Crystal structure of GH10 endo-b-1,4-xylanase (XynB) from Xanthomonas axonopodis pv citri in the native form

Experimental Data Snapshot

  • Resolution: 1.30 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.133 

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Molecular mechanisms associated with xylan degradation by xanthomonas plant pathogens.

Santos, C.R.Hoffmam, Z.B.de Matos Martins, V.P.Zanphorlin, L.M.de Paula Assis, L.H.Honorato, R.V.Lopes de Oliveira, P.S.Ruller, R.Murakami, M.T.

(2014) J Biol Chem 289: 32186-32200

  • DOI: https://doi.org/10.1074/jbc.M114.605105
  • Primary Citation of Related Structures:  
    4PMU, 4PMV, 4PMX, 4PMY, 4PMZ, 4PN2

  • PubMed Abstract: 

    Xanthomonas pathogens attack a variety of economically relevant plants, and their xylan CUT system (carbohydrate utilization with TonB-dependent outer membrane transporter system) contains two major xylanase-related genes, xynA and xynB, which influence biofilm formation and virulence by molecular mechanisms that are still elusive. Herein, we demonstrated that XynA is a rare reducing end xylose-releasing exo-oligoxylanase and not an endo-β-1,4-xylanase as predicted. Structural analysis revealed that an insertion in the β7-α7 loop induces dimerization and promotes a physical barrier at the +2 subsite conferring this unique mode of action within the GH10 family. A single mutation that impaired dimerization became XynA active against xylan, and high endolytic activity was achieved when this loop was tailored to match a canonical sequence of endo-β-1,4-xylanases, supporting our mechanistic model. On the other hand, the divergent XynB proved to be a classical endo-β-1,4-xylanase, despite the low sequence similarity to characterized GH10 xylanases. Interestingly, this enzyme contains a calcium ion bound nearby to the glycone-binding region, which is required for catalytic activity and structural stability. These results shed light on the molecular basis for xylan degradation by Xanthomonas and suggest how these enzymes synergistically assist infection and pathogenesis. Our findings indicate that XynB contributes to breach the plant cell wall barrier, providing nutrients and facilitating the translocation of effector molecules, whereas the exo-oligoxylanase XynA possibly participates in the suppression of oligosaccharide-induced immune responses.

  • Organizational Affiliation

    Biosciences National Laboratory and National Center for Research in Energy and Materials, Campinas, São Paulo, 13083-970, Brazil.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Xylanase306Xanthomonas citri pv. citri str. 306Mutation(s): 0 
Gene Names: xynBXAC4254
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CA

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 1.30 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.133 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.463α = 90
b = 71.834β = 90
c = 83.839γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil13/13309-0

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-08
    Type: Initial release
  • Version 1.1: 2014-10-15
    Changes: Database references, Structure summary
  • Version 1.2: 2014-11-26
    Changes: Database references
  • Version 1.3: 2018-11-07
    Changes: Data collection, Database references, Derived calculations, Other, Source and taxonomy
  • Version 1.4: 2019-04-17
    Changes: Author supporting evidence, Data collection
  • Version 1.5: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.6: 2023-12-27
    Changes: Data collection, Database references, Derived calculations, Refinement description