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On the Role of Tyrosine as Catalytic Base in Nitrile Hydratase
KTH, School of Biotechnology (BIO), Theoretical Chemistry.
KTH, School of Biotechnology (BIO), Theoretical Chemistry.
2008 (English)In: European Journal of Inorganic Chemistry, ISSN 1434-1948, E-ISSN 1099-0682, no 22, 3452-3459 p.Article in journal (Refereed) Published
Abstract [en]

Nitrile Hydratases (NHases) catalyze the conversion of nitriles to their corresponding amides. Two NHase classes exist, the Fe-III-NHases and the Co-III-NHases. Both harbour an intriguing active site, with a low-spin metal ion coordinated to deprotonated back-bone amides and oxidized cysteine residues. So far it has not been possible to conclusively determine the reaction mechanism of NHase. Here we employ density functional theory to investigate the recent proposal that a fully conserved second-shell tyrosine residue is the catalytic base of nitrile hydratase (J. Biol. Chem. 2007, 282, 7397-7404). In the proposed mechanism, the tyrosine is suggested to be in the tyrosinate state and to mediate nitrile hydration through activation of a water molecule, which attacks the metal-bound substrate. We have explored this mechanism employing quantum chemical active site models on the basis of the Co-III-NHase from P. thermophila JCM 3095 and the Fe-III-NHase from R. erythropolis N-771. Potential energy curves and optimized transition states are presented. The computed barriers for the two models are a few kcal/mol above the experimental value, indicating that the conserved second-shell tyrosine could function as the catalytic base of NHase. To further evaluate the likelihood of this mechanism, we estimated the pK(a) value of the second-shell tyrosine in each model. We also provide estimates of the energy involved in the exchange of a metal-bound water molecule with a nitrile substrate.

Place, publisher, year, edition, pages
2008. no 22, 3452-3459 p.
Keyword [en]
nitrile hydratase; enzyme catalysis; density functional theory; reaction mechanism
National Category
Chemical Sciences
Identifiers
URN: urn:nbn:se:kth:diva-8110DOI: 10.1002/ejic.200800250ISI: 000258681100007Scopus ID: 2-s2.0-53249111521OAI: oai:DiVA.org:kth-8110DiVA: diva2:13341
Note
QC 20100811. Uppdaterad från manuskript till artikel (20100811).Available from: 2008-03-18 Created: 2008-03-18 Last updated: 2010-08-11Bibliographically approved
In thesis
1. 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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