9KOV | pdb_00009kov

Crystal structure of an amidohydrolase mutant from Thermonema


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 
    0.264 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.222 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 
    0.224 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


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Literature

A thermostable OTA-detoxifying hydrolase from Thermonema rossianum: identification, characterization, structure, catalytic mechanism, and application.

Xu, N.Yan, M.Liang, X.Qin, H.Gao, J.Liu, W.

(2025) Food Chem 485: 144515-144515

  • DOI: https://doi.org/10.1016/j.foodchem.2025.144515
  • Primary Citation of Related Structures:  
    9KOV

  • PubMed Abstract: 

    Ochratoxin A (OTA) is highly toxic and widely distributed, posing serious threats to human and animal health. Searching for effective OTA-detoxifying enzyme is crucial for the prevention and control of OTA contaminations. Here, a new OTA-detoxifying enzyme, TrADH from Thermonema rossianum is identified, which exhibits highest temperature tolerance among OTA-detoxifying enzymes. TrADH maintains good activity in the range of 45-85 °C and retains about 50 % activity after heating at 70 °C for 30 min. Based on the solved crystal structures, the catalytic mechanism is proposed, and protein engineering of catalytic-related residues is performed to obtain a 2.1-fold upgraded variant TrADHS67E with the specific enzyme activity of 3990 U/mg, which is more efficient than the reported OTA-detoxifying enzymes. The efficient degradation of OTA in rum and walnut reveals the prospect of TrADH in food applications. The results indicate that TrADH has the potential in OTA bio-detoxification in food and feed industry.


  • Organizational Affiliation
    • School of Biological Engineering, Tianjin University of Science and Technology, No 9, 13th, Avenue, Tianjin Economic and Technological Development Area, Tianjin 300457, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China. Electronic address: xunuonuo@tib.cas.cn.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
trum-mut
A, B, C, D, E
A, B, C, D, E, F, G, H
422Pyrinomonas methylaliphatogenesMutation(s): 0 
UniProt
Find proteins for A0A846MQ93 (Thermonema lapsum)
Explore A0A846MQ93 
Go to UniProtKB:  A0A846MQ93
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A846MQ93
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free:  0.264 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.222 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 0.224 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.645α = 90
b = 205.755β = 103.08
c = 105.268γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-26
    Type: Initial release