Crystal Structure of Eicosapentanoic Acid Bound in the Cyclooxygenase Channel of Prostaglandin Endoperoxide H Synthase-1.

Experimental Data Snapshot

  • Resolution: 3.10 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.228 

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Structure of eicosapentaenoic and linoleic acids in the cyclooxygenase site of prostaglandin endoperoxide H synthase-1.

Malkowski, M.G.Thuresson, E.D.Lakkides, K.M.Rieke, C.J.Micielli, R.Smith, W.L.Garavito, R.M.

(2001) J Biol Chem 276: 37547-37555

  • DOI: https://doi.org/10.1074/jbc.M105982200
  • Primary Citation of Related Structures:  
    1IGX, 1IGZ

  • PubMed Abstract: 

    Prostaglandin endoperoxide H synthases-1 and -2 (PGHSs) can oxygenate 18-22 carbon polyunsaturated fatty acids, albeit with varying efficiencies. Here we report the crystal structures of eicosapentaenoic acid (EPA, 20:5 n-3) and linoleic acid (LA, 18:2 n-6) bound in the cyclooxygenase active site of Co(3+) protoporphyrin IX-reconstituted ovine PGHS-1 (Co(3+)-oPGHS-1) and compare the effects of active site substitutions on the rates of oxygenation of EPA, LA, and arachidonic acid (AA). Both EPA and LA bind in the active site with orientations similar to those seen previously with AA and dihomo-gamma-linolenic acid (DHLA). For EPA, the presence of an additional double bond (C-17/C-18) causes this substrate to bind in a "strained" conformation in which C-13 is misaligned with respect to Tyr-385, the residue that abstracts hydrogen from substrate fatty acids. Presumably, this misalignment is responsible for the low rate of EPA oxygenation. For LA, the carboxyl half binds in a more extended configuration than AA, which results in positioning C-11 next to Tyr-385. Val-349 and Ser-530, recently identified as important determinants for efficient oxygenation of DHLA by PGHS-1, play similar roles in the oxygenation of EPA and LA. Approximately 750- and 175-fold reductions in the oxygenation efficiency of EPA and LA were observed with V349A oPGHS-1, compared with a 2-fold change for AA. Val-349 contacts C-2 and C-3 of EPA and C-4 of LA orienting the carboxyl halves of these substrates so that the omega-ends are aligned properly for hydrogen abstraction. An S530T substitution decreases the V(max)/K(m) of EPA and LA by 375- and 140-fold. Ser-530 makes six contacts with EPA and four with LA involving C-8 through C-16; these interactions influence the alignment of the substrate for hydrogen abstraction. Interestingly, replacement of Phe-205 increases the volume of the cyclooxygenase site allowing EPA to be oxygenated more efficiently than with native oPGHS-1.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Prostaglandin Endoperoxide H Synthase-1576Ovis ariesMutation(s): 0 
Find proteins for P05979 (Ovis aries)
Explore P05979 
Go to UniProtKB:  P05979
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05979
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G07375KG
GlyCosmos:  G07375KG
GlyGen:  G07375KG
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G30233OG
GlyCosmos:  G30233OG
GlyGen:  G30233OG
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
EPA BindingDB:  1IGX IC50: 1.30e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 3.10 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.228 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 182.17α = 90
b = 182.17β = 90
c = 103.11γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-12-12
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-08-16
    Changes: Data collection, Database references, Refinement description, Structure summary