9J27 | pdb_00009j27

Fe-SaPolF-L-isoleucine copmplex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.266 (Depositor), 0.267 (DCC) 
  • R-Value Work: 
    0.217 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 
    0.220 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

A two-metalloenzyme cascade constructs the azetidine-containing pharmacophore.

Gong, R.Qu, Y.Liu, J.Zhang, X.Zhou, L.Tian, Z.Zeng, X.Jin, B.Li, Z.Yu, L.Chen, R.Zhou, Y.Liao, L.Yang, L.Song, X.Cai, Y.S.Shen, K.Deng, Z.Zhang, Z.Wang, B.Chen, W.

(2025) Nat Chem 

  • DOI: https://doi.org/10.1038/s41557-025-01949-y
  • Primary Citation of Related Structures:  
    9J27, 9J28, 9J29, 9J2A, 9J2B, 9J2C, 9J2E, 9J2M, 9J2P, 9J2R, 9J30, 9J33, 9J3G, 9J3V

  • PubMed Abstract: 

    Azetidine is a prominent pharmacophore present in dozens of drug-related molecules of both natural and synthetic origins. But how nature builds this moiety has long remained enigmatic. Here we address the full deciphering of a two-metalloenzyme cascade leading to polyoximic acid, an azetidine-containing moiety of the fungicide polyoxin. We demonstrate that the PolE enzyme functions as an Fe 2+ /pterin-dependent L-isoleucine desaturase. Moreover we illustrate that PolF is a new member of the emerging haem-oxygenase-like diiron oxidases, converting the desaturated L-isoleucine to polyoximic acid via an intramolecular C-N cyclization. Remarkably, we also establish that PolF exhibits dual functionality, orchestrating the sequential desaturation and cyclization with L-isoleucine as the initial substrate. Finally, our combined structural and quantum-mechanics/molecular-mechanics studies show that the PolF enzyme employs an extraordinary mechanism for the construction of the azetidine-containing moiety. These findings expand our knowledge on the catalysis of metalloenzymes and open the way for rational access of more azetidine-related molecules.


  • Organizational Affiliation
    • Department of Anesthesiology, Zhongnan Hospital of Wuhan University, TaiKang Center for Life and Medical Sciences, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SaPolF292Streptomyces armeniacusMutation(s): 0 
Gene Names: DVA86_03895
UniProt
Find proteins for A0A345XJU6 (Streptomyces armeniacus)
Explore A0A345XJU6 
Go to UniProtKB:  A0A345XJU6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A345XJU6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.266 (Depositor), 0.267 (DCC) 
  • R-Value Work:  0.217 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 0.220 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.168α = 90
b = 90.168β = 90
c = 64.733γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
CRANK2phasing

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)China31070027
National Natural Science Foundation of China (NSFC)China32170026
National Natural Science Foundation of China (NSFC)China32371303

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-08
    Type: Initial release
  • Version 1.1: 2025-10-15
    Changes: Database references