Quantum Chemical Studies of the Catalytic Mechanism of N-Terminal Nucleophile Hydrolase

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G. G. Chilov¹, A. V. Sidorova², and V. K. Svedas^1,2**

¹Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia

² Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119992 Moscow, Russia; fax: (495) 939-2355;; E-mail: vytas@belozersky.msu.ru

^* To whom correspondence should be addressed.

Received December 29, 2006; Revision received February 9, 2007

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Modeling of the catalytic mechanism of penicillin acylase, a member of the N-terminal nucleophile hydrolase superfamily, is for the first time conducted at ab initio quantum chemistry level. The uniqueness of this family of enzymes is that their active site lacks His and Asp (Glu) residues, comprising together with a serine residue the classical catalytic triad. The current investigation confirms that the amino group of the N-terminal serine residue in N-terminal hydrolases is capable of activating its own hydroxyl group. Using the MP2/RHF method with the 6--31+G** basis set, stationary points on the potential energy surface of the considered molecular system were located, corresponding to local minima (complexes of reagents, products, intermediate) and to saddle points (transition states). It turned out that the stage of acyl-serine formation proceeds via two transition states; the first one, which separates reagents from the so-called tetrahedral intermediate, has the highest relative energy (30 kcal/mol). In contrast to recently proposed empiric suggestions, we have found that participation of a bridging water molecule in proton shuttling is not necessary for the catalysis. The quantum chemical calculations showed a crucial role of a specific solvation in decreasing the activation barrier of the reaction by approximately 10 kcal/mol.

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KEY WORDS: penicillin acylase, Ntn-hydrolase, catalytic mechanism, quantum chemistry

DOI: 10.1134/S0006297907050057

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