PDBsum entry 7deq

Hydrolase

PDB id: 7deq

Contents

Protein chain

129 a.a.

Ligands

NAG-NAG-NAG-NAG

DOD ×210

Metals

_CL ×4

_NA

PDB id:

7deq

Name:

Hydrolase

Title:

Lysozyme-sugar complex in d2o

Structure:

LysozymE C. Chain: a. Synonym: 1,4-beta-n-acetylmuramidasE C,allergen gal d iv. Ec: 3.2.1.17

Source:

Gallus gallus. Chicken. Organism_taxid: 9031

Resolution:

1.03Å R-factor: 0.133 R-free: 0.149

Authors:

I.Tanaka,T.Chatake

Key ref:

I.Tanaka et al. (2021). Recent structural insights into the mechanism of lysozyme hydrolysis. Acta Crystallogr D Struct Biol, 77, 288-292. PubMed id: 33645532 DOI: 10.1107/S2059798321000346

Date:

04-Nov-20 Release date: 10-Mar-21

Protein chain

P00698  (LYSC_CHICK) -  Lysozyme C from Gallus gallus

Seq: 147 a.a.

Struc: 129 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: 10.1107/S2059798321000346

Acta Crystallogr D Struct Biol 77:288-292 (2021)

PubMed id: 33645532

Recent structural insights into the mechanism of lysozyme hydrolysis.

I.Tanaka, R.Nishinomiya, R.Goto, S.Shimazaki, T.Chatake.

ABSTRACT

Lysozyme hydrolyzes the glycosidic bonds between N-acetylmuramic acid and N-acetylglucosamine in peptidoglycans located in the bacterial cell wall. The mechanism of the hydrolysis reaction of lysozyme was first studied more than 50 years ago; however, it has not yet been fully elucidated and various mechanisms are still being investigated. One reaction system that has commonly been proposed is that the lysozyme intermediate undergoes covalent ligand binding during hydrolysis. However, these findings resulted from experiments performed under laboratory conditions using fluorine-based ligands, which facilitate the formation of covalent bonds between the ligands and the catalytic side chain of lysozyme. More recently, high-resolution X-ray structural analysis was used to study the complex of lysozyme with an N-acetylglucosamine tetramer. As a result, the carboxyl group of Asp52 was found to form a relatively strong hydrogen-bond network and had difficulty binding covalently to C1 of the carbohydrate ring. To confirm this hydrogen-bond network, neutron test measurements were successfully performed to a resolution of better than 1.9 Å.