Crystal structure of Brassica juncea chitinase catalytic module (Bjchi3)

Experimental Data Snapshot

  • Resolution: 1.53 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 

Starting Model: experimental
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Crystal structures of a family 19 chitinase from Brassica juncea show flexibility of binding cleft loops

Ubhayasekera, W.Tang, C.M.Ho, S.W.T.Berglund, G.Bergfors, T.Chye, M.-L.Mowbray, S.L.

(2007) FEBS J 274: 3695-3703

  • DOI: https://doi.org/10.1111/j.1742-4658.2007.05906.x
  • Primary Citation of Related Structures:  
    2Z37, 2Z38, 2Z39

  • PubMed Abstract: 

    Brassica juncea chitinase is an endo-acting, pathogenesis-related protein that is classified into glycoside hydrolase family 19, with highest homology (50-60%) in its catalytic domain to class I plant chitinases. Here we report X-ray structures of the chitinase catalytic domain from wild-type (apo, as well as with chloride ions bound) and a Glu234Ala mutant enzyme, solved by molecular replacement and refined at 1.53, 1.8 and 1.7 A resolution, respectively. Confirming our earlier mutagenesis studies, the active-site residues are identified as Glu212 and Glu234. Glu212 is believed to be the catalytic acid in the reaction, whereas Glu234 is thought to have a dual role, both activating a water molecule in its attack on the anomeric carbon, and stabilizing the charged intermediate. The molecules in the various structures differ significantly in the conformation of a number of loops that border the active-site cleft. The differences suggest an opening and closing of the enzyme during the catalytic cycle. Chitin is expected to dock first near Glu212, which will protonate it. Conformational changes then bring Glu234 closer, allowing it to assist in the following steps. These observations provide important insights into catalysis in family 19 chitinases.

  • Organizational Affiliation

     Department of Molecular Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden Department of Botany, The University of Hong Kong, Pokfulam, Hong Kong Department of Cell and Molecular Biology, Uppsala University, Sweden.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
244Brassica junceaMutation(s): 0 
Gene Names: Bjchi1
Find proteins for Q9SQF7 (Brassica juncea)
Explore Q9SQF7 
Go to UniProtKB:  Q9SQF7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SQF7
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.53 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.249α = 79.34
b = 61.821β = 89.52
c = 75.359γ = 88.9
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-06-19
    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: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2023-11-01
    Changes: Data collection, Database references, Refinement description