Crystal structure of human prostacyclin synthase

Experimental Data Snapshot

  • Resolution: 2.15 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 

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Crystal Structure of the Human Prostacyclin Synthase

Chiang, C.-W.Yeh, H.-C.Wang, L.-H.Chan, N.-L.

(2006) J Mol Biol 364: 266-274

  • DOI: https://doi.org/10.1016/j.jmb.2006.09.039
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Prostacyclin synthase (PGIS) catalyzes an isomerization of prostaglandin H(2) to prostacyclin, a potent mediator of vasodilation and anti-platelet aggregation. Here, we report the crystal structure of human PGIS at 2.15 A resolution, which represents the first three-dimensional structure of a class III cytochrome P450. While notable sequence divergence has been recognized between PGIS and other P450s, PGIS exhibits the typical triangular prism-shaped P450 fold with only moderate structural differences. The conserved acid-alcohol pair in the I helix of P450s is replaced by residues G286 and N287 in PGIS, but the distinctive disruption of the I helix and the presence of a nearby water channel remain conserved. The side-chain of N287 appears to be positioned to facilitate the endoperoxide bond cleavage, suggesting a functional conservation of this residue in O-O bond cleavage. A combination of bent I helix and tilted B' helix creates a channel extending from the heme distal pocket, which seemingly allows binding of various ligands; however, residue W282, placed in this channel at a distance of 8.4 A from the iron with its indole side-chain lying parallel with the porphyrin plane, may serve as a threshold to exclude most ligands from binding. Additionally, a long "meander" region protruding from the protein surface may impede electron transfer. Although the primary sequence of the PGIS cysteine ligand loop diverges significantly from the consensus, conserved tertiary structure and hydrogen bonding pattern are observed for this region. The substrate-binding model was constructed and the structural basis for prostacyclin biosynthesis is discussed.

  • 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
Prostacyclin synthase
A, B
482Homo sapiensMutation(s): 0 
Gene Names: PTGIS
UniProt & NIH Common Fund Data Resources
Find proteins for Q16647 (Homo sapiens)
Explore Q16647 
Go to UniProtKB:  Q16647
PHAROS:  Q16647
GTEx:  ENSG00000124212 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16647
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.15 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.733α = 90
b = 105.596β = 92.01
c = 73.95γ = 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: 2006-10-10
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Derived calculations