4XUO

Structure of the CBM22-1 xylan-binding domain from Paenibacillus barcinonensis Xyn10C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Exploring Multimodularity in Plant Cell Wall Deconstruction: STRUCTURAL AND FUNCTIONAL ANALYSIS OF Xyn10C CONTAINING THE CBM22-1-CBM22-2 TANDEM.

Sainz-Polo, M.A.Gonzalez, B.Menendez, M.Pastor, F.I.Sanz-Aparicio, J.

(2015) J.Biol.Chem. 290: 17116-17130

  • DOI: 10.1074/jbc.M115.659300
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Elucidating the molecular mechanisms regulating multimodularity is a challenging task. Paenibacillus barcinonensis Xyn10C is a 120-kDa modular enzyme that presents the CBM22/GH10/CBM9 architecture found in a subset of large xylanases. We report here ...

    Elucidating the molecular mechanisms regulating multimodularity is a challenging task. Paenibacillus barcinonensis Xyn10C is a 120-kDa modular enzyme that presents the CBM22/GH10/CBM9 architecture found in a subset of large xylanases. We report here the three-dimensional structure of the Xyn10C N-terminal region, containing the xylan-binding CBM22-1-CBM22-2 tandem (Xyn10C-XBD), which represents the first solved crystal structure of two contiguous CBM22 modules. Xyn10C-XBD is folded into two separate CBM22 modules linked by a flexible segment that endows the tandem with extraordinary plasticity. Each isolated domain has been expressed and crystallized, and their binding abilities have been investigated. Both domains contain the R(W/Y)YYE motif required for xylan binding. However, crystallographic analysis of CBM22-2 complexes shows Trp-308 as an additional binding determinant. The long loop containing Trp-308 creates a platform that possibly contributes to the recognition of precise decorations at subsite S2. CBM22-2 may thus define a subset of xylan-binding CBM22 modules directed to particular regions of the polysaccharide. Affinity electrophoresis reveals that Xyn10C-XBD binds arabinoxylans more tightly, which is more apparent when CBM22-2 is tested against highly substituted xylan. The crystal structure of the catalytic domain, also reported, shows the capacity of the active site to accommodate xylan substitutions at almost all subsites. The structural differences found at both Xyn10C-XBD domains are consistent with the isothermal titration calorimetry experiments showing two sites with different affinities in the tandem. On the basis of the distinct characteristics of CBM22, a delivery strategy of Xyn10C mediated by Xyn10C-XBD is proposed.


    Related Citations: 
    • Crystallization and preliminary X-ray diffraction analysis of the N-terminal domain of Paenibacillus barcinonensis xylanase 10C containing the CBM22-1-CBM22-2 tandem.
      Sainz-Polo, M.A.,Gonzalez, B.,Pastor, F.I.,Sanz-Aparicio, J.
      (2015) Acta Crystallogr F Struct Biol Commun 71: 136


    Organizational Affiliation

    the Departamento de Microbiología, Facultad de Biología, Universidad de Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain.,From the Departamentos de Cristalografía y Biología Estructural y xjulia@iqfr.csic.es.,From the Departamentos de Cristalografía y Biología Estructural y.,Química Física Biólogica, Instituto de Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, Serrano 119, 28006-Madrid and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endo-1,4-beta-xylanase C
A, B
159Paenibacillus barcinonensisMutation(s): 0 
Gene Names: xynC
EC: 3.2.1.8
Find proteins for O69230 (Paenibacillus barcinonensis)
Go to UniProtKB:  O69230
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.211 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 85.350α = 90.00
b = 85.350β = 90.00
c = 108.460γ = 120.00
Software Package:
Software NamePurpose
iMOSFLMdata reduction
REFMACrefinement
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-06-03
    Type: Initial release
  • Version 1.1: 2015-07-22
    Type: Database references
  • Version 1.2: 2018-04-18
    Type: Data collection, Database references