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PDBsum entry 1fe7
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References listed in PDB file
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Key reference
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Title
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Mutational and X-Ray crystallographic analysis of the interaction of dihomo-Gamma -Linolenic acid with prostaglandin endoperoxide h synthases.
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Authors
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E.D.Thuresson,
M.G.Malkowski,
K.M.Lakkides,
C.J.Rieke,
A.M.Mulichak,
S.L.Ginell,
R.M.Garavito,
W.L.Smith.
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Ref.
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J Biol Chem, 2001,
276,
10358-10365.
[DOI no: ]
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PubMed id
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Abstract
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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.
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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.
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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.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2001,
276,
10358-10365)
copyright 2001.
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Secondary reference #1
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Title
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Three-Dimensional structure of a presynaptic neurotoxic phospholipase a2 from daboia russelli pulchella at 2.4 a resolution.
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Authors
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V.Chandra,
P.Kaur,
A.Srinivasan,
T.P.Singh.
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Ref.
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J Mol Biol, 2000,
296,
1117-1126.
[DOI no: ]
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PubMed id
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Figure 3.
Figure 3. (a) Superimposition of C^α traces of DPLA[2]
(thick lines) and VPLA[2] (thin lines). The r.m.s. difference
for the C^α atoms is 1.2 Å. The corresponding shifts for
the neurotoxic (55–61 and 85–94), and anticoagulant
(53–77) fragments are 1.8 Å and 1.3 Å,
respectively. (b) Protruding side-chains of basic residues for
the anticoagulant site.
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Figure 4.
Figure 4. (a) The association of molecules A and B showing a
number of residues from both the molecules (black) and solvent
molecules (red) involved in the interactions between two
molecules: molecule A, Leu2, Leu17, Ala18, Ile19, Pro20, Trp31,
Arg43, Phe46, Ser70, Arg72, Met118, Leu119 and Asp122; molecule
B, Thr36, Ala40, Arg43, Phe46, Val47, Asn54, Glu97, Lys100,
Ile104, Gln108, Asn111, Leu130, Lys131 and Cys133 and 31 solvent
molecules. (b) Spatially two adjacent fragments 55–61 and
85–94. The segment 55–61 forms a β-turn I with a hydrogen
bond between Leu55 (O) and Cys61 (N). A tight loop, 85-94, is
stabilized by a number of intra-loop hydrogen bonds which are
indicated by dotted lines. The inter-segmental hydrogen bonds
(red, broken lines) are also indicated.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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