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PDBsum entry 2d0t
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Oxidoreductase
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PDB id
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2d0t
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References listed in PDB file
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Key reference
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Title
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Crystal structure of human indoleamine 2,3-Dioxygenase: catalytic mechanism of o2 incorporation by a heme-Containing dioxygenase.
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Authors
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H.Sugimoto,
S.Oda,
T.Otsuki,
T.Hino,
T.Yoshida,
Y.Shiro.
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Ref.
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Proc Natl Acad Sci U S A, 2006,
103,
2611-2616.
[DOI no: ]
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PubMed id
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Abstract
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Human indoleamine 2,3-dioxygenase (IDO) catalyzes the cleavage of the pyrrol
ring of L-Trp and incorporates both atoms of a molecule of oxygen (O2). Here we
report on the x-ray crystal structure of human IDO, complexed with the ligand
inhibitor 4-phenylimidazole and cyanide. The overall structure of IDO shows two
alpha-helical domains with the heme between them. A264 of the flexible loop in
the heme distal side is in close proximity to the iron. A mutant analysis shows
that none of the polar amino acid residues in the distal heme pocket are
essential for activity, suggesting that, unlike the heme-containing
monooxygenases (i.e., peroxidase and cytochrome P450), no protein group of IDO
is essential in dioxygen activation or proton abstraction. These characteristics
of the IDO structure provide support for a reaction mechanism involving the
abstraction of a proton from the substrate by iron-bound dioxygen. Inactive
mutants (F226A, F227A, and R231A) retain substrate-binding affinity, and an
electron density map reveals that 2-(N-cyclohexylamino)ethane sulfonic acid is
bound to these residues, mimicking the substrate. These findings suggest that
strict shape complementarities between the indole ring of the substrate and the
protein side chains are required, not for binding, but, rather, to permit the
interaction between the substrate and iron-bound dioxygen in the first step of
the reaction. This study provides the structural basis for a heme-containing
dioxygenase mechanism, a missing piece in our understanding of heme chemistry.
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Figure 1.
Fig. 1. Structure of IDO–PI complex. (A) Ribbon
representation of the overall structure of human IDO. The small
and large domains are represented by blue and green ribbons,
respectively. The helices A–S are named in the order of
appearance in the primary sequence. The connecting helices (K-L
and N) are colored in cyan. The long loop connecting the two
domains is colored in red. The heme (yellow), proximal ligand
H346 (white), and heme inhibitor 4-phynylimidazole (white) are
shown in a ball-and-stick model. The helices of the large domain
create the cavity for the heme. The connecting loop (red) and
small domain above the sixth-coordination site (heme distal
side) cover the top of cavity on the heme. (B) The four proximal
helices I, G, Q, and S run in parallel. The helices N (blue) and
K-L (cyan) connect the two domains. The connecting loop (red)
and small domain above the sixth-coordination site of the heme
cover the top of the cavity on the heme.
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Figure 3.
Fig. 3. Active site of IDO–PI complex. (A) Stereoview of
the residues around the heme of IDO viewed from the side of heme
plane. The proximal ligand H346 is H-bonded to wa1. The
6-propionate of the heme contacts with wa2 and R343 N  . The
wa2 is H-bonded to wa1, L388 O, and 6-propionate. Mutations of
F226, F227, and R231 do not lose the substrate affinity but
produce the inactive enzyme. Two CHES molecules are bound in the
distal pocket. The cyclohexan ring of CHES-1 (green) contacts
with F226 and R231. The 7-propionate of the heme interacts with
the amino group of CHES-1 and side chain of Ser-263. The
mutational analyses for these distal residues are shown in Table
1. (B) Top view of A by a rotation of 90°. The proximal
residues are omitted.
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