9C9A | pdb_00009c9a

Crystal structure of AprG complexed with a GlcNAc analog inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 
    0.186 (Depositor), 0.186 (DCC) 
  • R-Value Work: 
    0.168 (Depositor), 0.167 (DCC) 
  • R-Value Observed: 
    0.168 (Depositor) 

Starting Model: in silico
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This is version 1.1 of the entry. See complete history


Literature

Structure-Guided Mechanistic Investigation of Stereochemical Inversion during the Octose Formation Catalyzed by an Atypical Transaldolase AprG in the Biosynthesis of Apramycin.

Kim, W.Fan, P.H.Bu, J.Liu, H.W.Zhang, Y.J.

(2025) ACS Catal 15: 13778-13786

  • DOI: https://doi.org/10.1021/acscatal.5c03420
  • Primary Citation of Related Structures:  
    9C95, 9C99, 9C9A, 9C9B

  • PubMed Abstract: 

    Transaldolases are essential enzymes across all life domains, facilitating the exchange of aldol fragments in metabolic processes. AprG, a transaldolase in the apramycin biosynthetic pathway, catalyzes the incorporation of C7' and C8' moieties into the bicyclic octose core. Unlike canonical transaldolases, the AprG product exhibits unique stereochemical inversion, whose mechanism remains unclear. Here, by taking snapshots of AprG at different stages of the reaction, we identified active site residues essential for each reaction step. Strikingly, we discovered a 7'-epimer of the AprG product, directly implicating this inversion in the enzyme's mechanism and uncovering a key aspect of product inhibition. This unexpected epimer sheds a light on the stereochemical plasticity of transaldolases. Additionally, donor analogue studies provided insights into substrate recognition. These findings enhance our mechanistic understanding of AprG and suggest strategies for engineering biocatalysts with tailored stereochemical properties. More broadly, this work provides a framework for modifying transaldolase activity, expanding its potential applications in chemoenzymatic synthesis and metabolic engineering.


  • Organizational Affiliation
    • McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AprG
A, B
339Streptoalloteichus tenebrariusMutation(s): 0 
Gene Names: aprG
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free:  0.186 (Depositor), 0.186 (DCC) 
  • R-Value Work:  0.168 (Depositor), 0.167 (DCC) 
  • R-Value Observed: 0.168 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.15α = 90
b = 76.44β = 90
c = 123.47γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data scaling
xia2data reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM148356

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-06
    Type: Initial release
  • Version 1.1: 2025-09-10
    Changes: Database references