Structures of enzyme-substrate complexes of lysozyme.
Conformational energy calculations were used to determine the binding structures of two oligosaccharides (GlcNAc)(n), in which n = 5 and 6, in the rigid active site of lysozyme (mucopeptide N-acetylmuramoylhydrolase, EC 3.2.1.17). Starting with the lowest energy binding structures of (GlcNAc)(4) as determined in a previous publication, we added a fifth GlcNAc residue to this tetramer in three 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 fifth residue of the pentamer was closest to the left-handed helical one. During energy minimization, the fourth 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 it was found that the sixth residue of the hexamer binds in a conformation again close to the left-handed helical one. Stable binding regions of the rigid active site for the fifth and sixth residues were found to be 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 for addition of the fifth and sixth residues) is compared with recent experimental data, it is found that 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.
D000117:Acetylglucosamine / Q000378:metabolism; D000818:Animals; D001665:Binding Sites; D002645:Chickens; D005260:Female; D005944:Glucosamine / Q000031:analogs & derivatives; D008958:Models, Molecular; D009113:Muramidase / Q000378:metabolism; D009844:Oligosaccharides / Q000378:metabolism; D011487:Protein Conformation; D013329:Structure-Activity Relationship; D013816:Thermodynamics
D009844:Oligosaccharides; D009113:Muramidase; D005944:Glucosamine; D000117:Acetylglucosamine
Biochemistry. 1977 Feb 8;16(3):423-31
13816
Proc Natl Acad Sci U S A. 1976 Dec;73(12):4261-5
1069981
Biopolymers. 1976 Dec;15(12NA-NA-770103-770104):2485-521
1000053
J Mol Biol. 1976 Oct 5;106(4):1037-46
988188
Proc R Soc Lond B Biol Sci. 1967 Apr 18;167(1009):378-88
4382801
J Mol Biol. 1974 Sep 15;88(2):349-71
4453000
J Mol Biol. 1976 May 15;103(2):227-49
985660
Biochemistry. 1975 Mar 11;14(5):1088-94
1125174