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PDBsum entry 3vkt
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Oxidoreductase
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PDB id
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3vkt
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References listed in PDB file
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Key reference
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Title
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The reductive reaction mechanism of tobacco nitrite reductase derived from a combination of crystal structures and ultraviolet-Visible microspectroscopy.
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Authors
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S.Nakano,
M.Takahashi,
A.Sakamoto,
H.Morikawa,
K.Katayanagi.
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Ref.
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Proteins, 2012,
80,
2035-2045.
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PubMed id
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Abstract
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Assimilatory nitrite reductase (aNiR) reduces nitrite to an ammonium ion and has
siroheme and a [Fe(4)S(4)] cluster as prosthetic groups. A reaction mechanism
for Nii3, an aNiR from tobacco, is proposed based on high resolution X-ray
structures and UV-Vis (ultraviolet-visible) microspectroscopy of Nii3-ligand
complexes. Analysis of UV-Vis spectral changes in Nii3 crystals with increasing
X-ray exposure showed prosthetic group reductions. In Nii3-NO2(-) structures,
X-ray irradiation enhanced the progress of the reduction reaction, and cleavage
of the N-O bond was observed when X-ray doses were increased. Crystal structures
of Nii3 with other bound ligands, such as Nii3-NO and Nii3-NH(2)OH, were also
determined. Further, by combining information from these Nii3 ligand-bound
structures, including that of Nii3-NO2(-), with UV-Vis microspectral data
obtained using different X-ray doses, a reaction mechanism for aNiR was
suggested. Cleavage of the two N-O bonds of nitrite was envisaged as a two-step
process: first, the N-O bond close to Lys224 was cleaved, followed by cleavage
of the N-O bond close to Arg109. X-ray structures also indicated that
aNiR-catalyzed nitrite reduction proceeded without the need for conformation
changes in active site residues. Geometrical changes in the ligand molecules and
the placement of neighboring water molecules appeared to be important to the
stability of the active site residue interactions (Arg109, Arg179, and Lys224)
and the ligand molecule. These interactions may contribute to the efficiency of
aNiR reduction reactions.
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