PDBsum entry 1re2

Lysozyme

PDB id: 1re2

Contents

Protein chain

130 a.a. *

Ligands

NAG-GAL ×2

GOL ×2

Waters ×84

* Residue conservation analysis

PDB id:

1re2

Name:

Lysozyme

Title:

Human lysozyme labelled with two 2',3'-epoxypropyl beta-glycoside of n-acetyllactosamine

Structure:

Protein (lysozyme). Chain: a. Ec: 3.2.1.17

Source:

Homo sapiens. Human. Organism_taxid: 9606

Resolution:

2.30Å R-factor: 0.171 R-free: 0.247

Authors:

M.Muraki,K.Harata,N.Sugita,K.Sato

Key ref:

M.Muraki et al. (1999). 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. PubMed id: 9888793 DOI: 10.1021/bi981779g

Date:

05-Nov-98 Release date: 05-May-99

Protein chain

P61626  (LYSC_HUMAN) -  Lysozyme C from Homo sapiens

Seq: 148 a.a.

Struc: 130 a.a.

Enzyme reactions

• Enzyme class: E.C.3.2.1.17 - lysozyme.
• Reaction: Hydrolysis of the 1,4-beta-linkages between N-acetyl-D-glucosamine and N-acetylmuramic acid in peptidoglycan heteropolymers of the prokaryotes cell walls.

DOI no: 10.1021/bi981779g

Biochemistry 38:540-548 (1999)

PubMed id: 9888793

Dual affinity labeling of the active site of human lysozyme with an N-acetyllactosamine derivative: first ligand assisted recognition of the second ligand.

M.Muraki, K.Harata, N.Sugita, K.i.Sato.

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.