PDBsum entry 3krk

Oxidoreductase

PDB id: 3krk

Contents

Protein chains

551 a.a. *

Ligands

NAG-NAG ×3

NAG-NAG-MAN

ACD ×2

AKR ×4

GOL ×3

COH ×2

NAG ×2

BOG ×2

Waters ×632

* Residue conservation analysis

PDB id:

3krk

Name:

Oxidoreductase

Title:

X-ray crystal structure of arachidonic acid bound in the cyclooxygenase channel of l531f murine cox-2

Structure:

Prostaglandin g/h synthase 2. Chain: a, b. Fragment: unp residues 20-604. Synonym: cyclooxygenase-2, cox-2, prostaglandin-endoperoxide synthase 2, prostaglandin h2 synthase 2, pgh synthase 2, pghs-2, phs ii, glucocorticoid-regulated inflammatory cyclooxygenase, gripghs, tis10 protein, macrophage activation-associated marker protein p71/73, pes- 2. Engineered: yes.

Source:

Mus musculus. Mouse. Organism_taxid: 10090. Gene: cox-2, cox2, pghs-b, ptgs2, tis10. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108.

Resolution:

2.40Å R-factor: 0.182 R-free: 0.228

Authors:

A.J.Vecchio,D.M.Simmons,M.G.Malkowski

Key ref:

A.J.Vecchio et al. (2010). Structural basis of fatty acid substrate binding to cyclooxygenase-2. J Biol Chem, 285, 22152-22163. PubMed id: 20463020

Date:

18-Nov-09 Release date: 12-May-10

Protein chains

Q05769  (PGH2_MOUSE) -  Prostaglandin G/H synthase 2 from Mus musculus

Seq: 604 a.a.

Struc: 551 a.a.*

* PDB and UniProt seqs differ at 3 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

J Biol Chem 285:22152-22163 (2010)

PubMed id: 20463020

Structural basis of fatty acid substrate binding to cyclooxygenase-2.

A.J.Vecchio, D.M.Simmons, M.G.Malkowski.

ABSTRACT

The cyclooxygenases (COX-1 and COX-2) are membrane-associated, heme-containing homodimers that generate PGH2 from arachidonic acid (AA). While AA is the preferred substrate, other fatty acids are oxygenated by these enzymes with varying efficiencies. We determined the crystal structures of AA, eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA) bound to Co(3+)-protoporphyrin IX reconstituted murine COX-2 to 2.1A, 2.4A, and 2.65A, respectively. AA, EPA, and DHA bind in different conformations in each monomer constituting the homodimer in their respective structures such that one monomer exhibits non-productive binding and the other productive binding of the substrate in the cyclooxygenase channel. The interactions identified between protein and substrate when bound to COX-1 are conserved in our COX-2 structures, with the only notable difference being the lack of interaction of the carboxylate of AA and EPA with the side chain of Arg-120. Leu-531 exhibits a different side chain conformation when the non-productive and productive binding modes of AA are compared. Unlike COX-1, mutating this residue to Ala, Phe, Pro, or Thr did not result in a significant loss of activity or substrate binding affinity. Determination of the L531F:AA crystal structure resulted in AA binding in the same global conformation in each monomer. We speculate that the mobility of the Leu-531 side chain increases the volume available at the opening of the cyclooxygenase channel and contributes to the observed ability of COX-2 to oxygenate a broad spectrum of fatty acid and fatty ester substrates.