4PMV

Crystal structure of a novel reducing-end xylose-releasing exo-oligoxylanase (XynA) belonging to GH10 family (space group P43212)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history. 


Literature

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: 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 ...

    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: 

    From the Biosciences National Laboratory and mario.murakami@lnbio.cnpem.br.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Endo-1,4-beta-xylanase AA, B357Xanthomonas citri pv. citri str. 306Mutation(s): 0 
Gene Names: xynA, XAC4249
EC: 3.2.1.8
UniProt
Find proteins for Q8PEU1 (Xanthomonas axonopodis pv. citri (strain 306))
Explore Q8PEU1 
Go to UniProtKB:  Q8PEU1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8PEU1
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.819α = 90
b = 78.819β = 90
c = 303.969γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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View more in-depth experimental data

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: 2017-11-01
    Changes: Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy, Structure summary
  • Version 1.4: 2019-02-13
    Changes: Data collection, Source and taxonomy
  • Version 1.5: 2019-04-17
    Changes: Author supporting evidence, Data collection
  • Version 1.6: 2020-01-01
    Changes: Author supporting evidence