Structures of enzyme-substrate complexes of lysozyme

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Abstract
Conformational energy calculations were used to determine the binding structures of 2 oligosaccharides (GlcNAc)n, in which n = 5 and 6, in the rigid active site of lysozyme [henegg] (mucopeptide N-acetylmuramoylhydrolase, EC 3.2.1.17). Starting with the lowest energy binding structures of (GlcNAc)4, a 5th GlcNAc residue was added to this tetramer in 3 different conformations, corresponding to the left-handed and right-handed helical structures and an intermediate structure, and the energy of each complex was minimized. The most stable binding conformation of the 5th residue of the pentamer was closest to the left-handed helical one. During energy minimization, the 4th residue of the pentamer moved from its initial position near the surface of the active site farther into the active site cleft at binding site D. Binding structures of (GlcNAc)6 were then examined by addition of a residue to the lowest energy structure of (GlcNAc)5, and the 6th residue of the hexamer binded in a conformation again close to the left-handed helical one. Stable binding regions of the rigid active site for the 5th and 6th residues were near arginyl 45 and asparaginyl 46, on the opposite side of the active site cleft from arginyl 114. When the calculated structure of the lysozyme-(GlcNAc)4 complex (used here as the starting structure of addition of the 5th and 6th residues) is compared with recent experimental data, the calculated structure is a reasonable one. Of all binding regions available to the saccharide residues, the C site binds GlcNAc with the lowest energy, in agreement with experiments.