9UJD | pdb_00009ujd

Crystal structure of a Transaminase PaTA from Pseudonocardia ammonioxydans in complex with PLP and LLP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.248 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

Starting Model: in silico
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Literature

Rational engineering of R-selective transaminase from Pseudonocardia ammonioxydans for efficient synthesis of chiral beta-amino aryl ethers.

Gao, X.Zhang, W.Wang, Q.Zhang, Z.Wei, H.Wei, X.Zhao, L.Liu, W.Jia, X.You, S.

(2025) Bioresour Technol 443: 133802-133802

  • DOI: https://doi.org/10.1016/j.biortech.2025.133802
  • Primary Citation of Related Structures:  
    9UJD

  • PubMed Abstract: 

    R-transaminases show significant promise for the industrial synthesis of chiral amine pharmaceutical intermediates. However, the application is hindered by limited substrate acceptance and poor catalytic efficiency toward bulky substrates. Herein, the R-transaminase from Pseudonocardia ammonioxydans (PaTA) with the high activity towards the mexiletine precursor ketone (1c) was identified, and its crystal structure was resolved (PDB: 9UJD). Substrate specificity analysis revealed that PaTA exhibited obvious substrate preference for aryl-substituted phenoxyacetones (1c-16c). Based on the crystal structure, key sites affecting substrate selectivity were identified, followed by multiple rounds of engineering that yielded a series of variants with enhanced catalytic performance. Ultimately, the gram-scale synthesis of R-1d and 12d was conducted, achieving the space-time yields (STY) of 24 and 32 g/L·h, respectively. This study provides practical biocatalysts for the synthesis of chiral β-amino aryl ethers, along with insights into the relationship between the enzyme-substrate binding pocket and substrate selectivity.


  • Organizational Affiliation
    • School of Life Sciences and Biopharmaceutical Sciences, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe, Shenyang 110016, the People's Republic of China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Branched-chain amino acid aminotransferase348Pseudonocardia ammonioxydansMutation(s): 0 
Gene Names: SAMN05216207_10664
UniProt
Find proteins for A0A1I5HJ61 (Pseudonocardia ammonioxydans)
Explore A0A1I5HJ61 
Go to UniProtKB:  A0A1I5HJ61
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1I5HJ61
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Branched-chain amino acid aminotransferase
B, C, D
348Pseudonocardia ammonioxydansMutation(s): 0 
Gene Names: SAMN05216207_10664
UniProt
Find proteins for A0A1I5HJ61 (Pseudonocardia ammonioxydans)
Explore A0A1I5HJ61 
Go to UniProtKB:  A0A1I5HJ61
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1I5HJ61
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
LLP
Query on LLP
A
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.248 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 237.198α = 90
b = 237.198β = 90
c = 237.198γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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: 2025-12-31
    Type: Initial release