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Bioorg Chem. 2007 Dec;35(6):444-57. Epub 2007 Sep 27.

Quantum chemical modeling of enzymatic reactions: the case of 4-oxalocrotonate tautomerase.

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1
Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, AlbaNova University Center, SE-106 91 Stockholm, Sweden.

Abstract

The reaction mechanism of 4-oxalocrotonate tautomerase (4-OT) is studied using the density functional theory method B3LYP. This enzyme catalyzes the isomerisation of unconjugated alpha-keto acids to their conjugated isomers. Two different quantum chemical models of the active site are devised and the potential energy curves for the reaction are computed. The calculations support the proposed reaction mechanism in which Pro-1 acts as a base to shuttle a proton from the C3 to the C5 position of the substrate. The first step (proton transfer from C3 to proline) is shown to be the rate-limiting step. The energy of the charge-separated intermediate (protonated proline-deprotonated substrate) is calculated to be quite low, in accordance with measured pKa values. The results of the two models are used to evaluate the methodology employed in modeling enzyme active sites using quantum chemical cluster models.

PMID:
17904194
DOI:
10.1016/j.bioorg.2007.08.003
[Indexed for MEDLINE]
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