Probing stereoselectivity and pro-chirality of hydride transfer during short-chain alcohol dehydrogenase activity: A combined quantitative 2H NMR and computational approach

Kwiecień, Renata A.; Ayadi, Farouk; Nemmaoui, Youssef; Silvestre, Virginie; Zhang, Ben‐Li; Robins, Richard J.

doi:10.1016/j.abb.2008.11.019

Cited by 6 publications

(4 citation statements)

References 40 publications

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“…Moreover, the focus of these studies was mainly on the kinetic isotopic effect associated with H − transfer. Surprisingly, the theoretical studies of SDRs were much less frequent [30, 36–38, 45, 46] and we were unable to find works that investigated the mechanism with DFT methods. Therefore, despite the abundant literature on SDR, it seems that our paper might be one of the first, that addresses the mechanism with DFT calculations.…”

Section: Discussionmentioning

confidence: 93%

DFT-based prediction of reactivity of short-chain alcohol dehydrogenase

Stawoska

Dudzik

Wasylewski

et al. 2017

J Comput Aided Mol Des

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The reaction mechanism of ketone reduction by short chain dehydrogenase/reductase, (S)-1-phenylethanol dehydrogenase from Aromatoleum aromaticum, was studied with DFT methods using cluster model approach. The characteristics of the hydride transfer process were investigated based on reaction of acetophenone and its eight structural analogues. The results confirmed previously suggested concomitant transfer of hydride from NADH to carbonyl C atom of the substrate with proton transfer from Tyr to carbonyl O atom. However, additional coupled motion of the next proton in the proton-relay system, between O2′ ribose hydroxyl and Tyr154 was observed. The protonation of Lys158 seems not to affect the pKa of Tyr154, as the stable tyrosyl anion was observed only for a neutral Lys158 in the high pH model. The calculated reaction energies and reaction barriers were calibrated by calorimetric and kinetic methods. This allowed an excellent prediction of the reaction enthalpies (R2 = 0.93) and a good prediction of the reaction kinetics (R2 = 0.89). The observed relations were validated in prediction of log K eq obtained for real whole-cell reactor systems that modelled industrial synthesis of S-alcohols.Electronic supplementary materialThe online version of this article (doi:10.1007/s10822-017-0026-5) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 93%

DFT-based prediction of reactivity of short-chain alcohol dehydrogenase

Stawoska

Dudzik

Wasylewski

et al. 2017

J Comput Aided Mol Des

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“…These results support the hypothesis that SDRs enzymes are pro‐S, whereas the metal dependent medium‐chain ADH are pro‐R (Schneider‐Bernlohr et al, ). Structural studies on alcohol dehydrogenases from Saccharomyces cerevisiae and L. brevis described that the stereoselectivity of the reaction center had no correlation with the presence/absence of metal, the use of NADH or NADPH as cofactor or the size of the substrate that can be accepted (Kwiecien et al, ). The stereoselectivity is probably defined by the geometry of the active site (Kwiecien et al, ).…”

Section: Discussionmentioning

confidence: 99%

“…Structural studies on alcohol dehydrogenases from Saccharomyces cerevisiae and L. brevis described that the stereoselectivity of the reaction center had no correlation with the presence/absence of metal, the use of NADH or NADPH as cofactor or the size of the substrate that can be accepted (Kwiecien et al, ). The stereoselectivity is probably defined by the geometry of the active site (Kwiecien et al, ). In the docking and molecular structure studies we found that the S‐conformation allowed interactions with the 2C of the substrate and permit transference of hydrogen to the nicotinamide ring of NADP + ; in contrast the hydrogen in the R‐substrate is facing the opposite direction and prevents the interaction with the NADP + ring.…”

Section: Discussionmentioning

confidence: 99%

Functional Analysis of a Mosquito Short‐chain Dehydrogenase Cluster

Mayoral

Leonard

Nouzová

et al. 2012

Arch Insect Biochem Physiol

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The short chain dehydrogenases (SDR) constitute one the oldest and largest families of enzymes with over 46,000 members in sequence databases. About 25% of all known dehydrogenases belong to the SDR family. SDR enzymes have critical roles in lipid, amino acid, carbohydrate, hormone and xenobiotic metabolism as well as in redox sensor mechanisms. This family is present in archaea, bacteria, and eukaryota, emphasizing their versatility and fundamental importance for metabolic processes. We identified a cluster of eight SDRs in the mosquito Aedes aegypti (AaSDRs). Members of the cluster differ in tissue specificity and developmental expression. Heterologous expression produced recombinant proteins that had diverse substrate specificities, but distinct from the conventional insect alcohol (ethanol) dehydrogenases. They are all NADP+-dependent and they have S-enantioselectivity and preference for secondary alcohols with 8–15 carbons. Homology modeling was used to build the structure of AaSDR1 and two additional cluster members. The computational study helped explain the selectivity towards the (10S)-isomers as well as the reduced activity of AaSDR4 and AaSDR9 for longer isoprenoid substrates. Similar clusters of SDRs are present in other species of insects, suggesting similar selection mechanisms causing duplication and diversification of this family of enzymes.

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“…30,31) Rather, the specificity and stereoselectivity were probably defined by the geometry of the active site, resulting from X-ray crystallographic studies. 32) Therefore, the enzyme set, consisting of Gox2036, Gox0525, Gox1615, Gox0644, Gox1462, Gox1598, and Gox0290, was assembled so as to investigate their substrate selectivity and stereoselectivity toward the reduction of ketones.…”

Section: Selection Of Carbonyl Reductases and Analysis Of The Sequencesmentioning

confidence: 99%

A genomic search approach to identify carbonyl reductases in Gluconobacter oxydans for enantioselective reduction of ketones

Chen

Liu

Lin

et al. 2014

Bioscience, Biotechnology, and Biochemistry

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The versatile carbonyl reductases from Gluconobacter oxydans in the enantioselective reduction of ketones to the corresponding alcohols were exploited by genome search approach. All purified enzymes showed activities toward the tested ketoesters with different activities. In the reduction of 4-phenyl-2-butanone with in situ NAD(P)H regeneration system, (S)-alcohol was obtained with an e.e. of up to 100% catalyzed by Gox0644. Under the same experimental condition, all enzymes catalyzed ethyl 4-chloroacetoacetate to give chiral products with an excellent e.e. of up to 99%, except Gox0644. Gox2036 had a strict requirement for NADH as the cofactor and showed excellent enantiospecificity in the synthesis of ethyl (R)-4-chloro-3-hydroxybutanoate. For the reduction of ethyl 2-oxo-4-phenylbutyrate, excellent e.e. (>99%) and high conversion (93.1%) were obtained by Gox0525, whereas the other enzymes showed relatively lower e.e. and conversions. Among them, Gox2036 and Gox0525 showed potentials in the synthesis of chiral alcohols as useful biocatalysts.

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Probing stereoselectivity and pro-chirality of hydride transfer during short-chain alcohol dehydrogenase activity: A combined quantitative 2H NMR and computational approach

Cited by 6 publications

References 40 publications

DFT-based prediction of reactivity of short-chain alcohol dehydrogenase

DFT-based prediction of reactivity of short-chain alcohol dehydrogenase

Functional Analysis of a Mosquito Short‐chain Dehydrogenase Cluster

A genomic search approach to identify carbonyl reductases in Gluconobacter oxydans for enantioselective reduction of ketones

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