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PDBsum entry 4zk8
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Oxidoreductase
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PDB id
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4zk8
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References listed in PDB file
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Key reference
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Title
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Structural insights into the function of a thermostable copper-Containing nitrite reductase.
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Authors
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Y.Fukuda,
K.M.Tse,
M.Lintuluoto,
Y.Fukunishi,
E.Mizohata,
H.Matsumura,
H.Takami,
M.Nojiri,
T.Inoue.
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Ref.
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J Biochem (tokyo), 2014,
155,
123-135.
[DOI no: ]
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PubMed id
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Abstract
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Copper-containing nitrite reductase (CuNIR) catalyzes the reduction of nitrite
(NO(-)2) to nitric oxide (NO) during denitrification. We determined the crystal
structures of CuNIR from thermophilic gram-positive bacterium, Geobacillus
thermodenitrificans (GtNIR) in chloride- and formate-bound forms of wild type at
1.15 Å resolution and the nitrite-bound form of the C135A mutant at 1.90 Å
resolution. The structure of C135A with nitrite displays a unique η(1)-O
coordination mode of nitrite at the catalytic copper site (T2Cu), which has
never been observed at the T2Cu site in known wild-type CuNIRs, because the
mobility of two residues essential to catalytic activity, Asp98 and His244, are
sterically restricted in GtNIR by Phe109 on a characteristic loop structure that
is found above Asp98 and by an unusually short CH-O hydrogen bond observed
between His244 and water, respectively. A detailed comparison of the WT
structure with the nitrite-bound C135A structure implies the replacement of
hydrogen-bond networks around His244 and predicts the flow path of protons
consumed by nitrite reduction. On the basis of these observations, the reaction
mechanism of GtNIR through the η(1)-O coordination manner is proposed.
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