PDBsum entry 2dqa

Hydrolase

PDB id: 2dqa

Contents

Protein chains

123 a.a. *

Ligands

NAG-NAG-NAG ×2

BGC ×2

Metals

_PT ×8

Waters ×354

* Residue conservation analysis

PDB id:

2dqa

Name:

Hydrolase

Title:

Crystal structure of tapes japonica lysozyme

Structure:

Lysozyme. Chain: a, b. Fragment: recidues 1-123. Engineered: yes

Source:

Tapes japonica. Organism_taxid: 152465. Expressed in: pichia pastoris. Expression_system_taxid: 4922.

Resolution:

1.60Å R-factor: 0.176 R-free: 0.210

Authors:

T.Goto,Y.Kakuta,Y.Abe,K.Takeshita,T.Imoto,T.Ueda

Key ref:

T.Goto et al. (2007). Crystal Structure of Tapes japonica Lysozyme with Substrate Analogue: STRUCTURAL BASIS OF THE CATALYTIC MECHANISM AND MANIFESTATION OF ITS CHITINASE ACTIVITY ACCOMPANIED BY QUATERNARY STRUCTURAL CHANGE. J Biol Chem, 282, 27459-27467. PubMed id: 17631496 DOI: 10.1074/jbc.M704555200

Date:

24-May-06 Release date: 12-Jun-07

Protein chains

Q8IU26  (LYS_RUDPH) -  Invertebrate-type lysozyme from Ruditapes philippinarum

Seq: 136 a.a.

Struc: 123 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: 10.1074/jbc.M704555200

J Biol Chem 282:27459-27467 (2007)

PubMed id: 17631496

Crystal Structure of Tapes japonica Lysozyme with Substrate Analogue: STRUCTURAL BASIS OF THE CATALYTIC MECHANISM AND MANIFESTATION OF ITS CHITINASE ACTIVITY ACCOMPANIED BY QUATERNARY STRUCTURAL CHANGE.

T.Goto, Y.Abe, Y.Kakuta, K.Takeshita, T.Imoto, T.Ueda.

ABSTRACT

Tapes japonica lysozyme (TJL) is classified as a member of the recently established i-type lysozyme family. In this study, we solved the crystal structure of TJL complexed with a trimer of N-acetylglucosamine to 1.6A resolution. Based on structure and mutation analyses, we demonstrated that Glu-18 and Asp-30 are the catalytic residues of TJL. Furthermore, the present findings suggest that the catalytic mechanism of TJL is a retaining mechanism that proceeds through a covalent sugar-enzyme intermediate. On the other hand, the quaternary structure in the crystal revealed a dimer formed by the electrostatic interactions of catalytic residues (Glu-18 and Asp-30) in one molecule with the positive residues at the C terminus in helix 6 of the other molecule. Gel chromatography analysis revealed that the TJL dimer remained intact under low salt conditions but that it dissociated to TJL monomers under high salt conditions. With increasing salt concentrations, the chitinase activity of TJL dramatically increased. Therefore, this study provides novel evidence that the lysozyme activity of TJL is modulated by its quaternary structure.

Selected figure(s)

Figure 1.
FIGURE 1. The structure of TJL. Stereo view displaying the ribbon diagram of the TJL monomer complexed with (NAG)[3] and disulfide bond formation. The model was drawn using PyMOL software.

Figure 2.
FIGURE 2. Interactions at the active site cleft in TJL with (NAG)[3]. Stereo diagram displaying the interactions between TJL and (NAG)[3] in the A molecule. Possible hydrogen bonds between the protein and (NAG)[3] are displayed as gray dashed lines. Displayed in blue mesh is the F[o] - F[c] omit electron density map of (NAG)[3] contoured at 4.0 .

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 27459-27467) copyright 2007.

Figures were selected by an automated process.