8XM2 | pdb_00008xm2

The mutant crystal structure of phytase APPAmut9 from Yersinia intermedia


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 
    0.212 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.162 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.164 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Achieving thermostability of a phytase with resistance up to 100 °C.

Tu, T.Wang, Q.Dong, R.Liu, X.Penttinen, L.Hakulinen, N.Tian, J.Zhang, W.Wang, Y.Luo, H.Yao, B.Huang, H.

(2024) J Biological Chem 300: 107992-107992

  • DOI: https://doi.org/10.1016/j.jbc.2024.107992
  • Primary Citation of Related Structures:  
    8XM1, 8XM2

  • PubMed Abstract: 

    The development of enzymes with high-temperature resistance up to 100 °C is of significant and practical value in advancing the sustainability of industrial production. Phytase, a crucial enzyme in feed industrial applications, encounters challenges due to its limited heat resistance. Herein, we employed rational design strategies involving the introduction of disulfide bonds, free energy calculation, and B-factor analysis based on the crystal structure of phytase APPAmut4 (1.90 Å), a variant with enhanced expression levels derived from Yersinia intermedia, to improve its thermostability. Among the 144 variants experimentally verified, 29 exhibited significantly improved thermostability with higher t 1/2 values at 65 °C. Further combination and superposition led to APPAmut9 with an accumulation of five additional pairs of disulfide bonds and six single-point mutation sites, leading to an enhancement in its thermostability with a t 1/2 value of 256.7 min at 65 °C, which was more than 75-fold higher than that of APPAmut4 (3.4 min). APPAmut9 exhibited a T 50 value of 96 °C, representing a substantial increase of 40.9 °C compared to APPAmut4. Notably, approximately 70% of enzyme activity remained intact after exposure to boiling water at 100 °C for a holding period of 5 min. Significantly, these advantageous modifications were strategically positioned away from the catalytic pocket where enzymatic reactions occur to ensure minimal compromise on catalytic efficiency between APPAmut9 (11,500 ± 1100/mM/s) and APPAmut4 (12,300 ± 1600/mM/s). This study demonstrates the feasibility of engineering phytases with resistance to boiling using rational design strategies.


  • Organizational Affiliation
    • State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China. Electronic address: tutao@caas.cn.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phytase418Yersinia intermediaMutation(s): 20 
EC: 3.1.3.26
UniProt
Find proteins for Q000T0 (Yersinia intermedia)
Explore Q000T0 
Go to UniProtKB:  Q000T0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ000T0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free:  0.212 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.162 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.164 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.5α = 90
b = 70.45β = 90
c = 103.54γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32222082

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-03
    Type: Initial release
  • Version 1.1: 2024-10-09
    Changes: Structure summary
  • Version 1.2: 2025-01-15
    Changes: Database references