2BAA

THE REFINED CRYSTAL STRUCTURE OF AN ENDOCHITINASE FROM HORDEUM VULGARE L. SEEDS TO 1.8 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Work: 0.180 

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This is version 1.2 of the entry. See complete history


Literature

The refined crystal structure of an endochitinase from Hordeum vulgare L. seeds at 1.8 A resolution.

Hart, P.J.Pfluger, H.D.Monzingo, A.F.Hollis, T.Robertus, J.D.

(1995) J Mol Biol 248: 402-413

  • Primary Citation of Related Structures:  
    2BAA

  • PubMed Abstract: 
  • Class II chitinases (EC 3.2.1.14) are plant defense proteins. They hydrolyze chitin, an insoluble beta-1,4-linked polymer of N-acetylglucosamine (NAG), which is a major cell-wall component of many fungal hyphae. We previously reported the three-dimensional structure of the 26 kDa class II endochitinase from barley seeds at 2 ...

    Class II chitinases (EC 3.2.1.14) are plant defense proteins. They hydrolyze chitin, an insoluble beta-1,4-linked polymer of N-acetylglucosamine (NAG), which is a major cell-wall component of many fungal hyphae. We previously reported the three-dimensional structure of the 26 kDa class II endochitinase from barley seeds at 2.8 A resolution, determined using multiple isomorphous replacement (MIR) methods. Here, we report the crystallographic refinement of this chitinase structure against data to 1.8 A resolution using rounds of hand rebuilding coupled with molecular dynamics (X-PLOR). The final model has an R-value of 18.1% for the 5.0 to 1.8 A data shell and 19.8% for the 10.0 to 1.8 A shell, and root-mean-square deviations from standard bond lengths and angles of 0.017 A and 2.88 degrees, respectively. The 243 residue molecule has one beta-sheet, ten alpha-helices and three disulfide bonds; 129 water molecules are included in the final model. We show structural comparisons confirming that chitinase secondary structure resembles lysozyme at the active site region. Based on substrate binding to lysozyme, we have built a hypothetical model for the binding of a hexasaccharide into the pronounced active site cleft of chitinase. This provides the first view of likely substrate interactions from this family of enzymes; the model is consistent with a lysozyme-like mechanism of action in which Glu67 acts as proton donor and Glu89 is likely to stabilize the transition state oxycarbonium ion. These binding site residues, and many hydrophobic residues are conserved in a range of plant chitinases. This endochitinase structure will serve as a model for other plant chitinases, and that catalytic models based on this structure will be applicable to the entire enzyme family.


    Related Citations: 
    • Crystal Structure of an Endochitinase from Hordeum Vulgare L. Seeds
      Hart, P.J., Monzingo, A.F., Ready, M.P., Ernst, S.R., Robertus, J.D.
      (1993) J Mol Biol 229: 189
    • Crystallization of an Endochitinase from Hordeum Vulgare L. Seeds
      Hart, P.J., Ready, M.P., Robertus, J.D.
      (1992) J Mol Biol 225: 565
    • Biochemical and Molecular Characterization of Three Barley Seed Proteins with Antifungal Properties
      Leah, R., Tommerup, H., Svendsen, I., Mundy, J.
      (1991) J Biol Chem 266: 1564

    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Texas, Austin 78712, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ENDOCHITINASE (26 KD)A243Hordeum vulgareMutation(s): 0 
EC: 3.2.1.14
UniProt
Find proteins for P23951 (Hordeum vulgare)
Explore P23951 
Go to UniProtKB:  P23951
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23951
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Work: 0.180 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.5α = 90
b = 64.5β = 108
c = 43.1γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-01-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance