Chlorine Kinetic Isotope Effects on the Haloalkane Dehalogenase Reaction

Lewandowicz, Andrzej; Rudziński, Juliusz; Tronstad, Lisa; Widersten, Mikael; Ryberg, Per; Matsson, Olle; Paneth, Piotr

doi:10.1021/ja003503d

Cited by 49 publications

(56 citation statements)

References 63 publications

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“…An approach to further constrain this variability is to calculate reference values for a specific reaction acting on a specific molecule. This approach is only feasible if the structure of the transition state is sufficiently known, as was shown recently for chlorine isotope effects associated with dehalogenation of chlorinated alkanes by a haloalkane dehalogenase (106). A good agreement between calculated and experimental values was observed.…”

Section: Implications and Future Research Needsmentioning

confidence: 63%

A New Concept Linking Observable Stable Isotope Fractionation to Transformation Pathways of Organic Pollutants

Elsner

Zwank

Hunkeler

et al. 2005

Environ. Sci. Technol.

502

803

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Measuring stable isotope fractionation of carbon, hydrogen, and other elements by Compound Specific Isotope Analysis (CSIA) is a new, innovative approach to assess organic pollutant degradation in the environment. Central to this concept is the Rayleigh equation which relates degradation-induced decreases in concentrations directly to concomitant changes in bulk () average over the whole compound) isotope ratios. The extent of in situ transformation may therefore be inferred from measured isotope ratios in field samples, provided that an appropriate enrichment factor ( bulk ) is known. This bulk value, however, is usually only valid for a specific compound and for specific degradation conditions. Therefore, a direct comparison of bulk values for different compounds and for different types of reactions has in general not been feasible. In addition, it is often uncertain how robust and reproducible bulk values are and how confidently they can be used to quantify contaminant degradation in the field. To improve this situation and to achieve a more in-depth understanding, this critical review aims to relate fundamental insight about kinetic isotope effects (KIE) found in the physico(bio)chemical literature to apparent kinetic isotope effects (AKIE) derived from bulk values reported in environmentally oriented studies. Starting from basic rate laws, a quite general derivation of the Rayleigh equation is given, resulting in a novel set of simple equations that take into account the effects of (1) nonreacting positions and (2) intramolecular competition and that lead to position-specific AKIE values rather than bulk enrichment factors. Reevaluation of existing bulk literature values result in consistent ranges of AKIE values that generally are in good agreement with previously published data in the (bio)-chemical literature and are typical of certain degradation reactions (subscripts C and H indicate values for carbon and hydrogen): AKIE C ) 1.01-1.03 and AKIE H ) 2-23 for oxidation of C-H bonds; AKIE C ) 1.03-1.07 for S N 2-

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Section: Implications and Future Research Needsmentioning

confidence: 63%

A New Concept Linking Observable Stable Isotope Fractionation to Transformation Pathways of Organic Pollutants

Elsner

Zwank

Hunkeler

et al. 2005

Environ. Sci. Technol.

502

803

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“…47,116,169,217,220,[223][224][225][226][227][228][229] Bruice and co-workers have focused on identifying enzyme configurations that are most suitable for the nucleophilic attack. 116,227 However, Shurki et al suggested that these near attack conformations do not make important contributions to catalysis.…”

Section: Desolvation and Reactant State Effectsmentioning

confidence: 99%

Mechanisms and Free Energies of Enzymatic Reactions

Gao¹,

Ma²,

Major³

et al. 2006

ChemInform

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“…[23][24][25][26] The activation barrier for the reaction between acetate and DCE was calculated to be about 23 kcal mol À1 in the gas phase. Solvent effects have a pronounced influence on the barrier for the reaction.…”

Section: Introductionmentioning

confidence: 99%

The Catalytic Mechanism of Fluoroacetate Dehalogenase: A Computational Exploration of Biological Dehalogenation

Kamachi

Nakayama

Shitamichi

et al. 2009

Chemistry A European J

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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 10 800 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 alpha-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 His149, 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.

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Chlorine Kinetic Isotope Effects on the Haloalkane Dehalogenase Reaction

Cited by 49 publications

References 63 publications

A New Concept Linking Observable Stable Isotope Fractionation to Transformation Pathways of Organic Pollutants

A New Concept Linking Observable Stable Isotope Fractionation to Transformation Pathways of Organic Pollutants

Mechanisms and Free Energies of Enzymatic Reactions

The Catalytic Mechanism of Fluoroacetate Dehalogenase: A Computational Exploration of Biological Dehalogenation

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