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PDBsum entry 1o7h
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Oxidoreductase
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PDB id
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1o7h
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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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Crystal structure of naphthalene dioxygenase: side-On binding of dioxygen to iron.
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Authors
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A.Karlsson,
J.V.Parales,
R.E.Parales,
D.T.Gibson,
H.Eklund,
S.Ramaswamy.
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Ref.
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Science, 2003,
299,
1039-1042.
[DOI no: ]
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PubMed id
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Abstract
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Binding of oxygen to iron is exploited in several biological and chemical
processes. Although computational and spectroscopic results have suggested
side-on binding, only end-on binding of oxygen to iron has been observed in
crystal structures. We have determined structures of naphthalene dioxygenase
that show a molecular oxygen species bound to the mononuclear iron in a side-on
fashion. In a complex with substrate and dioxygen, the dioxygen molecule is
lined up for an attack on the double bond of the aromatic substrate. The
structures reported here provide the basis for a reaction mechanism and for the
high stereospecificity of the reaction catalyzed by naphthalene dioxygenase.
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Figure 1.
Fig. 1. (All panels are stereopairs.) (A) Binding of
naphthalene at the active site of NDO. The gray 2F[obs] -
F[calc] map is contoured at 1.0  . (B)
Binding of dioxygen to the mononuclear iron in the absence of
substrate. The gray 2F[obs] - F[calc] map is contoured at 1.15
and the
green F[obs] - F[calc] map (computed before the dioxygen
molecule was modeled) at 3.8 × RMS (root mean square). (C)
Binding of oxygen to the mononuclear iron in the presence of
indole. The gray 2F[obs] - F[calc] map is contoured at 1.0 and the
green F[obs] - F[calc] map (computed before the dioxygen
molecule was modeled) at 4.0 × RMS. (D) Naphthalene
cis-dihydrodiol bound to the active site of NDO. The gray
2F[obs] - F[calc] map is contoured at 1.0 .
Superposition of the product complex and the substrate complex
shows that the positions of the rings in the product and the
substrate are similar. The product cannot move any closer to the
iron, as it would bring the O from the product into van der
Waals short contact with the His ligand of the Fe. The current
distance between the O and the N of His is 2.9 Å. Color
code: yellow, carbon; blue, nitrogen; red, oxygen; purple, iron.
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Figure 2.
Fig. 2. (A) Scheme showing how the different structures in Fig.
1 can be arranged to follow the dihydroxylation reaction
catalyzed by NDO. Naphthalene and indole are both substrates for
the enzyme, and we have used them interchangeably in different
studies of the enzyme (23). For simplicity we show only
naphthalene here. The structures are as follows: 1, the resting
enzyme with oxidized Rieske center and ferrous active site
[Protein Data Bank (PDB) code 1O7H]; 2, the reduced enzyme (PDB
code 1O7W); 3, binary dioxgen complex (PDB code 1O7M); 4, binary
substrate complex, structures with both indole and naphthalene
[PDB codes 1EG9 (indole) and 1O7G (naphthalene)]; 5, ternary
substrate dioxygen species, structure with indole (PDB code
1O7N); and 6, product naphthalene cis-1,2-dihydrodiol (PDB code
1O7P). [2Fe-2S] refers to the nearest Rieske iron-sulfur
cluster. (B) Chemical steps in the dioxygenation reaction
carried out by Rieske dioxygenases.
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The above figures are
reprinted
by permission from the AAAs:
Science
(2003,
299,
1039-1042)
copyright 2003.
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