PDBsum entry 1u67

Oxidoreductase

PDB id: 1u67

Contents

Protein chain

553 a.a. *

Ligands

NAG-NDG ×2

NAG-NAG-BMA-BMA

BOG ×4

COH

ACD

Waters ×24

* Residue conservation analysis

PDB id:

1u67

Name:

Oxidoreductase

Title:

Crystal structure of arachidonic acid bound to a mutant of prostagladin h synthase-1 that forms predominantly 11-hpete.

Structure:

Prostaglandin g/h synthase 1 precursor. Chain: a. Synonym: cyclooxygenase-1, cox-1, prostaglandin-endoperoxide synthase 1, prostaglandin h2 synthase 1, pgh synthase 1, pghs-1, phs 1. Engineered: yes. Mutation: yes

Source:

Ovis aries. Sheep. Organism_taxid: 9940. Gene: ptgs1, cox1. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108.

Biol. unit:

Dimer (from PDB file)

Resolution:

3.10Å R-factor: 0.238 R-free: 0.311

Authors:

C.A.Harman,C.J.Rieke,R.M.Garavito,W.L.Smith

Key ref:

C.A.Harman et al. (2004). Crystal structure of arachidonic acid bound to a mutant of prostaglandin endoperoxide H synthase-1 that forms predominantly 11-hydroperoxyeicosatetraenoic acid. J Biol Chem, 279, 42929-42935. PubMed id: 15292194 DOI: 10.1074/jbc.M403013200

Date:

29-Jul-04 Release date: 07-Sep-04

Protein chain

P05979  (PGH1_SHEEP) -  Prostaglandin G/H synthase 1 from Ovis aries

Seq: 600 a.a.

Struc: 553 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.1.14.99.1 - prostaglandin-endoperoxide synthase.
• Reaction: (5Z,8Z,11Z,14Z)-eicosatetraenoate + AH2 + 2 O2 = prostaglandin H2 + A + H2O

(5Z,8Z,11Z,14Z)-eicosatetraenoate + AH2 + 2 × O2 = prostaglandin H2 + + H2O (Bound ligand (Het Group name = COH) matches with 51.11% similarity)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1074/jbc.M403013200

J Biol Chem 279:42929-42935 (2004)

PubMed id: 15292194

Crystal structure of arachidonic acid bound to a mutant of prostaglandin endoperoxide H synthase-1 that forms predominantly 11-hydroperoxyeicosatetraenoic acid.

C.A.Harman, C.J.Rieke, R.M.Garavito, W.L.Smith.

ABSTRACT

Kinetic studies and analysis of the products formed by native and mutant forms of ovine prostaglandin endoperoxide H synthase-1 (oPGHS-1) have suggested that arachidonic acid (AA) can exist in the cyclooxygenase active site of the enzyme in three different, catalytically competent conformations that lead to prostaglandin G2 (PGG2), 11R-hydroperoxyeicosatetraenoic acid (HPETE), and 15R,S-HPETE, respectively. We have identified an oPGHS-1 mutant (V349A/W387F) that forms predominantly 11R-HPETE. Thus, the preferred catalytically competent arrangement of AA in the cyclooxygenase site of this double mutant must be one that leads to 11-HPETE. The crystal structure of Co3+-protoporphyrin IX V349A/W387F oPGHS-1 in a complex with AA was determined to 3.1 A. Significant differences are observed in the positions of atoms C-3, C-4, C-5, C-6, C-10, C-11, and C-12 of bound AA between native and V349A/W387F oPGHS-1; in comparison, the positions of the side chains of cyclooxygenase active site residues are unchanged. The structure of the double mutant presented here provides structural insight as to how Val349 and Trp387 help position C-9 and C-11 of AA so that the incipient 11-peroxyl radical intermediate is able to add to C-9 to form the 9,11 endoperoxide group of PGG2. In the V349A/W387F oPGHS-1.AA complex the locations of C-9 and C-11 of AA with respect to one another make it difficult to form the endoperoxide group from the 11-hydroperoxyl radical. Therefore, the reaction apparently aborts yielding 11R-HPETE instead of PGG2. In addition, the observed differences in the positions of carbon atoms of AA bound to this mutant provides indirect support for the concept that the conformer of AA shown previously to be bound within the cyclooxygenase active site of native oPGHS-1 is the one that leads to PGG2.

Selected figure(s)

Figure 1.
FIG. 1. Reaction pathways for the formation of PGG[2] and 11R-HPETE.

Figure 3.
FIG. 3. Stereo view of AA bound within the active site of V349A/W387F oPGHS-1. The simulated annealing omit map F[o] - F[c] density contoured at 4.0 is shown in green. Carbon atoms of AA, which were originally built into the electron density, are shown in pink (atoms C-1-C-12). Carbon atoms of AA obtained from simulated annealing are shown in blue. Side chains of various amino acids that line the COX active site and contact the substrate are shown in a color scheme where carbons are gray, oxygens are red, nitrogens are dark blue, and sulfur is yellow. All of the figures were created using the program SETOR (22).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 42929-42935) copyright 2004.

Figures were selected by an automated process.