9C9B | pdb_00009c9b

Crystal structure of AprG complexed with an epimer of the octose product


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 
    0.193 (Depositor), 0.192 (DCC) 
  • R-Value Work: 
    0.167 (Depositor), 0.167 (DCC) 
  • R-Value Observed: 
    0.167 (Depositor) 

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

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Ligand Structure Quality Assessment 


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 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.

Macromolecule Content 

  • Total Structure Weight: 74.79 kDa 
  • Atom Count: 6,002 
  • Modeled Residue Count: 667 
  • Deposited Residue Count: 678 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
AprG
A, B
339Streptoalloteichus tenebrariusMutation(s): 0 
Gene Names: aprG

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1AVJ
(Subject of Investigation/LOI)

Query on A1AVJ



Download:Ideal Coordinates CCD File
E [auth B](1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 7-acetamido-2-amino-2,3,7-trideoxy-L-glycero-alpha-D-allo-octopyranoside
C16 H32 N4 O8
MJGXTLDNWXSQPF-JBBPOTEGSA-N
A1AU8
(Subject of Investigation/LOI)

Query on A1AU8



Download:Ideal Coordinates CCD File
C [auth A]N-(2-hydroxyethyl)acetamide
C4 H9 N O2
PVCJKHHOXFKFRP-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
D [auth B]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free:  0.193 (Depositor), 0.192 (DCC) 
  • R-Value Work:  0.167 (Depositor), 0.167 (DCC) 
  • R-Value Observed: 0.167 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.52α = 90
b = 76.72β = 90
c = 123.34γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data scaling
xia2data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



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