PDBsum entry 1d6p

Hydrolase

PDB id: 1d6p

Contents

Protein chain

130 a.a. *

Ligands

NAG-NAG

GOL

Waters ×43

* Residue conservation analysis

PDB id:

1d6p

Name:

Hydrolase

Title:

Human lysozyme l63 mutant labelled with 2',3'-epoxypropyl n,n'- diacetylchitobiose

Structure:

Lysozyme. Chain: a. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606

Resolution:

2.23Å R-factor: 0.181 R-free: 0.216

Authors:

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

Key ref:

M.Muraki et al. (2000). Protein-carbohydrate interactions in human lysozyme probed by combining site-directed mutagenesis and affinity labeling. Biochemistry, 39, 292-299. PubMed id: 10630988 DOI: 10.1021/bi991402q

Date:

15-Oct-99 Release date: 21-Jan-00

Protein chain

P61626  (LYSC_HUMAN) -  Lysozyme C from Homo sapiens

Seq: 148 a.a.

Struc: 130 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

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/bi991402q

Biochemistry 39:292-299 (2000)

PubMed id: 10630988

Protein-carbohydrate interactions in human lysozyme probed by combining site-directed mutagenesis and affinity labeling.

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

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.