4ZZ8

X-ray crystal structure of chitosan-binding module 2 in complex with chitotriose derived from chitosanase/glucanase from Paenibacillus sp. IK-5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


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Literature

Mechanism of chitosan recognition by CBM32 carbohydrate-binding modules from a Paenibacillus sp. IK-5 chitosanase/glucanase

Shinya, S.Nishimura, S.Kitaoku, Y.Numata, T.Kimoto, H.Kusaoke, H.Ohnuma, T.Fukamizo, T.

(2016) Biochem.J. 473: 1085-1095

  • DOI: 10.1042/BCJ20160045
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • An antifungal chitosanase/glucanase isolated from the soil bacterium Paenibacillus sp. IK-5 has two CBM32 chitosan-binding modules (DD1 and DD2) linked in tandem at the C-terminus. In order to obtain insights into the mechanism of chitosan recognitio ...

    An antifungal chitosanase/glucanase isolated from the soil bacterium Paenibacillus sp. IK-5 has two CBM32 chitosan-binding modules (DD1 and DD2) linked in tandem at the C-terminus. In order to obtain insights into the mechanism of chitosan recognition, the structures of DD1 and DD2 were solved by NMR spectroscopy and crystallography. DD1 and DD2 both adopted a β-sandwich fold with several loops in solution as well as in crystals. On the basis of chemical shift perturbations in(1)H-(15)N-HSQC resonances, the chitosan tetramer (GlcN)4 was found to bind to the loop region extruded from the core β-sandwich of DD1 and DD2. The binding site defined by NMR in solution was consistent with the crystal structure of DD2 in complex with (GlcN)3, in which the bound (GlcN)3 stood upright on its non-reducing end at the binding site. Glu(14)of DD2 appeared to make an electrostatic interaction with the amino group of the non-reducing end GlcN, and Arg(31), Tyr(36)and Glu(61)formed several hydrogen bonds predominantly with the non-reducing end GlcN. No interaction was detected with the reducing end GlcN. Since Tyr(36)of DD2 is replaced by glutamic acid in DD1, the mutation of Tyr(36)to glutamic acid was conducted in DD2 (DD2-Y36E), and the reverse mutation was conducted in DD1 (DD1-E36Y). Ligand-binding experiments using the mutant proteins revealed that this substitution of the 36th amino acid differentiates the binding properties of DD1 and DD2, probably enhancing total affinity of the chitosanase/glucanase toward the fungal cell wall.


    Organizational Affiliation

    Department of Advanced Bioscience, Kinki University, Nara 631-8505, Japan.,Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Japan.,Department of Advanced Bioscience, Kinki University, Nara 631-8505, Japan fukamizo@nara.kindai.ac.jp.,Department of Bioscience, Fukui Prefectural University, Fukui 910-1195, Japan.,Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka 599-8531, Japan.,Department of Environmental and Biotechnological Frontier Engineering, Fukui University of Technology, Fukui 910-8505, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glucanase/chitosanase
A, B
138Paenibacillus fukuinensisMutation(s): 0 
EC: 3.2.1.-
Find proteins for Q93IE7 (Paenibacillus fukuinensis)
Go to UniProtKB:  Q93IE7
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GCS
Query on GCS

Download SDF File 
Download CCD File 
A
D-GLUCOSAMINE
2-AMINO-2-DEOXY-D-GLUCOSE
C6 H13 N O5
MSWZFWKMSRAUBD-QZABAPFNSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

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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: 1.65 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 38.372α = 90.00
b = 65.548β = 90.00
c = 117.490γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PHASERphasing
Cootmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science, and TechnologyJapanS1101035

Revision History 

  • Version 1.0: 2016-04-13
    Type: Initial release
  • Version 1.1: 2016-04-20
    Type: Database references