PDBsum entry 1pxx

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Oxidoreductase PDB id
Protein chains
552 a.a. *
NAG ×8
BOG ×2
HEM ×4
DIF ×4
Waters ×317
* Residue conservation analysis

References listed in PDB file
Key reference
Title A novel mechanism of cyclooxygenase-2 inhibition involving interactions with ser-530 and tyr-385.
Authors S.W.Rowlinson, J.R.Kiefer, J.J.Prusakiewicz, J.L.Pawlitz, K.R.Kozak, A.S.Kalgutkar, W.C.Stallings, R.G.Kurumbail, L.J.Marnett.
Ref. J Biol Chem, 2003, 278, 45763-45769. [DOI no: 10.1074/jbc.M305481200]
PubMed id 12925531
A variety of drugs inhibit the conversion of arachidonic acid to prostaglandin G2 by the cyclooxygenase (COX) activity of prostaglandin endoperoxide synthases. Several modes of inhibitor binding in the COX active site have been described including ion pairing of carboxylic acid containing inhibitors with Arg-120 of COX-1 and COX-2 and insertion of arylsulfonamides and sulfones into the COX-2 side pocket. Recent crystallographic evidence suggests that Tyr-385 and Ser-530 chelate polar or negatively charged groups in arachidonic acid and aspirin. We tested the generality of this binding mode by analyzing the action of a series of COX inhibitors against site-directed mutants of COX-2 bearing changes in Arg-120, Tyr-355, Tyr-348, and Ser-530. Interestingly, diclofenac inhibition was unaffected by the mutation of Arg-120 to alanine but was dramatically attenuated by the S530A mutation. Determination of the crystal structure of a complex of diclofenac with murine COX-2 demonstrates that diclofenac binds to COX-2 in an inverted conformation with its carboxylate group hydrogen-bonded to Tyr-385 and Ser-530. This finding represents the first experimental demonstration that the carboxylate group of an acidic non-steroidal anti-inflammatory drug can bind to a COX enzyme in an orientation that precludes the formation of a salt bridge with Arg-120. Mutagenesis experiments suggest Ser-530 is also important in time-dependent inhibition by nimesulide and piroxicam.
Figure 1.
FIG. 1. COX substrate binding modes. Stereo diagram of the inhibitory binding mode of arachidonic acid to COX-2 (blue) aligned with the productive binding mode, observed in COX-1 (beige). The substrate is nominally rotated 180° between the two orientations, resulting in different coordination of the carboxylic acid group. Amino acids shown are within van der Waals contact of diclofenac except for Arg-120, Val-434, and Arg-513, added for reference. Red text indicates the position of the three amino acid differences between COX-1 and COX-2 within the active site. The superposition was performed using amino acids 113-122, 344-355, 385-391, and 522-532 and coordinate Protein Data Bank files 1CVU [PDB] and 1DIY [PDB] . All molecular graphics were generated with Ribbons and rendered with POV-Ray (36).
Figure 6.
FIG. 6. Comparison of inhibitor binding to COX-2. a, superposition of the structures of diclofenac (green) and indomethacin (gold carbons; Protein Data Bank number 4COX [PDB] ) shows their differential coordination to the protein, despite their comparable size and chemical composition. b, overlay of the structures of diclofenac and the inhibitory mode of arachidonic acid binding. Both ligands coordinate their acidic groups with the side chains of Tyr-385 and Ser-530 despite their dissimilar chemical structures.
The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 45763-45769) copyright 2003.
Secondary reference #1
Title Structural basis for selective inhibition of cyclooxygenase-2 by anti-Inflammatory agents.
Authors R.G.Kurumbail, A.M.Stevens, J.K.Gierse, J.J.Mcdonald, R.A.Stegeman, J.Y.Pak, D.Gildehaus, J.M.Miyashiro, T.D.Penning, K.Seibert, P.C.Isakson, W.C.Stallings.
Ref. Nature, 1996, 384, 644-648.
PubMed id 8967954
Secondary reference #2
Title Structural insights into the stereochemistry of the cyclooxygenase reaction.
Authors J.R.Kiefer, J.L.Pawlitz, K.T.Moreland, R.A.Stegeman, W.F.Hood, J.K.Gierse, A.M.Stevens, D.C.Goodwin, S.W.Rowlinson, L.J.Marnett, W.C.Stallings, R.G.Kurumbail.
Ref. Nature, 2000, 405, 97. [DOI no: 10.1038/35011103]
PubMed id 10811226
Full text Abstract
Figure 2.
Figure 2: COX-2 dimer interface solvent channel. The two monomers (coloured green and blue) of the COX-2 dimer are shown from the membrane face (a) or side (b). Cyclooxygenase and peroxidase active sites are marked by AA (red) and haem molecules (orange, superimposed onto the H207A-AA structure), respectively. Solvent molecules are shown as yellow spheres.
Figure 4.
Figure 4: Stereo diagram of the models of AA (a) and PGH[2] ( b) bound at the cyclooxygenase active site. Dashed lines indicate hydrogen bonds or ion pairs formed. The double bonds of the AA and PGH[2] are coloured blue. Protein side chains shown are within van der Waals contact of the ligand. The C13 pro(S)-hydrogen (purple) and pro(R)-hydrogen (gold) of AA are shown for reference.
The above figures are reproduced from the cited reference with permission from Macmillan Publishers Ltd
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