8KEU | pdb_00008keu

Crystal Structures of Endo-beta-1,4-xylanase II mutant T2CT28C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 
    0.149 (Depositor), 0.148 (DCC) 
  • R-Value Work: 
    0.135 (Depositor), 0.134 (DCC) 
  • R-Value Observed: 
    0.136 (Depositor) 

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8KEU

This is version 1.2 of the entry. See complete history

Literature

Rational design of GH11 xylanase to balance the activity-stability trade-off.

Li, Z.Li, X.Zhou, Y.Lu, M.Li, M.Zhu, Y.Wan, Q.

(2025) Int J Biol Macromol 311: 143063-143063

  • DOI: https://doi.org/10.1016/j.ijbiomac.2025.143063
  • Primary Citation Related Structures: 
    8KEU

  • PubMed Abstract: 

    Enhancements of enzyme stability often compromise activity; thus, achieving an optimal balance between stability and activity poses a significant challenge in enzyme engineering. Our study investigated the stability-activity trade-off using the GH11 xylanase XynII as a model. A rational design strategy integrating crystal structure analysis and molecular dynamics simulations was used to distinguish regions important for structural stability and catalytic activity. Structural stability and activity were significantly enhanced by the introduction of two disulfide bonds involving four residues (T2C/T28C/R81C/T168C), which conferred a 75 % increase in activity, a 12.1 °C increase in T m , and an 80-fold improvement in half-life compared to the wild-type enzyme. The incorporation of two additional mutations (Q125A/I129S) was shown to increase the catalytic activity by 30 % by enhancing the dynamics of the active site. Our results illustrate a successful strategy for simultaneously increasing activity and stability by optimizing the dynamics of the catalytic region and the rigidity of the noncatalytic region.


  • Organizational Affiliation
    • School of Biological Science, Jining Medical University, Rizhao 276827, China.

Macromolecule Content 

  • Total Structure Weight: 21.59 kDa 
  • Atom Count: 1,797 
  • Modeled Residue Count: 190 
  • Deposited Residue Count: 190 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Endo-1,4-beta-xylanase II190Trichoderma reeseiMutation(s): 2 
EC: 3.2.1.8
UniProt
Find proteins for G0RUP7 (Hypocrea jecorina (strain QM6a))
Explore G0RUP7 
Go to UniProtKB:  G0RUP7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0RUP7
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free:  0.149 (Depositor), 0.148 (DCC) 
  • R-Value Work:  0.135 (Depositor), 0.134 (DCC) 
  • R-Value Observed: 0.136 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.119α = 90
b = 59.298β = 90
c = 69.782γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data

  • Released Date: 2024-08-14 
  • Deposition Author(s): Li, Z.

Funding OrganizationLocationGrant Number
Not fundedChina--

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-14
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Structure summary
  • Version 1.2: 2025-09-03
    Changes: Database references