Catalytic reaction mechanism of goose egg-white lysozyme by molecular modelling of enzyme-substrate complex.
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.
Hirakawa
Hideki
H
Kyushu University, Hakozaki, Higashi-ku, Fukuoka, Japan.
Ochi
Atsuko
A
Kawahara
Yoshihiro
Y
Kawamura
Shunsuke
S
Torikata
Takao
T
Kuhara
Satoru
S
D000117:Acetylglucosamine / Q000737:chemistry; D000818:Animals; D001665:Binding Sites; D002384:Catalysis; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D005777:Geese / Q000378:metabolism; D007700:Kinetics; D008958:Models, Molecular; D009113:Muramidase / Q000737:chemistry* / Q000378:metabolism; D011487:Protein Conformation
C421864:hen egg lysozyme; D009113:Muramidase; D000117:Acetylglucosamine