Crystal structure of glycosidic hydrolase family 10 (GH10) xylanase XynA contains an additional proline-rich sequence in the C-terminus

Experimental Data Snapshot

  • Resolution: 2.56 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.219 

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Effectiveness of ruminal xylanase with an extra proline-rich C-terminus on lignocellulosic biomass degradation.

Dong, R.Liao, M.Liu, X.Penttinen, L.Hakulinen, N.Qin, X.Wang, X.Huang, H.Luo, H.Yao, B.Bai, Y.Tu, T.

(2023) Bioresour Technol 372: 128695-128695

  • DOI: https://doi.org/10.1016/j.biortech.2023.128695
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The efficient degradation of plant polysaccharides in agricultural waste requires xylanases with high catalytic activity. In this study, the C-terminal proline-rich GH10 xylanase XynA from sheep rumen was investigated using product analysis, structural characterization, truncated and site-directed mutagenesis, molecular dynamics simulation, and application evaluation, revealing that the proline-rich C-terminus contributes to the interaction at the substrate-binding pocket to reduce the binding free energy. Compared to the C-terminally truncated enzyme XynA-Tr, XynA has a more favorable conformation for proton transfer and affinity attack, facilitating the degradation of oligomeric and beechwood xylan without altering the hydrolysis pattern. Moreover, both the reduced sugar yield and weight loss of the pretreated wheat bran, corn cob, and corn stalk hydrolyzed by XynA for 12 h increased by more than 30 %. These findings are important to better understand the relationship between enzyme activities and their terminal regions and suggest candidate materials for lignocellulosic biomass utilization.

  • Organizational Affiliation

    State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
383uncultured organismMutation(s): 0 
Find proteins for L7UY53 (uncultured organism)
Explore L7UY53 
Go to UniProtKB:  L7UY53
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupL7UY53
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.56 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.219 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.922α = 90
b = 99.461β = 100.907
c = 87.833γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-22
    Type: Initial release
  • Version 1.1: 2023-08-30
    Changes: Data collection, Source and taxonomy