1RE2

HUMAN LYSOZYME LABELLED WITH TWO 2',3'-EPOXYPROPYL BETA-GLYCOSIDE OF N-ACETYLLACTOSAMINE

Summary for 1RE2

• Entry DOI: 10.2210/pdb1re2/pdb
• Descriptor: PROTEIN (LYSOZYME), beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, ... (4 entities in total)
• Functional Keywords: lysozyme, muramidase, ec 3.2.1.17, hydrolase(o-glycosyl), n-acetyllactosamine, affinity labeling
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 1
• Total formula weight: 15671.58

Authors

Muraki, M.,Harata, K.,Sugita, N.,Sato, K. (deposition date: 1998-11-05, release date: 1999-05-05, Last modification date: 2024-12-25)

Primary citation

Muraki, M.,Harata, K.,Sugita, N.,Sato, K.
Dual affinity labeling of the active site of human lysozyme with an N-acetyllactosamine derivative: first ligand assisted recognition of the second ligand.
Biochemistry, 38:540-548, 1999

PubMed Abstract: Among the three kinds of the 2',3'-epoxypropyl beta-glycoside of disaccharides (GlcNAc-beta1,4-GlcNAc, Gal-beta1,4-GlcNAc, and Man-beta1,4-GlcNAc), the derivative of N-acetyllactosamine (Gal-beta1,4-GlcNAc-Epo) caused the dual labeling of human lysozyme (HL) most efficiently. The labeled HL was crystallized and analyzed by X-ray diffraction methodology. The X-ray analysis located the two Gal-beta1,4-GlcNAc-Epo moieties inside the catalytic cleft of HL. The attachment sites were the side-chain carboxylate groups of the catalytic residues Glu35 and Asp53 in HL. The first Gal-beta1, 4-GlcNAc-Epo moiety occupied virtually the same position as observed in the HL labeled with single Gal-beta1,4-GlcNAc-Epo molecule. The second Gal-beta1,4-GlcNAc-Epo moiety was recognized via the carbohydrate-carbohydrate interaction with the first Gal-beta1, 4-GlcNAc-Epo moiety in addition to the protein-carbohydrate interaction with the "right-side" catalytic cleft of HL through a number of hydrogen bonds including water-mediated ones as well as many van der Waals contacts. The two N-acetylglucosamine residues stacked with each other, while the two rings of galactose residues approximately shared the same plane. The dual labeling with two Gal-beta1,4-GlcNAc-Epo molecules was supposed to have occurred sequentially, which was accompanied with the alteration to the pKa of Glu35 derived from the esterification of Asp53 in the first labeling. Both asymmetric carbons in the connection parts between HL and N-acetyllactosamine moieties showed the same stereoconfiguration derived from the reaction with (2'R) stereoisomer concerning the epoxide group in the labeling reagent. The results demonstrated that the HL labeled with single Gal-beta1,4-GlcNAc-Epo was functional as a novel N-acetyllactosamine-binding protein, and the second labeling was performed by way of the first-ligand assisted recognition of the second ligand.

PubMed: 9888793
DOI: 10.1021/bi981779g

Experimental method

X-RAY DIFFRACTION (2.3 Å)