic efficiency of haloalkane d...

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Biodegradation of chlorinated aliphatic compounds

Cited by 39 publications

References 46 publications

Dehalogenation of Haloalkanes byMycobacterium tuberculosisH37Rv and Other Mycobacteria

Dehalogenation of Haloalkanes byMycobacterium tuberculosisH37Rv and Other Mycobacteria

Non-enzymatic and enzymatic hydrolysis of alkyl halides: A haloalkane dehalogenation enzyme evolved to stabilize the gas-phase transition state of an S _N 2 displacement reaction

Nonenzymatic and enzymatic hydrolysis of alkyl halides: A theoretical study of the S_N2 reactions of acetate and hydroxide ions with alkyl chlorides

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Biodegradation of chlorinated aliphatic compounds

Cited by 39 publications

References 46 publications

Dehalogenation of Haloalkanes byMycobacterium tuberculosisH37Rv and Other Mycobacteria

Dehalogenation of Haloalkanes byMycobacterium tuberculosisH37Rv and Other Mycobacteria

Non-enzymatic and enzymatic hydrolysis of alkyl halides: A haloalkane dehalogenation enzyme evolved to stabilize the gas-phase transition state of an S N 2 displacement reaction

Nonenzymatic and enzymatic hydrolysis of alkyl halides: A theoretical study of the SN2 reactions of acetate and hydroxide ions with alkyl chlorides

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Non-enzymatic and enzymatic hydrolysis of alkyl halides: A haloalkane dehalogenation enzyme evolved to stabilize the gas-phase transition state of an S _N 2 displacement reaction

Nonenzymatic and enzymatic hydrolysis of alkyl halides: A theoretical study of the S_N2 reactions of acetate and hydroxide ions with alkyl chlorides