4PMZ

Crystal structure of GH10 endo-b-1,4-xylanase (XynB) from Xanthomonas axonopodis pv citri complexed with xylobiose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.5 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
  • Structures With Same Primary Citation

  • 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 influe ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Xylanase
A, B
303Xanthomonas citri pv. citri str. 306Mutation(s): 0 
Gene Names: xynBXAC4254
EC: 3.2.1.8
Find proteins for Q8PET6 (Xanthomonas axonopodis pv. citri (strain 306))
Go to UniProtKB:  Q8PET6
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BXP
Query on BXP

Download CCD File 
A, B
4-O-beta-D-xylopyranosyl-beta-D-xylopyranose
C10 H18 O9
LGQKSQQRKHFMLI-SJYYZXOBSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.056α = 90
b = 49.238β = 90
c = 83.035γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History 

  • 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: 2015-02-04
    Changes: Derived calculations
  • Version 1.4: 2019-04-17
    Changes: Advisory, Author supporting evidence, Data collection, Database references, Derived calculations, Other, Source and taxonomy, Structure summary
  • Version 1.5: 2020-01-01
    Changes: Author supporting evidence