QM/MM study of the mechanism of enzymatic limonene 1,2-epoxide hydrolysis

Hou, Qianqian; Sheng, Xiang; Wang, J.H.; Liu, Yanjie; Liu, C.B.

doi:10.1016/j.bbapap.2011.08.014

Cited by 13 publications

(14 citation statements)

References 36 publications

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“…Epoxide‐ring opening by LEH has been studied previously by Himo and co‐workers on the basis of a quantum‐mechanical cluster model12 and by Hou et al. by QM/MM 13. Upon binding of the substrate in the active site, activation occurs by hydrogen‐bonding between the epoxide O atom and protonated aspartate (D101).…”

Section: Methodsmentioning

confidence: 99%

“…As the activation of the epoxide by D101 is considered essential for reaction, only docking poses in which this interaction is present have been considered. Furthermore, the directionality of this interaction is important 13. For the WT model, two almost degenerate binding poses of substrate 1 contain a H‐bond to the protonated D101 residue: In one pose the pro‐ R , R and in the other the pro‐ S , S carbon atom is placed close to the water molecule.…”

Section: Methodsmentioning

confidence: 99%

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Reshaping an Enzyme Binding Pocket for Enhanced and Inverted Stereoselectivity: Use of Smallest Amino Acid Alphabets in Directed Evolution

et al. 2015

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Directed evolution based on saturation mutagenesis at sites lining the binding pocket is a commonly practiced strategy for enhancing or inverting the stereoselectivity of enzymes for use in organic chemistry or biotechnology. However, as the number of residues in a randomization site increases to five or more, the screening effort for 95 % library coverage increases astronomically until it is no longer feasible. We propose the use of a single amino acid for saturation mutagenesis at superlarge randomization sites comprising 10 or more residues. When used to reshape the binding pocket of limonene epoxide hydrolase, this strategy, which drastically reduces the search space and thus the screening effort, resulted in R,R- and S,S-selective mutants for the hydrolytic desymmetrization of cyclohexene oxide and other epoxides. X-ray crystal structures and docking studies of the mutants unveiled the source of stereoselectivity and shed light on the mechanistic intricacies of this enzyme.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Reshaping an Enzyme Binding Pocket for Enhanced and Inverted Stereoselectivity: Use of Smallest Amino Acid Alphabets in Directed Evolution

et al. 2015

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“…A minor class of epoxide hydrolases, with the limonene 1,2-epoxide hydroxylase (LEH) from Rhodococcus erythropolis as a prominent example, act through a distinct mechanism. [113] LEH catalyzes the direct hydrolysis of epoxides by activating a water molecule in the active site, thereby enabling the nucleophilic attack while the oxygen atom of the oxirane leaving group is protonated by an aspartate (Figure 11 B). The proposed mechanism for HHDH involves the activation of the epoxide by hydrogen bonding, which allows the attack of a nucleophile that is expected to bind in a halide-binding pocket (Figure 11 C).…”

Section: Methodsmentioning

confidence: 99%

New Generation of Biocatalysts for Organic Synthesis

et al. 2014

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The use of enzymes as catalysts for the preparation of novel compounds has received steadily increasing attention over the past few years. High demands are placed on the identification of new biocatalysts for organic synthesis. The catalysis of more ambitious reactions reflects the high expectations of this field of research. Enzymes play an increasingly important role as biocatalysts in the synthesis of key intermediates for the pharmaceutical and chemical industry, and new enzymatic technologies and processes have been established. Enzymes are an important part of the spectrum of catalysts available for synthetic chemistry. The advantages and applications of the most recent and attractive biocatalysts--reductases, transaminases, ammonia lyases, epoxide hydrolases, and dehalogenases--will be discussed herein and exemplified by the syntheses of interesting compounds.

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“…Dabei bildet sich eine kovalente Zwischenstufe, deren Esterbindung hydrolysiert wird (Abbildung 11 a). Im Unterschied zu den Reaktionen der klassischen Epoxidhydrolasen, die über einen zweistufigen Mechanismus unter Bildung eines kovalenten Enzym‐Substrat‐Komplexes ablaufen, hydrolysiert Limonen‐1,2‐Epoxidhydrolase (LEH) ihre Substrate in einem einzigen Schritt 113. Hierbei katalysiert die LEH aus Rhodococcus erythropolis die direkte Hydrolyse des Epoxids durch die Aktivierung eines Wassermoleküls im aktiven Zentrum des Enzyms (Abbildung 11 b).…”

Section: Biokatalyse Als Alternative Zur Generierung Chiraler Epoxunclassified

Biokatalysatoren für die organische Synthese – die neue Generation

et al. 2014

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Die Verwendung von Enzymen als Katalysatoren zur Synthese neuartiger Verbindungen ist in den letzten Jahren zunehmend in den Fokus gerückt. Entsprechend hohe Erwartungen werden an die Entdeckung und Identifizierung neuer Biokatalysatoren für die organische Synthese gestellt. Dies spiegelt sich auch in der Komplexität der adressierten Reaktionen wider. Der Anwendungsbereich von Biokatalysatoren umfasst die Synthese wichtiger Zwischenprodukte für die pharmazeutische und chemische Industrie sowie die Entwicklung neuer enzymatischer Techniken und Prozesse. Enzyme sind ein wichtiger Teil des Spektrums an Katalysatoren, die der Synthesechemie zur Verfügung stehen. Die Vorteile und Anwendungsmöglichkeiten der neuesten und höchst vielversprechenden Generation von Biokatalysatoren – Reduktasen, Transaminasen, Ammoniak‐Lyasen, Epoxidhydrolasen und Dehalogenasen – werden hier vorgestellt und anhand der Synthese von Schlüsselmolekülen beispielhaft diskutiert.

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QM/MM study of the mechanism of enzymatic limonene 1,2-epoxide hydrolysis

Cited by 13 publications

References 36 publications

Reshaping an Enzyme Binding Pocket for Enhanced and Inverted Stereoselectivity: Use of Smallest Amino Acid Alphabets in Directed Evolution

Reshaping an Enzyme Binding Pocket for Enhanced and Inverted Stereoselectivity: Use of Smallest Amino Acid Alphabets in Directed Evolution

New Generation of Biocatalysts for Organic Synthesis

Biokatalysatoren für die organische Synthese – die neue Generation

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