4.2.1.127: linalool dehydratase
This is an abbreviated version!
For detailed information about linalool dehydratase, go to the full flat file.
Word Map on EC 4.2.1.127
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4.2.1.127
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castellaniella
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defragrans
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isomerization
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monoterpene
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acyclic
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s-+-linalool
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alkene
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in-frame
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terpene
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betaproteobacterium
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beta-myrcene
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biotechnology
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synthesis
- 4.2.1.127
- castellaniella
- defragrans
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isomerization
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monoterpene
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acyclic
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s-+-linalool
- alkene
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in-frame
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terpene
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betaproteobacterium
- beta-myrcene
- biotechnology
- synthesis
Reaction
Synonyms
bifunctional linalool dehydratase isomerase, LDI, ldi/LDI, linalool dehydratase isomerase, linalool dehydratase-isomerase, linalool dehydratase/isomerase, LinD, LIS, More
ECTree
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General Information
General Information on EC 4.2.1.127 - linalool dehydratase
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malfunction
metabolism
physiological function
additional information
an in-frame deletion mutant with an inactivated ldi gene shows no growth with the acyclic beta-myrcene, but grows like the wild type on limonene or alpha-phellandrene
malfunction
deletion of gene ldi affects growth on acyclic monoterpenes, e.g. beta-myrcene, phenotype, overview
malfunction
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deletion of gene ldi affects growth on acyclic monoterpenes, e.g. beta-myrcene, phenotype, overview
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malfunction
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an in-frame deletion mutant with an inactivated ldi gene shows no growth with the acyclic beta-myrcene, but grows like the wild type on limonene or alpha-phellandrene
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beta-myrcene is enantiospecifically hydrated to (S)-(+)-linalool and further isomerized to geraniol by the linalool dehydrataseisomerase
metabolism
the bifunctional linalool dehydratase-isomerase ldi/LDI is the initial enzyme in the anaerobic beta-myrcene degradation pathway and catalyzes the hydration of beta-myrcene to (S)-(+)-linalool and its isomerization to geraniol. A high-affinity geraniol dehydrogenase geoA/GeDH and a geranial dehydrogenase geoB/GaDH contribute to the formation of geranic acid
metabolism
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the bifunctional linalool dehydratase-isomerase ldi/LDI is the initial enzyme in the anaerobic beta-myrcene degradation pathway and catalyzes the hydration of beta-myrcene to (S)-(+)-linalool and its isomerization to geraniol. A high-affinity geraniol dehydrogenase geoA/GeDH and a geranial dehydrogenase geoB/GaDH contribute to the formation of geranic acid
metabolism
the enzyme is responsible for the first two steps in myrcene degradation in Castellaniella defragrans as geraniol is further oxidized shifting the reaction equilibrium
metabolism
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the enzyme is responsible for the first two steps in myrcene degradation in Castellaniella defragrans as geraniol is further oxidized shifting the reaction equilibrium
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metabolism
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the bifunctional linalool dehydratase-isomerase ldi/LDI is the initial enzyme in the anaerobic beta-myrcene degradation pathway and catalyzes the hydration of beta-myrcene to (S)-(+)-linalool and its isomerization to geraniol. A high-affinity geraniol dehydrogenase geoA/GeDH and a geranial dehydrogenase geoB/GaDH contribute to the formation of geranic acid
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metabolism
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beta-myrcene is enantiospecifically hydrated to (S)-(+)-linalool and further isomerized to geraniol by the linalool dehydrataseisomerase
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essential requirement of the linalool dehydratase-isomerase for growth on acyclic monoterpenes, e.g. beta-myrcene, but not on cyclic monoterpenes, e.g. cyclic alpha-phellandrene or limonene
physiological function
linalool dehydratase/isomerase (Ldi), an enzyme of terpene degradation in Castellaniella defragrans, isomerizes the primary monoterpene alcohol geraniol into the tertiary alcohol (3S)-linalool and dehydrates (3S)-linalool to the alkene beta-myrcene
physiological function
the bifunctional linalool dehydratase isomerase (LinD) from the bacterium Castellaniella defragrans catalyzes in nature the hydration of beta-myrcene to (3S)-linalool and the subsequent isomerization to geraniol
physiological function
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linalool dehydratase/isomerase (Ldi), an enzyme of terpene degradation in Castellaniella defragrans, isomerizes the primary monoterpene alcohol geraniol into the tertiary alcohol (3S)-linalool and dehydrates (3S)-linalool to the alkene beta-myrcene
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physiological function
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essential requirement of the linalool dehydratase-isomerase for growth on acyclic monoterpenes, e.g. beta-myrcene, but not on cyclic monoterpenes, e.g. cyclic alpha-phellandrene or limonene
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growth on cyclic monoterpenes independent of the initial enzyme linalool dehydratase suggests the presence of a second enzyme system activating unsaturated hydrocarbons
additional information
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growth on cyclic monoterpenes independent of the initial enzyme linalool dehydratase suggests the presence of a second enzyme system activating unsaturated hydrocarbons
additional information
catalytic mechanism of enzyme LinD by a combined quantum mechanics and molecular mechanics (QM/MM), computational modeling resulting in two models. Model I (LinD-linalool) is derived from the crystal structure of the selenomethionine derivative of LinD (SeMet-LinD) in complex with the natural substrate geraniol, whereas model II (LinD-beta-myrcene) is constructed from the crystal structure of LinD in complex with beta-myrcene. Model II as the active one, which implies that hydration and dehydration are sensitive to the protonation state and fine structure of the active site: Firstly, beta-myrcene is hydrated by a crystal water (W14) and is converted into the stable intermediate (3S)-linalool, then linalool is isomerized to geraniol with an overall energy barrier of 24.6 kcal/mol. Besides, linalool can also reversibly convert into the reactant with an energy barrier of 24.1 kcal/mol. The intermediate IM1 can directly transform to geraniol without first converting to (3S)-linalool. His128 and Tyr65 form hydrogen bonds to stabilize the structure of the active site, but they do not act as general acid/base catalysts during the catalytic reactions
additional information
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catalytic mechanism of enzyme LinD by a combined quantum mechanics and molecular mechanics (QM/MM), computational modeling resulting in two models. Model I (LinD-linalool) is derived from the crystal structure of the selenomethionine derivative of LinD (SeMet-LinD) in complex with the natural substrate geraniol, whereas model II (LinD-beta-myrcene) is constructed from the crystal structure of LinD in complex with beta-myrcene. Model II as the active one, which implies that hydration and dehydration are sensitive to the protonation state and fine structure of the active site: Firstly, beta-myrcene is hydrated by a crystal water (W14) and is converted into the stable intermediate (3S)-linalool, then linalool is isomerized to geraniol with an overall energy barrier of 24.6 kcal/mol. Besides, linalool can also reversibly convert into the reactant with an energy barrier of 24.1 kcal/mol. The intermediate IM1 can directly transform to geraniol without first converting to (3S)-linalool. His128 and Tyr65 form hydrogen bonds to stabilize the structure of the active site, but they do not act as general acid/base catalysts during the catalytic reactions
additional information
structure of LinD in complex with the prodxaduct geraniol, structure-function relationship, overview. Cys171 is well positioned to protonate the linalool hydroxyl of the (S)-configuration, and a covalent LinD-terpene complex is formed as the hydroxyl is eliminated as water. The covalent intermediate underxadgoes either hydrolysis, by a water molecule activated by His129, to give geraniol in an isomerization reaction, or base-catalyzed elimixadnation, most likely by Asp39 or Tyr45 at the methyl group, to give myrcene in a dehydration process. In the second proposal, involvxading a carbocation intermediate, Cys180 does not interact directly with the substrate terminal C=C double bond. Dehydration of (3S)-linalool, catalyzed by Cys171, results in a carbocation intermediate that undergoes either rehydration, catalyzed by His129 or Cys180 to form geraniol, or base-catalyzed deprotonation to form myrcene by Tyr45 and Asp39
additional information
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structure of LinD in complex with the prodxaduct geraniol, structure-function relationship, overview. Cys171 is well positioned to protonate the linalool hydroxyl of the (S)-configuration, and a covalent LinD-terpene complex is formed as the hydroxyl is eliminated as water. The covalent intermediate underxadgoes either hydrolysis, by a water molecule activated by His129, to give geraniol in an isomerization reaction, or base-catalyzed elimixadnation, most likely by Asp39 or Tyr45 at the methyl group, to give myrcene in a dehydration process. In the second proposal, involvxading a carbocation intermediate, Cys180 does not interact directly with the substrate terminal C=C double bond. Dehydration of (3S)-linalool, catalyzed by Cys171, results in a carbocation intermediate that undergoes either rehydration, catalyzed by His129 or Cys180 to form geraniol, or base-catalyzed deprotonation to form myrcene by Tyr45 and Asp39
additional information
the active site of the enzyme is proposed to be located at the interface of two neighboring monomers and, therefore, to be made up of amino acid residues M125, C171, C180, H129, Q179 and Y420 from chain A and D39 and Y45 from chain B. Residues Y45, M125, H129, C171 and C180 are involved in the mechanism of the isomerization of geraniol as well as the dehydration of linalool. Reaction mechanisms, one via a covalent intermediate, and one acid-base mechanism via a carbocation intermediate. In both cases, C171, Y45 and D39 act as general acid and base for the protonation of the hydroxyl leaving group of the substrate (S)-linalool and the dehydration at the chiral carbon atom. Water is activated by H129 or C180 and added to the covalent or carbocation intermediate
additional information
the substrates are embedded inside a hydrophobic channel between two monomers of the (alpha,alpha)6 barrel fold class and flanked by three clusters of polar residues involved in acid-base catalysis, modelling of the cytosolic enzyme domain. The substrate binding site in (alpha,alpha)6 barrel enzymes is embedded inside a cavity at the barrel entrance whereas the substrate cavity in Ldi is partly capped by the irregular segment 36'-52' of the neighbor monomer of the homopentamer
additional information
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the substrates are embedded inside a hydrophobic channel between two monomers of the (alpha,alpha)6 barrel fold class and flanked by three clusters of polar residues involved in acid-base catalysis, modelling of the cytosolic enzyme domain. The substrate binding site in (alpha,alpha)6 barrel enzymes is embedded inside a cavity at the barrel entrance whereas the substrate cavity in Ldi is partly capped by the irregular segment 36'-52' of the neighbor monomer of the homopentamer
additional information
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the active site of the enzyme is proposed to be located at the interface of two neighboring monomers and, therefore, to be made up of amino acid residues M125, C171, C180, H129, Q179 and Y420 from chain A and D39 and Y45 from chain B. Residues Y45, M125, H129, C171 and C180 are involved in the mechanism of the isomerization of geraniol as well as the dehydration of linalool. Reaction mechanisms, one via a covalent intermediate, and one acid-base mechanism via a carbocation intermediate. In both cases, C171, Y45 and D39 act as general acid and base for the protonation of the hydroxyl leaving group of the substrate (S)-linalool and the dehydration at the chiral carbon atom. Water is activated by H129 or C180 and added to the covalent or carbocation intermediate
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additional information
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the substrates are embedded inside a hydrophobic channel between two monomers of the (alpha,alpha)6 barrel fold class and flanked by three clusters of polar residues involved in acid-base catalysis, modelling of the cytosolic enzyme domain. The substrate binding site in (alpha,alpha)6 barrel enzymes is embedded inside a cavity at the barrel entrance whereas the substrate cavity in Ldi is partly capped by the irregular segment 36'-52' of the neighbor monomer of the homopentamer
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additional information
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growth on cyclic monoterpenes independent of the initial enzyme linalool dehydratase suggests the presence of a second enzyme system activating unsaturated hydrocarbons
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