5OFL

Crystal structure of CbXyn10C variant E140Q/E248Q complexed with cellohexaose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.871 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.152 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1074/jbc.M117.807768
  • Primary Citation of Related Structures:  

  • 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 <i>Cb </i>Xyn10C/C ...

    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

    the Department of Chemistry, University of Eastern Finland, Joensuu Campus, Joensuu FIN-80101, Finland, nina.hakulinen@uef.fi.,the Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China, and.,From the Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.,From the Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China, binyao@caas.cn.,the Key Laboratory of Molecular Animal Nutrition and Feed Sciences, College of Animal Science, Zhejiang University, Hangzhou 310058, China.,the Department of Chemistry, University of Eastern Finland, Joensuu Campus, Joensuu FIN-80101, Finland.,From the Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China, suxiaoyun@caas.cn.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycoside hydrolase family 48
A
339Caldicellulosiruptor bescii (strain ATCC BAA-1888 / DSM 6725 / Z-1320)Mutation(s): 2 
Find proteins for B9MKT7 (Caldicellulosiruptor bescii (strain ATCC BAA-1888 / DSM 6725 / Z-1320))
Go to UniProtKB:  B9MKT7
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
BGC
Query on BGC

Download SDF File 
Download CCD File 
A
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.871 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.152 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 185.830α = 90.00
b = 185.830β = 90.00
c = 56.320γ = 90.00
Software Package:
Software NamePurpose
xia2data scaling
xia2data reduction
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Academy of FinlandFinland256937
Academy of FinlandFinland292705

Revision History 

  • Version 1.0: 2017-10-04
    Type: Initial release
  • Version 1.1: 2017-10-18
    Type: Database references
  • Version 1.2: 2017-12-06
    Type: Database references