9J2P | pdb_00009j2p

Fe2+/pterin-dependent,BH4-L-isoleucine-SnPolE complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.229 (Depositor), 0.231 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 
    0.199 (Depositor) 

Starting Model: experimental
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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
SnPolE
A, B
373Streptomyces sp. NTH33Mutation(s): 0 
Gene Names: C1I97_07030
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
H4B (Subject of Investigation/LOI)
Query on H4B

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
5,6,7,8-TETRAHYDROBIOPTERIN
C9 H15 N5 O3
FNKQXYHWGSIFBK-RPDRRWSUSA-N
ILE (Subject of Investigation/LOI)
Query on ILE

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
ISOLEUCINE
C6 H13 N O2
AGPKZVBTJJNPAG-WHFBIAKZSA-N
FE2
Query on FE2

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.229 (Depositor), 0.231 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 0.199 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.918α = 90
b = 91.25β = 90
c = 113.002γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
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)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