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Journal of Biochemistry Advance Access originally published online on October 9, 2008
Journal of Biochemistry 2008 144(6):753-761; doi:10.1093/jb/mvn133
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© The Authors 2008. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved

Catalytic Reaction Mechanism of Goose Egg-white Lysozyme by Molecular Modelling of Enzyme–Substrate Complex

Hideki Hirakawa1, Atsuko Ochi2, Yoshihiro Kawahara2, Shunsuke Kawamura3, Takao Torikata3 and Satoru Kuhara1,2,*

1Faculty of Agriculture; 2Graduate School of Genetic Resources Technology, Kyushu University, Hakozaki, Higashi-ku, Fukuoka 812-8581; and 3Department of Bioscience, School of Agriculture, Tokai University, Aso, Kumamoto 869-1404, Japan

*To whom correspondence should be addressed. Tel: +81-92-642-3043, Fax: +81-92-642-3043, E-mail: kuhara{at}grt.kyushu-u.ac.jp

Received July 7, 2008; Accepted September 17, 2008


  Abstract

Despite the low similarity between their amino acid sequences, the core structures of the fold between chicken-type and goose-type lysozymes are conserved. However, their enzymatic activities are quite different. Both of them exhibit hydrolytic activities, but the goose-type lysozyme does not exhibit transglycosylation activity. The chicken-type lysozyme has a retaining-type reaction mechanism, while the reaction mechanism of the goose-type lysozyme has not been clarified. To clarify the latter mechanism, goose egg-white lysozyme (GEL)–N-acetyl-D-glucosamine (GlcNAc)6 complexes were modelled and compared with hen egg-white lysozyme (HEL)–(GlcNAc)6 complexes. By systematic conformational search, 48 GEL–(GlcNAc)6 complexes were modelled. The right and left side, and the amino acid residues in subsites E–G were identified in GEL. The GlcNAc residue D could bind towards the right side without distortion and there was enough room for a water molecule to attack the C1 carbon of GlcNAc residue D from {alpha}-side in the right side and not for acceptor molecule. The result of molecular dynamics simulation suggests that GEL would be an inverting enzyme, and Asp97 would act as a second carboxylate and that the narrow space of the binding cleft at subsites E–G in GEL may prohibit the sugar chain to bind alternative site that might be essential for transglycosylation.

Key Words: binding simulation, goose-type lysozyme, inverting enzyme, molecular dynamics simulation, systematic conformational search

Abbreviations: GEL, goose egg-white lysozyme; HEL, hen egg-white lysozyme; GlcNAc, N-acetyl-D-glucosamine; MD, molecular dynamics


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