5K2L

Crystal structure of LysM domain from Volvox carteri chitinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.139 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Chitin oligosaccharide binding to the lysin motif of a novel type of chitinase from the multicellular green alga, Volvox carteri.

Kitaoku, Y.Fukamizo, T.Numata, T.Ohnuma, T.

(2017) Plant Mol. Biol. 93: 97-108

  • DOI: 10.1007/s11103-016-0549-5

  • PubMed Abstract: 
  • The chitinase-mediated defense system in higher plants has been intensively studied from physiological and structural viewpoints. However, the defense system in the most primitive plant species, such as green algae, has not yet been elucidated in det ...

    The chitinase-mediated defense system in higher plants has been intensively studied from physiological and structural viewpoints. However, the defense system in the most primitive plant species, such as green algae, has not yet been elucidated in details. In this study, we solved the crystal structure of a family CBM-50 LysM module attached to the N-terminus of chitinase from Volvox carteri, and successfully analyzed its chitin-binding ability by NMR spectroscopy and isothermal titration calorimetry. Trp96 of the LysM module appeared to make a CH-π stacking interaction with the reducing end sugar residue of the ligand. We believe the data included in this manuscript provide novel insights into the molecular basis of chitinase-mediated defense system in green algae. A chitinase from the multicellular green alga, Volvox carteri, contains two N-terminal lysin motifs (VcLysM1 and VcLysM2), that belong to the CBM-50 family, in addition to a catalytic domain. We produced a recombinant protein of VcLysM2 in order to examine its structure and function. The X-ray crystal structure of VcLysM2 was successfully solved at a resolution of 1.2 Å, and revealed that the protein adopts the βααβ fold typical of members belonging to the CBM-50 family. NMR spectra of 13 C- and 15 N-labeled proteins were analyzed in order to completely assign the main chain resonances of the 1 H, 15 N-HSQC spectrum in a sequential manner. NMR-based titration experiments of chitin oligosaccharides, (GlcNAc) n (n = 3-6), revealed the ligand-binding site of VcLysM2, in which the Trp96 side chain appeared to interact with the terminal GlcNAc residue of the ligand. We then mutated Trp96 to alanine (VcLysM2-W96A), and the mutant protein was characterized. Based on isothermal titration calorimetry, the affinity of (GlcNAc) 6 toward VcLysM2 (-6.9 kcal/mol) was found to be markedly higher than that of (GlcNAc) 3 (-4.1 kcal/mol), whereas the difference in affinities between (GlcNAc) 6 and (GlcNAc) 3 in VcLysM2-W96A (-5.1 and -4.0 kcal/mol, respectively) was only moderate. This suggests that the Trp96 side chain of VcLysM2 interacts with the sugar residue of (GlcNAc) 6 not with (GlcNAc) 3 . VcLysM2 appears to preferentially bind (GlcNAc) n with longer chains and plays a major role in the degradation of the chitinous components of enzyme targets.


    Organizational Affiliation

    Department of Advanced Bioscience, Kindai University, 3327-204 Nakamachi, Nara, 631-8505, Japan.,Department of Advanced Bioscience, Kindai University, 3327-204 Nakamachi, Nara, 631-8505, Japan. fukamizo@nara.kindai.ac.jp.,Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8566, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Chitinase, lysozyme
A
49Volvox carteri f. nagariensisMutation(s): 0 
Gene Names: chi4
Find proteins for D8UFB5 (Volvox carteri f. nagariensis)
Go to UniProtKB:  D8UFB5
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.139 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 29.130α = 90.00
b = 29.130β = 90.00
c = 94.257γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Strategic Project to Support the Formation of Research Bases at Private Universities: Matching Fund Subsidy from the MEXTJapanS1101035

Revision History 

  • Version 1.0: 2017-02-22
    Type: Initial release