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PDBsum entry 1v3t
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Oxidoreductase
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PDB id
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1v3t
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Structural basis of leukotriene b4 12-Hydroxydehydrogenase/15-Oxo-Prostaglandin 13-Reductase catalytic mechanism and a possible src homology 3 domain binding loop.
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Authors
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T.Hori,
T.Yokomizo,
H.Ago,
M.Sugahara,
G.Ueno,
M.Yamamoto,
T.Kumasaka,
T.Shimizu,
M.Miyano.
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Ref.
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J Biol Chem, 2004,
279,
22615-22623.
[DOI no: ]
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PubMed id
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Abstract
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The bifunctional leukotriene B(4) 12-hydroxydehydrogenase/15-oxo-prostaglandin
13-reductase (LTB(4) 12-HD/PGR) is an essential enzyme for eicosanoid
inactivation. It is involved in the metabolism of the E and F series of
15-oxo-prostaglandins (15-oxo-PGs), leukotriene B(4) (LTB(4)), and
15-oxo-lipoxin A(4) (15-oxo-LXA(4)). Some nonsteroidal anti-inflammatory drugs
(NSAIDs), which primarily act as cyclooxygenase inhibitors also inhibit LTB(4)
12-HD/PGR activity. Here we report the crystal structure of the LTB(4)
12-HD/PGR, the binary complex structure with NADP(+), and the ternary complex
structure with NADP(+) and 15-oxo-PGE(2). In the ternary complex, both in the
crystalline form and in solution, the enolate anion intermediate accumulates as
a brown chromophore. PGE(2) contains two chains, but only the omega-chain of
15-oxo-PGE(2) was defined in the electron density map in the ternary complex
structure. The omega-chain was identified at the hydrophobic pore on the dimer
interface. The structure showed that the 15-oxo group forms hydrogen bonds with
the 2'-hydroxyl group of nicotine amide ribose of NADP(+) and a bound water
molecule to stabilize the enolate intermediate during the reductase reaction.
The electron-deficient C13 atom of the conjugated enolate may be directly
attacked by a hydride from the NADPH nicotine amide in a stereospecific manner.
The moderate recognition of 15-oxo-PGE(2) is consistent with a broad substrate
specificity of LTB(4) 12-HD/PGR. The structure also implies that a Src homology
domain 3 may interact with the left-handed proline-rich helix at the dimer
interface and regulate LTB(4) 12-HD/PGR activity by disruption of the substrate
binding pore to accommodate the omega-chain.
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Figure 3.
FIG. 3. NADP+ and 15-oxo-PGE[2] binding to LTB[4]
12-HD/PGR. A, a stereo view of the bound NADP+ in the binary
complex structure. The|F[o]| -|F[c]| simulated annealing omit
electron density map is contoured at 3.0  (orange) and 6.0 (cyan).
The carbon atoms of NADP+ are yellow, and those of side chains
involved in NADP+ binding are green. Single-letter codes are
used for amino acid residues. The water molecules, oxygen,
nitrogen, and phosphorus atoms are colored pink, red, blue, and
orange, respectively. The hydrogen bonds are indicated by dashed
lines. The main chain nitrogen or carbonyl groups interacting
with the bound NADP+ are labeled by residue numbers. B, a photo
of the ternary complex crystals (0.3 x 0.2 x 0.1 mm). C,
absorption spectrum changes of a ternary complex solution
mixture. A 1:10 dilution of the ternary mixture after NaOH
addition was measured. D, stereo view of the  -chain of bound
15-oxo-PGE[2] in the ternary complex structure. The carbon atoms
of the -chain of 15-oxo-PGE[2]
are colored in cyan, and NADP+ in yellow. The residues from the
same subunit of the bound NADP+ around the -chain hydrophobic pore
are colored in green, and those from the other subunit are in
magenta.|F[o]| -|F[c]| simulated annealing omit electron density
map is contoured at 2.4 (orange) and 3.5 (blue).
The residues Ala-241, Tyr-245, and Met-248 are located on the
loop  E-  F. Tyr-273 was refined
as two conformers. E, a stereo view of the interaction between
the -chain and NADP+. The
hydrogen bonds and the  - orbital interactions
between the nicotine amide ring and the conjugated double bonds
of the -chain are indicated in
dashed lines. The shortest distance of the - orbital interactions is
3.2 Å between the carbonyl oxygen atom of 15-oxo-PGE[2]
and the nitrogen atom of the nicotine amide ring.
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Figure 5.
FIG. 5. Schematic drawing of the enolate anion intermediate
in 15-oxo-PGE[2] reductase reaction mechanism. Only the -chain
and the cyclopentane ring are represented (see "Results and
Discussion" for further details).
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2004,
279,
22615-22623)
copyright 2004.
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