Crystal structure of CbXyn10C variant E140Q/E248Q complexed with cellohexaose

Experimental Data Snapshot

  • Resolution: 1.87 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.153 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history


Insights into the roles of non-catalytic residues in the active site of a GH10 xylanase with activity on cellulose.

Chu, Y.Tu, T.Penttinen, L.Xue, X.Wang, X.Yi, Z.Gong, L.Rouvinen, J.Luo, H.Hakulinen, N.Yao, B.Su, X.

(2017) J Biol Chem 292: 19315-19327

  • DOI: https://doi.org/10.1074/jbc.M117.807768
  • Primary Citation of Related Structures:  
    5OFJ, 5OFK, 5OFL

  • PubMed Abstract: 

    Bifunctional glycoside hydrolases have potential for cost-savings in enzymatic decomposition of plant cell wall polysaccharides for biofuels and bio-based chemicals. The N-terminal GH10 domain of a bifunctional multimodular enzyme Cb Xyn10C/Cel48B from Caldicellulosiruptor bescii is an enzyme able to degrade xylan and cellulose simultaneously. However, the molecular mechanism underlying its substrate promiscuity has not been elucidated. Herein, we discovered that the binding cleft of Cb Xyn10C would have at least six sugar-binding subsites by using isothermal titration calorimetry analysis of the inactive E140Q/E248Q mutant with xylo- and cello-oligosaccharides. This was confirmed by determining the catalytic efficiency of the wild-type enzyme on these oligosaccharides. The free form and complex structures of Cb Xyn10C with xylose- or glucose-configured oligosaccharide ligands were further obtained by crystallographic analysis and molecular modeling and docking. Cb Xyn10C was found to have a typical (β/α) 8 -TIM barrel fold and "salad-bowl" shape of GH10 enzymes. In complex structures with xylo-oligosaccharides, seven sugar-binding subsites were found, and many residues responsible for substrate interactions were identified. Site-directed mutagenesis indicated that 6 and 10 amino acid residues were key residues for xylan and cellulose hydrolysis, respectively. The most important residues are centered on subsites -2 and -1 near the cleavage site, whereas residues playing moderate roles could be located at more distal regions of the binding cleft. Manipulating the residues interacting with substrates in the distal regions directly or indirectly improved the activity of Cb Xyn10C on xylan and cellulose. Most of the key residues for cellulase activity are conserved across GH10 xylanases. Revisiting randomly selected GH10 enzymes revealed unreported cellulase activity, indicating that the dual function may be a more common phenomenon than has been expected.

  • Organizational Affiliation

    From the Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycoside hydrolase family 48339Caldicellulosiruptor bescii DSM 6725Mutation(s): 2 
Gene Names: Athe_1857
Find proteins for B9MKT7 (Caldicellulosiruptor bescii (strain ATCC BAA-1888 / DSM 6725 / KCTC 15123 / Z-1320))
Explore B9MKT7 
Go to UniProtKB:  B9MKT7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB9MKT7
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G09454VW
GlyCosmos:  G09454VW
GlyGen:  G09454VW
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Resolution: 1.87 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.153 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 185.83α = 90
b = 185.83β = 90
c = 56.32γ = 90
Software Package:
Software NamePurpose
xia2data reduction
xia2data scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Academy of FinlandFinland256937
Academy of FinlandFinland292705

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-04
    Type: Initial release
  • Version 1.1: 2017-10-18
    Changes: Database references
  • Version 1.2: 2017-12-06
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary