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PDBsum entry 2nwb
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Oxidoreductase
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PDB id
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2nwb
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References listed in PDB file
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Key reference
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Title
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Molecular insights into substrate recognition and catalysis by tryptophan 2,3-Dioxygenase.
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Authors
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F.Forouhar,
J.L.Anderson,
C.G.Mowat,
S.M.Vorobiev,
A.Hussain,
M.Abashidze,
C.Bruckmann,
S.J.Thackray,
J.Seetharaman,
T.Tucker,
R.Xiao,
L.C.Ma,
L.Zhao,
T.B.Acton,
G.T.Montelione,
S.K.Chapman,
L.Tong.
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Ref.
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Proc Natl Acad Sci U S A, 2007,
104,
473-478.
[DOI no: ]
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PubMed id
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Abstract
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Tryptophan 2,3-dioxygenase (TDO) and indoleamine 2,3-dioxygenase (IDO)
constitute an important, yet relatively poorly understood, family of
heme-containing enzymes. Here, we report extensive structural and biochemical
studies of the Xanthomonas campestris TDO and a related protein SO4414 from
Shewanella oneidensis, including the structure at 1.6-A resolution of the
catalytically active, ferrous form of TDO in a binary complex with the substrate
L-Trp. The carboxylate and ammonium moieties of tryptophan are recognized by
electrostatic and hydrogen-bonding interactions with the enzyme and a propionate
group of the heme, thus defining the L-stereospecificity. A second, possibly
allosteric, L-Trp-binding site is present at the tetramer interface. The sixth
coordination site of the heme-iron is vacant, providing a dioxygen-binding site
that would also involve interactions with the ammonium moiety of L-Trp and the
amide nitrogen of a glycine residue. The indole ring is positioned correctly for
oxygenation at the C2 and C3 atoms. The active site is fully formed only in the
binary complex, and biochemical experiments confirm this induced-fit behavior of
the enzyme. The active site is completely devoid of water during catalysis,
which is supported by our electrochemical studies showing significant
stabilization of the enzyme upon substrate binding.
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Figure 2.
Fig. 2. The structure of TDO. (a) Schematic representation
of the structure of the monomer of X. campestris TDO. The  -helices
are shown in yellow and labeled. Heme is shown in gray, and
L-Trp is shown in orange (labeled W). The water molecule is
shown as a red sphere (labeled wat). (b) Schematic
representation of the tetramer of X. campestris TDO. The four
monomers are colored in yellow, cyan, violet, and green. Helices
in the tetramer interface are labeled. The Trp molecules in the
tetramer interface are also shown. Produced with Molscript (35)
and rendered with Raster3D (36).
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Figure 3.
Fig. 3. Molecular basis for substrate recognition by TDO.
(a) Final 2F[o]–F[c] electron density at 1.6-Å
resolution for heme, L-Trp, and a water in the active site.
Contoured at 1  . (b) Stereo drawing
showing the active site of X. campestris TDO in the binary
complex with L-Trp. The segment in cyan is from another monomer
of the tetramer. Hydrogen-bonding interactions are indicated
with dashed lines in magenta. (c) Overlay of the structures of
the free enzyme (in orchid) and the binary complex (yellow and
cyan) in the active-site region. Regions of conformational
differences are indicated with the red arrows. (d) Overlay of
the active-site region of the second monomer (in green) and that
of the first monomer (in yellow). Only the side-chain atoms of
Trp are shown in the second monomer (in magenta). (e) Final
2F[o]–F[c] electron density at 1.6-Å resolution for
heme, L-Trp, and a water in the active site of the second TDO
molecule in the crystal. Contoured at 1 . Two conformations for
the main chain atoms are shown, but neither fit the density
well. For the stereo version of c and d, please see SI Fig. 7.
Produced with Molscript (35) and rendered with Raster3D (36).
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