1D6P image
Deposition Date 1999-10-15
Release Date 2000-01-21
Last Version Date 2024-12-25
Entry Detail
PDB ID:
1D6P
Keywords:
Title:
HUMAN LYSOZYME L63 MUTANT LABELLED WITH 2',3'-EPOXYPROPYL N,N'-DIACETYLCHITOBIOSE
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
Resolution:
2.23 Å
R-Value Free:
0.21
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:LYSOZYME
Mutations:Y63L
Chain IDs:A
Chain Length:130
Number of Molecules:1
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Protein-carbohydrate interactions in human lysozyme probed by combining site-directed mutagenesis and affinity labeling.
Biochemistry 39 292 299 (2000)
PMID: 10630988 DOI: 10.1021/bi991402q

Abstact

The synergism between apolar and polar interactions in the carbohydrate recognition by human lysozyme (HL) was probed by site-directed mutagenesis and affinity labeling. The three-dimensional structures of the Tyr63-->Leu mutant HL labeled with 2',3'-epoxypropyl beta-glycoside of N,N'-diacetylchitobiose (L63-HL/NAG-NAG-EPO complex) and the Asp102-->Glu mutant HL labeled with the 2',3'-epoxypropyl beta-glycoside of N-acetyllactosamine were revealed by X-ray diffraction at 2.23 and 1.96 A resolution, respectively. Compared to the wild-type HL labeled with the 2', 3'-epoxypropyl beta-glycoside of N,N'-diacetylchitobiose, the N-acetylglucosamine residue at subsite B of the L63-HL/NAG-NAG-EPO complex markedly moved away from the 63rd residue, with substantial loss of hydrogen-bonding interactions. Evidently, the stacking interaction with the aromatic side chain of Tyr63 is essential in positioning the N-acetylglucosamine residue in the productive binding mode. On the other hand, the position of the galactose residue in subsite B of HL is almost unchanged by the mutation of Asp102 to Glu. Most hydrogen bonds, including the one between the carboxylate group of Glu102 and the axial 4-OH group of the galactose residue, were maintained by local movement of the backbone from residues 102-104. In both structures, the conformation of the disaccharide was conserved, reflecting an intrinsic conformational rigidity of the disaccharides. The structural analysis suggested that CH-pi interactions played an important role in the recognition of the carbohydrate residue at subsite B of HL.

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Primary Citation of related structures