PDBsum entry 2z2e

Hydrolase

PDB id: 2z2e

Contents

Protein chains

129 a.a. *

Ligands

SO4 ×2

Waters ×215

* Residue conservation analysis

PDB id:

2z2e

Name:

Hydrolase

Title:

Crystal structure of canine milk lysozyme stabilized against non- enzymatic deamidation

Structure:

LysozymE C, milk isozyme. Chain: a, b. Synonym: 1,4-beta-n-acetylmuramidasE C. Engineered: yes. Mutation: yes

Source:

Canis lupus familiaris. Dog. Organism_taxid: 9615. Strain: familiaris. Expressed in: pichia pastoris. Expression_system_taxid: 4922.

Resolution:

2.01Å R-factor: 0.280 R-free: 0.413

Authors:

Y.Nonaka,D.Akieda,N.Watanabe,I.Tanaka,M.Kamiya,T.Aizawa,K.Nitta, M.Demura,K.Kawano

Key ref:

Y.Nonaka et al. (2008). Spontaneous asparaginyl deamidation of canine milk lysozyme under mild conditions. Proteins, 72, 313-322. PubMed id: 18214981 DOI: 10.1002/prot.21927

Date:

21-May-07 Release date: 27-Nov-07

Protein chains

P81708  (LYSC1_CANLF) -  Lysozyme C, milk isozyme from Canis lupus familiaris

Seq: 129 a.a.

Struc: 129 a.a.*

* PDB and UniProt seqs differ at 5 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.

DOI no: 10.1002/prot.21927

Proteins 72:313-322 (2008)

PubMed id: 18214981

Spontaneous asparaginyl deamidation of canine milk lysozyme under mild conditions.

Y.Nonaka, T.Aizawa, D.Akieda, M.Yasui, M.Watanabe, N.Watanabe, I.Tanaka, M.Kamiya, M.Mizuguchi, M.Demura, K.Kawano.

ABSTRACT

Asparaginyl deamidation is a common form of nonenzymatic degradation of proteins and peptides. As it introduces a negative charge spontaneously and irreversibly, charge heterogeneity can be accumulated in protein solution during purification, preservation, and experiments. In this study, canine milk lysozyme (CML), a useful model for the study of the molten globule state, exhibited charge heterogeneity after sample purification. Four Asn residues in CML deamidated rapidly under mild conditions: pH 8.0 and 30 degrees C. Other than these residues, one Asn residue, which was stable in the native state, was labile to deamidation in the unfolded state. This suggests that the structural formation around Asn can suppress deamidation. Substitutions of these labile Asn residues to Gln residues prevented deamidation effectively. Because the substitutions did not disrupt the structural formation of the native and molten globule states, they will enable more precise analyses for physical and structural studies.

Selected figure(s)

Figure 1.
Figure 1. The currently accepted mechanism of asparagine nonenzymatic deamidation.[11][12] The succinimide intermediate formation arises from a nucleophilic attack of the backbone NH group of the next residue on the side-chain carbonyl of the asparaginyl residue. The ring is hydrolyzed to open, resulting in either an aspartic acid or isoaspartic acid product.

Figure 6.
Figure 6. (a) Crystal structure of 5NQ. The substituted residues are represented in yellow. (b) Superposition of the backbone structures of CML wild type (red, PDB 2CWI) and 5NQ (blue) by X-ray crystallography. The root-mean-square deviation of the backbones of the two structures is 0.511 Å.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2008, 72, 313-322) copyright 2008.

Figures were selected by the author.