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PDBsum entry 2dws
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Oxidoreductase
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PDB id
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2dws
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References listed in PDB file
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Key reference
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Title
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Ph dependence of copper geometry, Reduction potential, And nitrite affinity in nitrite reductase.
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Authors
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F.Jacobson,
A.Pistorius,
D.Farkas,
W.De grip,
O.Hansson,
L.Sjölin,
R.Neutze.
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Ref.
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J Biol Chem, 2007,
282,
6347-6355.
[DOI no: ]
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PubMed id
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Abstract
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Many properties of copper-containing nitrite reductase are pH-dependent, such as
gene expression, enzyme activity, and substrate affinity. Here we use x-ray
diffraction to investigate the structural basis for the pH dependence of
activity and nitrite affinity by examining the type 2 copper site and its
immediate surroundings in nitrite reductase from Rhodobacter sphaeroides 2.4.3.
At active pH the geometry of the substrate-free oxidized type 2 copper site
shows a near perfect tetrahedral geometry as defined by the positions of its
ligands. At higher pH values the most favorable copper site geometry is altered
toward a more distorted tetrahedral geometry whereby the solvent ligand adopts a
position opposite to that of the His-131 ligand. This pH-dependent variation in
type 2 copper site geometry is discussed in light of recent computational
results. When co-crystallized with substrate, nitrite is seen to bind in a
bidentate fashion with its two oxygen atoms ligating the type 2 copper,
overlapping with the positions occupied by the solvent ligand in the high and
low pH structures. Fourier transformation infrared spectroscopy is used to
assign the pH dependence of the binding of nitrite to the active site, and EPR
spectroscopy is used to characterize the pH dependence of the reduction
potential of the type 2 copper site. Taken together, these spectroscopic and
structural observations help to explain the pH dependence of nitrite reductase,
highlighting the subtle relationship between copper site geometry, nitrite
affinity, and enzyme activity.
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Figure 2.
FIGURE 2. Stereo view of nitrite bound to the type 2 copper
ion in RsNiR. a, at pH 6.0 showing full occupancy and with 2F[o]
- F[c] electron density contoured at  level 1.0. b, at pH 8.4
with half-occupancy and with 2F[o] - F[c] electron density
contoured at level 0.9. The
flexibility of His-287 at pH 8.4 can be seen as a rotation of
the imidazole ring (b).
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Figure 3.
FIGURE 3. Stereo view illustrating the ligating solvent
molecule that coordinates the oxidized type 2 copper ion in
Cu-NiRs. a and b, pH6(a) and at pH 8.4 (b), both with 2F[o] -
F[c] electron density contoured at level 1.0. Asp-129
forms an H-bond to the solvent ligand at pH 6.0 (a), but this
bond is absent at pH 8.4 (b). The flexibility of His-287 at pH
8.4 can be seen as a movement of the imidazole ring toward the
type 2 copper ion (b).
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2007,
282,
6347-6355)
copyright 2007.
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