Xylopentaose binding mutated (X-2 L110F) CBM4-2 Carbohydrate Binding Module from a Thermostable Rhodothermus marinus Xylanase

Experimental Data Snapshot

  • Resolution: 1.40 Å
  • R-Value Free: 0.200 
  • R-Value Observed: 0.143 

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Structural basis for carbohydrate-binding specificity--a comparative assessment of two engineered carbohydrate-binding modules.

von Schantz, L.Hakansson, M.Logan, D.T.Walse, B.Osterlin, J.Nordberg-Karlsson, E.Ohlin, M.

(2012) Glycobiology 22: 948-961

  • DOI: https://doi.org/10.1093/glycob/cws063
  • Primary Citation of Related Structures:  
    2Y64, 2Y6G, 2Y6H, 2Y6J, 2Y6K, 2Y6L

  • PubMed Abstract: 

    Detection, immobilization and purification of carbohydrates can be done using molecular probes that specifically bind to targeted carbohydrate epitopes. Carbohydrate-binding modules (CBMs) are discrete parts of carbohydrate-hydrolyzing enzymes that can be engineered to bind and detect specifically a number of carbohydrates. Design and engineering of CBMs have benefited greatly from structural studies that have helped us to decipher the basis for specificity in carbohydrate-protein interactions. However, more studies are needed to predict which modifications in a CBM would generate probes with predetermined binding properties. In this report, we present the crystal structures of two highly related engineered CBMs with different binding specificity profiles: X-2, which is specific for xylans and the L110F mutant of X-2, which binds xyloglucans and β-glucans in addition to xylans. The structures of the modules were solved both in the apo form and complexed with oligomers of xylose, as well as with an oligomer of glucose in the case of X-2 L110F. The mutation, leucine to phenylalanine, converting the specific module into a cross-reactive one, introduces a crucial hydrogen-π interaction that allows the mutant to retain glucan-based ligands. The cross-reactivity of X-2 L110F is furthermore made possible by the plasticity of the protein, in particular, of residue R142, which permits accommodation of an extra hydroxymethyl group present in cellopentaose and not xylopentaose. Altogether, this study shows, in structural detail, altered protein-carbohydrate interactions that have high impact on the binding properties of a carbohydrate probe but are introduced through simple mutagenesis.

  • Organizational Affiliation

    Department of Immunotechnology, Lund University, Lund, Sweden.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
XYLANASE167Rhodothermus marinusMutation(s): 7 
Find proteins for Q7WTN6 (Rhodothermus marinus)
Explore Q7WTN6 
Go to UniProtKB:  Q7WTN6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7WTN6
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G47101GE
GlyCosmos:  G47101GE
Experimental Data & Validation

Experimental Data

  • Resolution: 1.40 Å
  • R-Value Free: 0.200 
  • R-Value Observed: 0.143 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.46α = 90
b = 50.68β = 90
c = 62.55γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-03-07
    Type: Initial release
  • Version 1.1: 2012-08-01
    Changes: Database references
  • Version 1.2: 2018-01-17
    Changes: Data collection, Database references, Structure summary
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
  • Version 2.1: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary