PDBsum entry: 1at5

Hydrolase

PDB id: 1at5

Contents

Protein chain

129 a.a. *

Ligands

NAG-NAG-NAG

Metals

_CL

_NA

Waters ×95

* Residue conservation analysis

PDB id:

1at5

Name:

Hydrolase

Title:

Hen egg white lysozyme with a succinimide residue

Structure:

Lysozyme. Chain: a. Other_details: succinimide at residue 101

Source:

Gallus gallus. Chicken. Organism_taxid: 9031. Cell: egg. Cellular_location: cytoplasm (white)

Resolution:

1.80Å R-factor: 0.182 R-free: 0.233

Authors:

S.Noguchi,K.Miyawaki,Y.Satow

Key ref:

S.Noguchi et al. (1998). Succinimide and isoaspartate residues in the crystal structures of hen egg-white lysozyme complexed with tri-N-acetylchitotriose. J Mol Biol, 278, 231-238. PubMed id: 9571046 DOI: 10.1006/jmbi.1998.1674

Date:

18-Aug-97 Release date: 25-Feb-98

Protein chain

P00698  (LYSC_CHICK) -  Lysozyme C

Seq: 147 a.a.

Struc: 129 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

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.

 Gene Ontology (GO) functional annotation 

• Cellular component: extracellular region (2 terms)
• Biological process: metabolic process (4 terms)
• Biochemical function: catalytic activity (4 terms)

DOI no: 10.1006/jmbi.1998.1674

J Mol Biol 278:231-238 (1998)

PubMed id: 9571046

Succinimide and isoaspartate residues in the crystal structures of hen egg-white lysozyme complexed with tri-N-acetylchitotriose.

S.Noguchi, K.Miyawaki, Y.Satow.

ABSTRACT

The isomerization of Asp101 to isoaspartate autocatalytically proceeds via a succinimide intermediate in hen egg-white lysozyme at a mildly acidic condition. The crystal structures of succinimide and isoaspartate forms of the lysozyme proteins, each complexed with a tri-N-acetylchitotriose ligand, have been determined at 1.8 A resolution, and distinctively elucidate coplanar cyclic aminosuccinyl and beta-linked isoaspartyl residues. Compared with the liganded native protein with normal Asp101, succinimide 101 protrudes toward the ligand, and isoaspartate 101 extends away from the ligand. The formations of these residues caused the loss of three hydrogen-bonds between the ligand and the side-chains of Asp101 and Asn103 along with 0.5 A displacement of the ligand location.

Selected figure(s)

Figure 1.
Figure 1. Schematic diagram for the isoaspartate formation pathway via succinimide. Either an α-linked aspartate or a β-linked isoaspartate is formed via cyclic succinimide intermediate. The succinimide intermediate formed by spontaneous deamidation of asparagine follows the same pathway. Note that racemization at the α carbon is possible since the succinimide intermediate is racemization-labile [Geiger and Clarke 1987].

Figure 4.
Figure 4. Stereo views of the lysozyme regions from Val99 to Gly104. (a) Succinimide protein; (b) isoaspartate protein. C, N, and O atoms are drawn with dark gray, light blue, and red spheres, respectively. Covalent bonds in the Suc101–Gly102 and isoAsp101 moieties are colored with red sticks, those of the remaining parts of the proteins with blue, and those of tri- N -acetylchitotriose with green.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 278, 231-238) copyright 1998.

Figures were selected by an automated process.