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Journal of Biochemistry Advance Access published online on October 9, 2008
Journal of Biochemistry, doi:10.1093/jb/mvn133
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© 2008 The Japanese Biochemical Society

Catalytic reaction mechanism of goose egg-white lysozyme by molecular modeling of enzyme-substrate complex

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

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

Corresponding author: Satoru Kuhara, Ph.D. Mailing address: 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan. Telephone number: +81-92-642-3043, Fax number: +81-92-642-3043; E-mail address: 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, GEL-(GlcNAc)6 complexes were modeled and compared with HEL-(GlcNAc)6 complexes.

By systematic conformational search, 48 GEL-(GlcNAc)6 complexes were modeled. The right- and left-side, and the amino acid residues in subsites E - G were identified in GEL. The GlcNAc residue D could bind toward 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: goose-type lysozyme, binding simulation, systematic conformational search, molecular dynamics simulation, inverting enzyme


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