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Catalytic mechanism of limonene epoxide hydrolase: a theoretical study
KTH, School of Biotechnology (BIO), Theoretical Chemistry.
Biophysics, Department of Medical Biochemistry and Biophysics, Karolinska Institutet.
KTH, School of Biotechnology (BIO), Theoretical Chemistry.
2005 (English)In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 127, no 41, 14339-14347 p.Article in journal (Refereed) Published
Abstract [en]

The catalytic mechanism of limonene epoxide hydrolase (LEH) was investigated theoretically using the density functional theory method B3LYP. LEH is part of a novel limonene degradation pathway found in Rhodococcus erythropolis DCL14, where it catalyzes the hydrolysis of limonene-1,2-epoxide to give limonene-1,2-diol. The recent crystal structure of LEH was used to build a model of the LEH active site composed of five amino acids and a crystallographically observed water molecule. With this model, hydrolysis of different substrates was investigated. It is concluded that LEH employs a concerted general acid/general base-catalyzed reaction mechanism involving protonation of the substrate by Asp101, nucleophilic attack by water on the epoxide, and abstraction of a proton from water by Asp132. Furthermore, we provide an explanation for the experimentally observed regioselective hydrolysis of the four stereoisomers of limonene-1,2-epoxide.

Place, publisher, year, edition, pages
2005. Vol. 127, no 41, 14339-14347 p.
Keyword [en]
Amino acids; Catalysis; Degradation; Hydrolysis; Mathematical models; Probability density function; Limonene degradation; Limonene epoxide hydrolase (LEH); Regioselective hydrolysis; Rhodococcus erythropolis DCL14
National Category
Chemical Sciences
Identifiers
URN: urn:nbn:se:kth:diva-7168DOI: 10.1021/ja050940pISI: 000232605600057Scopus ID: 2-s2.0-26844530203OAI: oai:DiVA.org:kth-7168DiVA: diva2:12095
Note
QC 20100811Available from: 2007-05-22 Created: 2007-05-22 Last updated: 2010-08-11Bibliographically approved
In thesis
1. Quantum chemical studies of epoxide-transforming enzymes
Open this publication in new window or tab >>Quantum chemical studies of epoxide-transforming enzymes
2007 (English)Licentiate thesis, comprehensive summary (Other scientific)
Abstract [en]

Density functional theory is employed to study the reaction mechanisms of different epoxide-transforming enzymes. Calculations are based on quantum chemical active site models, which are build from X-ray crystal structures. The models are used to study conversion of various epoxides into their corresponding diols or substituted alcohols. Epoxide-transforming enzymes from three different families are studied. The human soluble epoxide hydrolase (sEH) belongs to the α/β-hydrolase fold family. sEH employs a covalent mechanism to hydrolyze various epoxides into vicinal diols. The Rhodococcus erythrobacter limonene epoxide hydrolase (LEH) constitutes a novel epoxide hydrolase, which is considered the founding member of a new family of enzymes. LEH mediates transformation of limone-1,2-epoxide into the corresponding vicinal diol by employing a general acid/general base-mediated mechanism. The Agrobacterium radiobacter AD1 haloalcohol dehalogenase HheC is related to the short-chain dehydrogenase/reductases. HheC is able to convert epoxides using various nucleophiles such as azide, cyanide, and nitrite. Reaction mechanisms of these three enzymes are analyzed in depth and the role of different active site residues is studied through in silico mutations. Steric and electronic factors influencing the regioselectivity of epoxide opening are identified. The computed energetics help to explain preferred reaction pathways and experimentally observed regioselectivities. Our results confirm the usefulness of the employed computational methodology for investigating enzymatic reactions.

Place, publisher, year, edition, pages
Stockholm: KTH, 2007. x, 58 p.
Series
Trita-BIO-Report, ISSN 1654-2312 ; 2007:3
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:kth:diva-4390 (URN)978-91-7178-640-1 (ISBN)
Presentation
2007-05-11, FD41, AlbaNova, 10:00
Opponent
Supervisors
Note
QC 20101108Available from: 2007-05-22 Created: 2007-05-22 Last updated: 2010-11-08Bibliographically approved
2. Nitrile Hydratases and Epoxide-Transforming Enzymes: Quantum Chemical Modeling of Reaction Mechanisms and Selectivities
Open this publication in new window or tab >>Nitrile Hydratases and Epoxide-Transforming Enzymes: Quantum Chemical Modeling of Reaction Mechanisms and Selectivities
2008 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Quantum chemical studies of enzymatic reactions are able to provide detailed insight into mechanisms and catalytic strategies. The energetic feasibility of proposed mechanisms can be established, and new possible reaction pathways can be put forward. The role of the involved active site residues can be analyzed in detail and the origins for experimentally observed selectivities can be investigated. Density functional theory (DFT), in particular the hybrid functional B3LYP, is the method of choice in this kind of studies.

In this thesis, the reaction mechanisms of several enzymes have been explored using the B3LYP functional. The studied enzymes include limonene epoxide hydrolase (LEH), soluble epoxide hydrolase (sEH), haloalcohol dehalogenase (HheC), and nitrile hydratase (NHase). Transition states and intermediates along various reaction pathways were optimized and evaluated.

For the three epoxide-transforming enzymes, the role of the proposed catalytic residues could be confirmed. Analysis of in silico mutations helped to quantify the effect of various functional groups on the barriers and regioselectivities of epoxide opening. A detailed analysis of the factors governing the enzymatic regioselectivities is given.

For nitrile hydratase, various putative first- and second-shell mechanisms have been studied. Active site models based on both the Co(III)-NHase and the Fe(III)-NHase were employed. The studied mechanisms include general base-catalyzed reaction pathways with water as nucleophile as well as two pathways involving cysteine-sulfenate as nucleophile. Several computed mechanisms exhibit similar barriers, making it difficult to pinpoint the true NHase mechanism.

Place, publisher, year, edition, pages
Stockholm: KTH, 2008. x, 74 p.
Series
Trita-BIO-Report, ISSN 1654-2312 ; 2008:1
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:kth:diva-4668 (URN)978-91-7178-885-6 (ISBN)
Public defence
2008-04-04, FB52, AlbaNova, Roslagstullsbacken 21, Stockholm, 10:30
Opponent
Supervisors
Note
QC 20100811Available from: 2008-03-18 Created: 2008-03-18 Last updated: 2010-08-11Bibliographically approved

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