9KPP | pdb_00009kpp

Crystal structure of FrazP2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.197 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.164 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 
    0.166 (Depositor) 

Starting Model: in silico
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Literature

Cytochrome P450 Mediated Cyclohexane Ring Formation in Forazoline Biosynthesis.

Chen, X.Zhang, Y.Li, S.Liao, W.Tao, W.Deng, Z.Bugni, T.S.Su, H.Zhang, F.

(2025) Angew Chem Int Ed Engl 64: e202504925-e202504925

  • DOI: https://doi.org/10.1002/anie.202504925
  • Primary Citation of Related Structures:  
    9KPP, 9KPU

  • PubMed Abstract: 

    Forazoline A, produced by the marine actinomycete Actinomadura sp. WMMB-499, is a unique PK/NRP hybrid macrolactone with promising antifungal in vivo efficacy through a previously unreported mechanism. Although a PKS/NRPS gene cluster was identified as a candidate for forazoline production, the precise biosynthetic pathway and the functions of the tailoring enzymes remain unclear. In this work, the functions of three cytochrome P450 mono-oxygenases (FrazP1P2P3) were characterized. Notably, FrazP2 was found to mediate cyclohexane ring formation from an 1,3,6-triene precursor during forazoline A biosynthesis, as confirmed by genetic and biochemical analysis. To gain structural and mechanistic insight into the activity of FrazP2, the crystal structure of a FrazP2-substrate complex has been solved at 2.3 Å resolution. The molecular dynamics simulations and DFT calculations revealed an unprecedented enzyme-catalyzed oxidative cyclization reaction by FrazP2. These findings expand our understanding of the catalytic diversity of cytochrome P450s, contributing to the diversification of natural products and enabling the creation of unnatural derivatives with increased antifungal potency.


  • Organizational Affiliation
    • Department of Pulmonary and Critical Care Medicine, Zhongnan Hospital of Wuhan University, TaiKang Center for Life and Medical Sciences, School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei, 430071, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome P450393Actinomadura sp.Mutation(s): 0 
Gene Names: F7P10_30360
UniProt
Find proteins for A0A239NBQ6 (Actinomadura meyerae)
Explore A0A239NBQ6 
Go to UniProtKB:  A0A239NBQ6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A239NBQ6
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.197 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.164 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 0.166 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.15α = 117.68
b = 52.96β = 104.06
c = 54.02γ = 93.26
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
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)ChinaNo. 82273826

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-21
    Type: Initial release
  • Version 1.1: 2025-07-16
    Changes: Database references