8IOZ | pdb_00008ioz

Crystal structure of transaminase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 
    0.265 (Depositor), 0.263 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 
    0.208 (Depositor) 

Starting Model: in silico
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Literature

Protein engineering of transaminase facilitating enzyme cascade reaction for the biosynthesis of azasugars.

Zhu, Y.Chen, P.Dong, Q.Li, Q.Liu, D.Liu, T.Liu, W.Sun, Y.

(2024) iScience 27: 109034-109034

  • DOI: https://doi.org/10.1016/j.isci.2024.109034
  • Primary Citation of Related Structures:  
    8IOZ, 8ISC, 8IVP

  • PubMed Abstract: 

    Azasugars, such as 1-deoxynojirimycin (1-DNJ), exhibit unique physiological functions and hold promising applications in medicine and health fields. However, the biosynthesis of 1-DNJ is hindered by the low activity and thermostability of the transaminase. In this study, the transaminase from Mycobacterium vanbaalenii (MvTA) with activity toward d-fructose was engineered through semi-rational design and high-throughput screening method. The final mutant M9-1 demonstrated a remarkable 31.2-fold increase in specific activity and an impressive 200-fold improvement in thermostability compared to the wild-type enzyme. Molecular dynamics (MD) simulations revealed that the mutation sites of H69R and K145R in M9-1 played crucial roles in the binding of the amino acceptor and donor, leading to the stable conformation of substrates within the active pocket. An enzyme cascade reaction was developed using M9-1 and the dehydrogenase from Paenibacillus polymyxa (GutB1) for the production of mannojirimycin (MJ), which provided a new idea for the in vitro biosynthesis of 1-DNJ.


  • Organizational Affiliation
    • Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Branched chain amino acid: 2-keto-4-methylthiobutyrate aminotransferase
A, B
337Mycolicibacterium vanbaalenii PYR-1Mutation(s): 0 
Gene Names: Mvan_4516
EC: 2.6.1
UniProt
Find proteins for A1TDP1 (Mycolicibacterium vanbaalenii (strain DSM 7251 / JCM 13017 / BCRC 16820 / KCTC 9966 / NRRL B-24157 / PYR-1))
Explore A1TDP1 
Go to UniProtKB:  A1TDP1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1TDP1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free:  0.265 (Depositor), 0.263 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.443α = 90
b = 71.443β = 90
c = 499.721γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
Aimlessdata scaling
PHASERphasing
HKL-2000data reduction

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: 2024-01-24
    Type: Initial release
  • Version 1.1: 2025-08-06
    Changes: Database references, Structure summary