9U53 | pdb_00009u53

Crystal structure of the CYP154C2 Q230A from Streptomyces avermitilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 
    0.234 (Depositor), 0.242 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 
    0.181 (Depositor) 

Starting Model: experimental
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Literature

Conformational gating in CYP154C2: Gln230-mediated substrate recognition and catalytic switching revealed by structural dynamics.

Yang, J.Huang, J.He, X.Fushinobu, S.Xu, L.H.

(2025) Biosci Biotechnol Biochem 89: 1144-1153

  • DOI: https://doi.org/10.1093/bbb/zbaf076
  • Primary Citation Related Structures: 
    9U53

  • PubMed Abstract: 

    Previously, we reported that CYP154C2 from Streptomyces avermitilis is capable of catalyzing the 2α-hydroxylation of the two model substrates, testosterone (TES) and androstenedione (ASD), and resolved the closed structures of both the substrate-free form and the TES-bound form. In this study, we extend these findings by determining the open-conformation structures of the substrate-free and ASD-bound forms-a rare achievement among bacterial P450s. Structural analyses revealed coordinated conformational shifts in the FG helices, HI helices, and BC loop during open-to-closed transitions. Despite divergent overall conformations, both substrates positioned their C2 atoms near the heme iron, aligning for 2α-hydroxylation. Mutagenesis studies established Gln230's pivotal role in substrate recognition and catalytic activation. High-resolution crystallography (1.97 Å) of the Q230A mutant revealed polyethylene glycol-occupied catalytic pockets (indicating complete loss of TES binding) while maintaining the open conformation. These results provide atomic-level evidence that Gln230 coordinates both substrate-driven conformational gating and catalytic site optimization.


  • Organizational Affiliation
    • College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome P450420Streptomyces avermitilisMutation(s): 1 
Gene Names: SAV14893_032670SAV31267_054670
UniProt
Find proteins for A0A4D4LTT1 (Streptomyces avermitilis)
Explore A0A4D4LTT1 
Go to UniProtKB:  A0A4D4LTT1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4D4LTT1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free:  0.234 (Depositor), 0.242 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 0.181 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.505α = 90
b = 79.353β = 90
c = 116.995γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data scaling
HKL-3000data reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2025-09-24 
  • Deposition Author(s): Xu, L.H.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-24
    Type: Initial release
  • Version 1.1: 2026-04-08
    Changes: Database references