2DQA

Crystal Structure of Tapes japonica Lysozyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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

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

(2007) J.Biol.Chem. 282: 27459-27467

  • DOI: 10.1074/jbc.M704555200

  • PubMed 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 an ...

    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.


    Organizational Affiliation

    Graduate School of Pharmaceutical Sciences, Agricultural Sciences of Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme
A, B
124Ruditapes philippinarumMutation(s): 0 
EC: 3.2.1.17
Find proteins for Q8IU26 (Ruditapes philippinarum)
Go to UniProtKB:  Q8IU26
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PT
Query on PT

Download SDF File 
Download CCD File 
A, B, C, D
PLATINUM (II) ION
Pt
HRGDZIGMBDGFTC-UHFFFAOYSA-N
 Ligand Interaction
BGC
Query on BGC

Download SDF File 
Download CCD File 
B
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.175 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.749α = 90.00
b = 88.760β = 116.04
c = 43.644γ = 90.00
Software Package:
Software NamePurpose
SOLVEphasing
CrystalCleardata reduction
CNSrefinement
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
CrystalCleardata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-06-12
    Type: Initial release
  • Version 1.1: 2007-09-17
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance