4TOQ

Crystal structure of class III chitinase from pomegranate provides the insight into its metal storage capacity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Crystal structure of class III chitinase from pomegranate provides the insight into its metal storage capacity.

Masuda, T.Zhao, G.Mikami, B.

(2015) Biosci Biotechnol Biochem 79: 45-50

  • DOI: 10.1080/09168451.2014.962475
  • Primary Citation of Related Structures:  
    4TOQ

  • PubMed Abstract: 
  • Chitinase hydrolyzes the β-1,4-glycosidic bond in chitin. In higher plants, this enzyme has been regarded as a pathogenesis-related protein. Recently, we identified a class III chitinase, which functions as a calcium storage protein in pomegranate (Punica granatum) seed (PSC, pomegranate seed chitinase) ...

    Chitinase hydrolyzes the β-1,4-glycosidic bond in chitin. In higher plants, this enzyme has been regarded as a pathogenesis-related protein. Recently, we identified a class III chitinase, which functions as a calcium storage protein in pomegranate (Punica granatum) seed (PSC, pomegranate seed chitinase). Here, we solved a crystal structure of PSC at 1.6 Å resolution. Although its overall structure, including the structure of catalytic site and non-proline cis-peptides, was closely similar to those of other class III chitinases, PSC had some unique structural characteristics. First, there were some metal-binding sites with coordinated water molecules on the surface of PSC. Second, many unconserved aspartate residues were present in the PSC sequence which rendered the surface of PSC negatively charged. This acidic electrostatic property is in contrast to that of hevamine, well-characterized plant class III chitinase, which has rather a positively charged surface. Thus, the crystal structure provides a clue for metal association property of PSC.


    Organizational Affiliation

    a Laboratory of Food Quality Design and Development, Division of Agronomy and Horticultural Science, Graduate School of Agriculture , Kyoto University , Gokasho, Uji, Kyoto , Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Class III chitinaseA, B, C, D273Punica granatumMutation(s): 0 
Gene Names: PSCCDL15_Pgr011527
EC: 3.2.1.14
UniProt
Find proteins for G1UH28 (Punica granatum)
Explore G1UH28 
Go to UniProtKB:  G1UH28
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
J [auth A], K [auth A], N [auth B], O [auth B], P [auth B], U [auth C]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A] , F [auth A] , G [auth A] , H [auth A] , I [auth A] , L [auth B] , M [auth B] , Q [auth C] , 
E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], L [auth B], M [auth B], Q [auth C], R [auth C], S [auth C], T [auth C], V [auth D], W [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.462α = 90
b = 79.969β = 102.97
c = 97.532γ = 90
Software Package:
Software NamePurpose
HKL-2000data processing
MOLREPphasing
PDB_EXTRACTdata extraction
Cootmodel building
PHENIXrefinement
MOLREPmodel building
HKLdata reduction
HKLdata scaling

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-10
    Type: Initial release
  • Version 1.1: 2014-10-15
    Changes: Database references
  • Version 1.2: 2015-02-04
    Changes: Database references
  • Version 1.3: 2015-11-04
    Changes: Data collection
  • Version 1.4: 2020-01-29
    Changes: Data collection, Derived calculations