The structure of chi1, a chitinase from Yersinia entomophaga

Experimental Data Snapshot

  • Resolution: 1.74 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 

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Structural analysis of Chi1 Chitinase from Yen-Tc: the multisubunit insecticidal ABC toxin complex of Yersinia entomophaga

Busby, J.N.Landsberg, M.J.Simpson, R.M.Jones, S.A.Hankamer, B.Hurst, M.R.H.Lott, J.S.

(2012) J Mol Biol 415: 359-371

  • DOI: https://doi.org/10.1016/j.jmb.2011.11.018
  • Primary Citation of Related Structures:  
    3OA5, 4A5Q

  • PubMed Abstract: 

    Yersinia entomophaga MH96 is a native New Zealand soil bacterium that secretes a large ABC-type protein toxin complex, Yen-Tc, similar to those produced by nematode-associated bacteria such as Photorhabdus luminescens. Y. entomophaga displays an exceptionally virulent pathogenic phenotype in sensitive insect species, causing death within 72 h of infection. Because of this phenotype, there is intrinsic interest in the mechanism of action of Yen-Tc, and it also has the potential to function as a novel class of biopesticide. We have identified genes that encode chitinases as part of the toxin complex loci in Y. entomophaga MH96, P. luminescens, Photorhabdus asymbiotica and Xenorhabdus nematophila. Furthermore, we have shown that the secreted toxin complex from Y. entomophaga MH96 includes two chitinases as an integral part of the complex, a feature not described previously in other ABC toxins and possibly related to the severe disease caused by this bacterium. We present here the structure of the Y. entomophaga MH96 Chi1 chitinase, determined by X-ray crystallography to 1.74 Å resolution, and show that a ring of five symmetrically arranged lobes on the surface of the Yen-Tc toxin complex structure, as determined by single-particle electron microscopy, provides a good fit to the Chi1 monomer. We also confirm that the isolated chitinases display endochitinase activity, as does the complete toxin complex.

  • Organizational Affiliation

    AgResearch Structural Biology Laboratory, School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
574Yersinia entomophagaMutation(s): 0 
Gene Names: chi1
Find proteins for B6A876 (Yersinia entomophaga)
Explore B6A876 
Go to UniProtKB:  B6A876
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6A876
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.74 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.012α = 102.85
b = 67.172β = 108.06
c = 81.679γ = 92.1
Software Package:
Software NamePurpose
Blu-Icedata collection
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-10
    Type: Initial release
  • Version 1.1: 2011-12-07
    Changes: Database references
  • Version 1.2: 2013-06-19
    Changes: Database references
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description