9WAT | pdb_00009wat

Crystal structure of CYP204A3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.248 (Depositor), 0.258 (DCC) 
  • R-Value Work: 
    0.212 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 
    0.214 (Depositor) 

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


Literature

Unveiling cytochrome P450 enzymes that catalyze steroid side-chain cleavage in bacteria.

Tian, W.Wei, G.Duan, B.Peng, H.Liu, H.Zheng, M.Lin, Z.Deng, Z.Zhang, Z.Qu, X.

(2025) Nat Commun 

  • DOI: https://doi.org/10.1038/s41467-025-67278-3
  • Primary Citation of Related Structures:  
    9WAT

  • PubMed Abstract: 

    Steroids are among the most valuable and widely used pharmaceuticals. The cholesterol side-chain cleavage enzyme (P450scc) is critical for steroid metabolism and hormone biosynthesis. While mammalian eukaryotic P450scc enzymes are well-characterized, bacterial counterparts remain underexplored despite their industrial promise and potential contributions to bacterial steroid catabolism. Here, we identify a series of CYP204 family P450 enzymes, widely distributed across diverse steroid-degrading bacterial species, that catalyze the side-chain cleavage of cholesterol, phytosterol, and cholestenone to produce pregnenolone and progesterone. Unlike mammalian enzymes, which exhibit strict cholesterol specificity, bacterial P450scc enzymes display relaxed substrate specificity, preferentially converting cholestenone to progesterone-a key precursor in steroid drug semi-synthesis. Structural and mechanistic analyses demonstrate that CYP204 enzymes employ a flexible, dual-regioselective C-H activation mechanism distinct from the sequential hydroxylation of mammalian P450scc enzymes. Iterative saturation mutagenesis identified critical residues for side-chain cleavage, improving catalytic efficiency up to 6.5-fold, and computational analyses clarified sequence-function relationships. This finding of bacterial P450scc enzymes not only underscores their potential function in bacterial steroid catabolism but also lays a foundation for promising biocatalytic strategies for pregnenolone and progesterone synthesis.


  • Organizational Affiliation
    • State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome P450440Novosphingobium sp. 28-62-57Mutation(s): 0 
Gene Names: B7Y36_09295
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
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: 2.10 Å
  • R-Value Free:  0.248 (Depositor), 0.258 (DCC) 
  • R-Value Work:  0.212 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 0.214 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.43α = 90
b = 78.077β = 90
c = 108.281γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
PHENIXmodel building
Aimlessdata scaling
PHASERphasing
XDSdata reduction

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. 22407088

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-17
    Type: Initial release
  • Version 1.1: 2025-12-24
    Changes: Database references