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PDBsum entry 1fe2

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Oxidoreductase PDB id
1fe2
Jmol
Contents
Protein chain
553 a.a. *
Ligands
NAG-NAG ×2
NAG-NAG-BMA-BMA-
BMA
BOG ×3
COH
LAX
Waters ×60
* Residue conservation analysis

References listed in PDB file
Key reference
Title Mutational and X-Ray crystallographic analysis of the interaction of dihomo-Gamma -Linolenic acid with prostaglandin endoperoxide h synthases.
Authors E.D.Thuresson, M.G.Malkowski, K.M.Lakkides, C.J.Rieke, A.M.Mulichak, S.L.Ginell, R.M.Garavito, W.L.Smith.
Ref. J Biol Chem, 2001, 276, 10358-10365. [DOI no: 10.1074/jbc.M009378200]
PubMed id 11121413
Abstract
Prostaglandin endoperoxide H synthases-1 and -2 (PGHSs) catalyze the committed step in prostaglandin biosynthesis. Both isozymes can oxygenate a variety of related polyunsaturated fatty acids. We report here the x-ray crystal structure of dihomo-gamma-linolenic acid (DHLA) in the cyclooxygenase site of PGHS-1 and the effects of active site substitutions on the oxygenation of DHLA, and we compare these results to those obtained previously with arachidonic acid (AA). DHLA is bound within the cyclooxygenase site in the same overall L-shaped conformation as AA. C-1 and C-11 through C-20 are in the same positions for both substrates, but the positions of C-2 through C-10 differ by up to 1.74 A. In general, substitutions of active site residues caused parallel changes in the oxygenation of both AA and DHLA. Two significant exceptions were Val-349 and Ser-530. A V349A substitution caused an 800-fold decrease in the V(max)/K(m) for DHLA but less than a 2-fold change with AA; kinetic evidence indicates that C-13 of DHLA is improperly positioned with respect to Tyr-385 in the V349A mutant thereby preventing efficient hydrogen abstraction. Val-349 contacts C-5 of DHLA and appears to serve as a structural bumper positioning the carboxyl half of DHLA, which, in turn, positions properly the omega-half of this substrate. A V349A substitution in PGHS-2 has similar, minor effects on the rates of oxygenation of AA and DHLA. Thus, Val-349 is a major determinant of substrate specificity for PGHS-1 but not for PGHS-2. Ser-530 also influences the substrate specificity of PGHS-1; an S530T substitution causes 40- and 750-fold decreases in oxygenation efficiencies for AA and DHLA, respectively.
Figure 2.
Fig. 2. Comparison of the binding of AA and DHLA within the cyclooxygenase active site. A stereo view of DHLA (red) and AA (light blue) (7) bound within in the cyclooxygenase active site channel of oPGHS-1. Active site residues are colored as in Fig. 1. The absence of the C5/C6 double bond in DHLA allows for greater conformational flexibility in the carboxyl half of the substrates as compared with AA. This is reflected in the 1.1-Å r.m.s. deviation between carbon positions in DHLA versus AA for C-1 to C-10. Additionally, the position of the C -2 atom of Ile-523 (orange in DHLA versus blue in AA) and the O atom on Ser-530 (light green in DHLA versus magenta in AA) move to accommodate DHLA in the active site.
Figure 3.
Fig. 3. Interactions between DHLA and cyclooxygenase active site residues. A schematic diagram of the interactions between DHLA and residues within the cyclooxygenase channel. Every other carbon atom of DHLA is labeled, and the hydrogens for C-13 have been modeled. All dashed lines represent interactions within 4.0 Å between the specific side chain atom of the protein and DHLA. Only 3 of the 62 contacts between DHLA and cyclooxygenase channel residues are hydrophilic.
The above figures are reprinted by permission from the ASBMB: J Biol Chem (2001, 276, 10358-10365) copyright 2001.
Secondary reference #1
Title Structure of prostaglandin synthase complexed with arachidonic acid.
Authors M.G.Malkowski, S.L.Ginell, W.L.Smith, R.M.Garavito.
Ref. TO BE PUBLISHED ...
PROCHECK
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