2DKV

Crystal structure of class I chitinase from Oryza sativa L. japonica


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of full-length class I chitinase from rice revealed by X-ray crystallography and small-angle X-ray scattering.

Kezuka, Y.Kojima, M.Mizuno, R.Suzuki, K.Watanabe, T.Nonaka, T.

(2010) Proteins 78: 2295-2305

  • DOI: 10.1002/prot.22742
  • Primary Citation of Related Structures:  
    2DKV, 3IWR

  • PubMed Abstract: 
  • The rice class I chitinase OsChia1b, also referred to as RCC2 or Cht-2, is composed of an N-terminal chitin-binding domain (ChBD) and a C-terminal catalytic domain (CatD), which are connected by a proline- and threonine-rich linker peptide. Because of the ability to inhibit fungal growth, the OsChia1b gene has been used to produce transgenic plants with enhanced disease resistance ...

    The rice class I chitinase OsChia1b, also referred to as RCC2 or Cht-2, is composed of an N-terminal chitin-binding domain (ChBD) and a C-terminal catalytic domain (CatD), which are connected by a proline- and threonine-rich linker peptide. Because of the ability to inhibit fungal growth, the OsChia1b gene has been used to produce transgenic plants with enhanced disease resistance. As an initial step toward elucidating the mechanism of hydrolytic action and antifungal activity, the full-length structure of OsChia1b was analyzed by X-ray crystallography and small-angle X-ray scattering (SAXS). We determined the crystal structure of full-length OsChia1b at 2.00-A resolution, but there are two possibilities for a biological molecule with and without interdomain contacts. The SAXS data showed an extended structure of OsChia1b in solution compared to that in the crystal form. This extension could be caused by the conformational flexibility of the linker. A docking simulation of ChBD with tri-N-acetylchitotriose exhibited a similar binding mode to the one observed in the crystal structure of a two-domain plant lectin complexed with a chitooligosaccharide. A hypothetical model based on the binding mode suggested that ChBD is unsuitable for binding to crystalline alpha-chitin, which is a major component of fungal cell walls because of its collisions with the chitin chains on the flat surface of alpha-chitin. This model also indicates the difference in the binding specificity of plant and bacterial ChBDs of GH19 chitinases, which contribute to antifungal activity.


    Related Citations: 
    • Sequence variation, differential expression and chromosomal location of rice chitinase genes
      Nishizawa, Y., Kishimoto, N., Saito, A., Hibi, T.
      (1993) Mol Gen Genet 241: 1
    • Crystallization and preliminary X-ray analysis of plant class I chitinase from rice
      Kezuka, Y., Kitazaki, K., Itoh, Y., Watanabe, J., Takaha, O., Watanabe, T., Nishizawa, Y., Nonaka, T.
      (2004) Protein Pept Lett 11: 401

    Organizational Affiliation

    Department of Structural Biology, School of Pharmacy, Iwate Medical University, Yahaba, Iwate 028-3694, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
chitinaseA309Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: Cht2RC7Os05g0399300LOC_Os05g33130OsJ_18467
EC: 3.2.1.14
UniProt
Find proteins for Q7DNA1 (Oryza sativa subsp. japonica)
Explore Q7DNA1 
Go to UniProtKB:  Q7DNA1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7DNA1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MES
Query on MES

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.452α = 90
b = 66.452β = 90
c = 123.636γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-01
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-01-01
    Changes: Database references