Beta-1,4-xylanase from Chaetomium thermophilum complexed with methyl thioxylopentoside

Experimental Data Snapshot

  • Resolution: 1.55 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 

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Determination of thioxylo-oligosaccharide binding to family 11 xylanases using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry and X-ray crystallography

Janis, J.Hakanpaa, J.Hakulinen, N.Ibatullin, F.M.Hoxha, A.Derrick, P.J.Rouvinen, J.Vainiotalo, P.

(2005) FEBS J 272: 2317-2333

  • DOI: https://doi.org/10.1111/j.1742-4658.2005.04659.x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Noncovalent binding of thioxylo-oligosaccharide inhibitors, methyl 4-thio-alpha-xylobioside (S-Xyl2-Me), methyl 4,4II-dithio-alpha-xylotrioside (S-Xyl3-Me), methyl 4,4II,4III-trithio-alpha-xylotetroside (S-Xyl4-Me), and methyl 4,4II,4III,4IV-tetrathio-alpha-xylopentoside (S-Xyl5-Me), to three family 11 endo-1,4-beta-xylanases from Trichoderma reesei (TRX I and TRX II) and Chaetomium thermophilum (CTX) was characterized using electrospray ionization Fourier transform ion cyclotron resonance (FT-ICR) MS and X-ray crystallography. Ultra-high mass-resolving power and mass accuracy inherent to FT-ICR allowed mass measurements for noncovalent complexes to within |DeltaM|average of 2 p.p.m. The binding constants determined by MS titration experiments were in the range 10(4)-10(3) M-1, decreasing in the series of S-Xyl5-Me>or=S-Xyl4-Me>S-Xyl3-Me. In contrast, S-Xyl2-Me did not bind to any xylanase at the initial concentration of 5-200 microM, indicating increasing affinity with increasing number of xylopyranosyl units, with a minimum requirement of three. The crystal structures of CTX-inhibitor complexes gave interesting insights into the binding. Surprisingly, none of the inhibitors occupied any of the aglycone subsites of the active site. The binding to only the glycone subsites is nonproductive for catalysis, and yet this has also been observed for other family 11 xylanases in complex with beta-d-xylotetraose [Wakarchuk WW, Campbell RL, Sung WL, Davoodi J & Makoto Y (1994) Protein Sci3, 465-475, and Sabini E, Wilson KS, Danielsen S, Schulein M & Davies GJ (2001) Acta CrystallogrD57, 1344-1347]. Therefore, the role of the aglycone subsites remains controversial despite their obvious contribution to catalysis.

  • Organizational Affiliation

    Department of Chemistry, University of Joensuu, Finland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
endoxylanase 11A
A, B
196Thermochaetoides thermophilaMutation(s): 0 
Find proteins for Q8J1V6 (Thermochaetoides thermophila)
Explore Q8J1V6 
Go to UniProtKB:  Q8J1V6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8J1V6
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
4-thio-beta-D-xylopyranose-(1-4)-4-thio-beta-D-xylopyranose-(1-4)-methyl 4-thio-alpha-D-xylopyranoside
C, D
Glycosylation Resources
GlyTouCan:  G54887LV
GlyCosmos:  G54887LV
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on PCA
A, B
Experimental Data & Validation

Experimental Data

  • Resolution: 1.55 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.241α = 90
b = 57.593β = 90
c = 66.205γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-05-10
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2018-07-11
    Changes: Data collection
  • Version 2.0: 2019-12-25
    Changes: Database references, Derived calculations, Polymer sequence
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 3.1: 2020-10-14
    Changes: Structure summary
  • Version 3.2: 2023-10-25
    Changes: Data collection, Database references, Refinement description