Crystal structure of a rice cell wall degrading esterase LipA from Xanthomonas oryzae

Experimental Data Snapshot

  • Resolution: 1.86 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.161 

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A Cell Wall-Degrading Esterase of Xanthomonas oryzae Requires a Unique Substrate Recognition Module for Pathogenesis on Rice

Aparna, G.Chatterjee, A.Sonti, R.V.Sankaranarayanan, R.

(2009) Plant Cell 21: 1860-1873

  • DOI: https://doi.org/10.1105/tpc.109.066886
  • Primary Citation of Related Structures:  
    3H2G, 3H2H, 3H2I, 3H2J

  • PubMed Abstract: 

    Xanthomonas oryzae pv oryzae (Xoo) causes bacterial blight, a serious disease of rice (Oryza sativa). LipA is a secretory virulence factor of Xoo, implicated in degradation of rice cell walls and the concomitant elicitation of innate immune responses, such as callose deposition and programmed cell death. Here, we present the high-resolution structural characterization of LipA that reveals an all-helical ligand binding module as a distinct functional attachment to the canonical hydrolase catalytic domain. We demonstrate that the enzyme binds to a glycoside ligand through a rigid pocket comprising distinct carbohydrate-specific and acyl chain recognition sites where the catalytic triad is situated 15 A from the anchored carbohydrate. Point mutations disrupting the carbohydrate anchor site or blocking the pocket, even at a considerable distance from the enzyme active site, can abrogate in planta LipA function, exemplified by loss of both virulence and the ability to elicit host defense responses. A high conservation of the module across genus Xanthomonas emphasizes the significance of this unique plant cell wall-degrading function for this important group of plant pathogenic bacteria. A comparison with the related structural families illustrates how a typical lipase is recruited to act on plant cell walls to promote virulence, thus providing a remarkable example of the emergence of novel functions around existing scaffolds for increased proficiency of pathogenesis during pathogen-plant coevolution.

  • Organizational Affiliation

    Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500007, India.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
esterase397Xanthomonas oryzae pv. oryzaeMutation(s): 0 
Gene Names: LipA
EC: 3.1.1
Find proteins for Q5H5J0 (Xanthomonas oryzae pv. oryzae (strain KACC10331 / KXO85))
Explore Q5H5J0 
Go to UniProtKB:  Q5H5J0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5H5J0
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.86 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.161 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.66α = 90
b = 54.68β = 92.65
c = 66.33γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-08-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance