1IGX

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

Summary for 1IGX

• Entry DOI: 10.2210/pdb1igx/pdb
• Related: 1DIY 1FE2 1IGZ
• Descriptor: Prostaglandin Endoperoxide H Synthase-1, 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... (9 entities in total)
• Functional Keywords: membrane protein, fatty acid, eicosapentanoic acid, oxidoreductase, peroxidase, dioxygenase
• Biological source: Ovis aries (sheep)
• Total number of polymer chains: 1
• Total formula weight: 69611.36

Authors

Malkowski, M.G.,Thuresson, E.D.,Smith, W.L.,Garavito, R.M. (deposition date: 2001-04-18, release date: 2001-12-12, Last modification date: 2023-08-16)

Primary citation

Malkowski, M.G.,Thuresson, E.D.,Lakkides, K.M.,Rieke, C.J.,Micielli, R.,Smith, W.L.,Garavito, R.M.
Structure of eicosapentaenoic and linoleic acids in the cyclooxygenase site of prostaglandin endoperoxide H synthase-1.
J.Biol.Chem., 276:37547-37555, 2001

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.

PubMed: 11477109
DOI: 10.1074/jbc.M105982200

Experimental method

X-RAY DIFFRACTION (3.1 Å)