4XUR

Structure of the CBM22-2 xylan-binding domain from Paenibacillus barcinonensis Xyn10C in complex with xylotetraose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 

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This is version 2.0 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:  
    4W8L, 4XUN, 4XUO, 4XUP, 4XUQ, 4XUR, 4XUT

  • 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 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 ...

    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

    From the Departamentos de Cristalografía y Biología Estructural y xjulia@iqfr.csic.es.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Endo-1,4-beta-xylanase CA, B, C181Paenibacillus barcinonensisMutation(s): 0 
Gene Names: xynC
EC: 3.2.1.8
UniProt
Find proteins for O69230 (Paenibacillus barcinonensis)
Explore O69230 
Go to UniProtKB:  O69230
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO69230
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranoseD 4N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G60650FG
GlyCosmos:  G60650FG
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-xylopyranose-(1-4)-beta-D-xylopyranoseE 2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G87728WL
GlyCosmos:  G87728WL
Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranoseF 3N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G87429QT
GlyCosmos:  G87429QT
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XYP
Query on XYP

Download Ideal Coordinates CCD File 
H [auth B],
J [auth C]
beta-D-xylopyranose
C5 H10 O5
SRBFZHDQGSBBOR-KKQCNMDGSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
G [auth A],
I [auth B],
K [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 2 Unique
Entity ID: 3
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900116
Query on PRD_900116
E4beta-beta-xylobioseOligosaccharide / Metabolism Ligand Interaction
Entity ID: 4
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900117
Query on PRD_900117
F4beta-beta-xylotrioseOligosaccharide / Metabolism Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.769α = 90
b = 92.769β = 90
c = 48.571γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-03
    Type: Initial release
  • Version 1.1: 2015-07-22
    Changes: Database references
  • Version 1.2: 2018-04-18
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary