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PDBsum entry 3w2e
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Oxidoreductase
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PDB id
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3w2e
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References listed in PDB file
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Key reference
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Title
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Elucidations of the catalytic cycle of nadh-Cytochrome b5 reductase by X-Ray crystallography: new insights into regulation of efficient electron transfer.
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Authors
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M.Yamada,
T.Tamada,
K.Takeda,
F.Matsumoto,
H.Ohno,
M.Kosugi,
K.Takaba,
Y.Shoyama,
S.Kimura,
R.Kuroki,
K.Miki.
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Ref.
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J Mol Biol, 2013,
425,
4295-4306.
[DOI no: ]
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PubMed id
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Abstract
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NADH-Cytochrome b5 reductase (b5R), a flavoprotein consisting of NADH and flavin
adenine dinucleotide (FAD) binding domains, catalyzes electron transfer from the
two-electron carrier NADH to the one-electron carrier cytochrome b5 (Cb5). The
crystal structures of both the fully reduced form and the oxidized form of
porcine liver b5R were determined. In the reduced b5R structure determined at
1.68Å resolution, the relative configuration of the two domains was slightly
shifted in comparison with that of the oxidized form. This shift resulted in an
increase in the solvent-accessible surface area of FAD and created a new
hydrogen-bonding interaction between the N5 atom of the isoalloxazine ring of
FAD and the hydroxyl oxygen atom of Thr66, which is considered to be a key
residue in the release of a proton from the N5 atom. The isoalloxazine ring of
FAD in the reduced form is flat as in the oxidized form and stacked together
with the nicotinamide ring of NAD(+). Determination of the oxidized b5R
structure, including the hydrogen atoms, determined at 0.78Å resolution
revealed the details of a hydrogen-bonding network from the N5 atom of FAD to
His49 via Thr66. Both of the reduced and oxidized b5R structures explain how
backflow in this catalytic cycle is prevented and the transfer of electrons to
one-electron acceptors such as Cb5 is accelerated. Furthermore, crystallographic
analysis by the cryo-trapping method suggests that re-oxidation follows a
two-step mechanism. These results provide structural insights into the catalytic
cycle of b5R.
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