Crystal structure of zebrafish prostacyclin synthase (cytochrome P450 8A1)

Experimental Data Snapshot

  • Resolution: 2.08 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 

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Structures of Prostacyclin Synthase and Its Complexes with Substrate Analog and Inhibitor Reveal a Ligand-specific Heme Conformation Change

Li, Y.-C.Chiang, C.-W.Yeh, H.-C.Hsu, P.-Y.Whitby, F.G.Wang, L.-H.Chan, N.-L.

(2008) J Biol Chem 283: 2917-2926

  • DOI: https://doi.org/10.1074/jbc.M707470200
  • Primary Citation of Related Structures:  
    3B6H, 3B98, 3B99

  • PubMed Abstract: 

    Prostacyclin synthase (PGIS) is a cytochrome P450 (P450) enzyme that catalyzes production of prostacyclin from prostaglandin H(2). PGIS is unusual in that it catalyzes an isomerization rather than a monooxygenation, which is typical of P450 enzymes. To understand the structural basis for prostacyclin biosynthesis in greater detail, we have determined the crystal structures of ligand-free, inhibitor (minoxidil)-bound and substrate analog U51605-bound PGIS. These structures demonstrate a stereo-specific substrate binding and suggest features of the enzyme that facilitate isomerization. Unlike most microsomal P450s, where large substrate-induced conformational changes take place at the distal side of the heme, conformational changes in PGIS are observed at the proximal side and in the heme itself. The conserved and extensive heme propionate-protein interactions seen in all other P450s, which are largely absent in the ligand-free PGIS, are recovered upon U51605 binding accompanied by water exclusion from the active site. In contrast, when minoxidil binds, the propionate-protein interactions are not recovered and water molecules are largely retained. These findings suggest that PGIS represents a divergent evolution of the P450 family, in which a heme barrier has evolved to ensure strict binding specificity for prostaglandin H(2), leading to a radical-mediated isomerization with high product fidelity. The U51605-bound structure also provides a view of the substrate entrance and product exit channels.

  • Organizational Affiliation

    Institute of Biochemistry, College of Life Sciences, National Chung Hsing University, Taichung City 402, Taiwan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Prostaglandin I2 synthase
A, B
475Danio rerioMutation(s): 0 
Gene Names: pgis
Membrane Entity: Yes 
Find proteins for F1RE08 (Danio rerio)
Explore F1RE08 
Go to UniProtKB:  F1RE08
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF1RE08
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C34 H32 Fe N4 O4
Experimental Data & Validation

Experimental Data

  • Resolution: 2.08 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.667α = 90
b = 87.896β = 90
c = 190.854γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-11-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description