1D6P

HUMAN LYSOZYME L63 MUTANT LABELLED WITH 2',3'-EPOXYPROPYL N,N'-DIACETYLCHITOBIOSE

Summary for 1D6P

• Entry DOI: 10.2210/pdb1d6p/pdb
• Related: 1D6Q 1REY
• Descriptor: LYSOZYME, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, ... (4 entities in total)
• Functional Keywords: lysozyme, muramidase, hydrolase (o-glycosyl), site-directed mutagenesis, n, n'-diacetylchitobiose, affinity labeling, hydrolase
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 1
• Total formula weight: 15187.17

Authors

Muraki, M.,Harata, K.,Sugita, N.,Sato, K. (deposition date: 1999-10-15, release date: 2000-01-21, Last modification date: 2021-11-03)

Primary citation

Muraki, M.,Harata, K.,Sugita, N.,Sato, K.I.
Protein-carbohydrate interactions in human lysozyme probed by combining site-directed mutagenesis and affinity labeling.
Biochemistry, 39:292-299, 2000

PubMed Abstract: 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.

PubMed: 10630988
DOI: 10.1021/bi991402q

Experimental method

X-RAY DIFFRACTION (2.23 Å)