9VK4 | pdb_00009vk4

Crystal structure of Xyn10A from Thermoascus crustaceus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.225 (Depositor), 0.226 (DCC) 
  • R-Value Work: 
    0.184 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

Starting Model: in silico
View more details

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Enzymatic properties and potential for agro-food byproduct upcycling of xylanase TcrXyn10A expressed in Escherichia coli.

Kim, K.M.Han, D.G.Kim, B.S.Kim, S.R.Nam, K.H.Kim, I.J.

(2025) Int J Biol Macromol 329: 147880-147880

  • DOI: https://doi.org/10.1016/j.ijbiomac.2025.147880
  • Primary Citation of Related Structures:  
    9VK4

  • PubMed Abstract: 

    Xylanases play a crucial role in xylan degradation by cleaving its backbone and releasing xylooligosaccharides (XOSs) or xylose, which are compounds widely used in the food, paper, feed, and fuel industries. A xylanase from Thermoascus crustaceus (TcrXyn10A) exhibits high activity suitable for industrial use when expressed in Pichia pastoris; however, the high cost of this enzyme precludes its economic use. To improve economic feasibility, we expressed TcrXyn10A in Escherichia coli with a level of >30 mg per liter of culture, and the enzyme displayed optimal hydrolytic activity against beechwood xylan at pH 5.0 and 50-60 °C with a specific activity of 525.8 U/mg. The crystal structure of TcrXyn10A was determined at 2.1 Å resolution, revealing that Trp300 in the β8-α13 loop adopts a distinct conformation from that in homologous GH10 xylanases. TcrXyn10A expressed in E. coli did not form a disulfide bond between Cys280 and Cys286, which may have contributed to its different enzymatic properties from those of TcrXyn10A expressed in P. pastoris. TcrXyn10A expressed in E. coli efficiently produced XOSs from xylan extracted from agricultural byproducts, including corncobs and perilla stalks, suggesting its potential for industrial applications. These findings expand our knowledge of the molecular properties of TcrXyn10A and provide insights into its potential industrial use in biomass degradation.


  • Organizational Affiliation
    • Division of Applied Life Sciences, Institute of Agriculture and Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-xylanase
A, B
327Thermoascus crustaceusMutation(s): 0 
EC: 3.2.1.8
UniProt
Find proteins for A0A3G2WJY4 (Thermoascus crustaceus)
Explore A0A3G2WJY4 
Go to UniProtKB:  A0A3G2WJY4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3G2WJY4
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.225 (Depositor), 0.226 (DCC) 
  • R-Value Work:  0.184 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.618α = 90
b = 87.745β = 90
c = 101.991γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2025-07-02 
  • Deposition Author(s): Nam, K.H.

Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic OfNational Research Foundation of Korea

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-02
    Type: Initial release
  • Version 1.1: 2025-11-05
    Changes: Database references