EC Number   |
General Information |
Reference |
|---|
   4.2.1.127 | malfunction |
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 |
-, 729502 |
| 4.2.1.127 | malfunction |
deletion of gene ldi affects growth on acyclic monoterpenes, e.g. beta-myrcene, phenotype, overview |
-, 719178 |
| 4.2.1.127 | metabolism |
beta-myrcene is enantiospecifically hydrated to (S)-(+)-linalool and further isomerized to geraniol by the linalool dehydrataseisomerase |
-, 729502 |
| 4.2.1.127 | 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 |
-, 719178, 731033 |
| 4.2.1.127 | 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 |
-, 747625 |
| 4.2.1.127 | more |
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 |
748867 |
| 4.2.1.127 | more |
growth on cyclic monoterpenes independent of the initial enzyme linalool dehydratase suggests the presence of a second enzyme system activating unsaturated hydrocarbons |
-, 719178 |
| 4.2.1.127 | more |
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 |
748734 |
| 4.2.1.127 | more |
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 |
-, 747625 |
| 4.2.1.127 | more |
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 |
-, 747771 |
