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PDBsum entry 1krh
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Oxidoreductase
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PDB id
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1krh
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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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X-Ray crystal structure of benzoate 1,2-Dioxygenase reductase from acinetobacter sp. Strain ADP1.
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Authors
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A.Karlsson,
Z.M.Beharry,
D.Matthew eby,
E.D.Coulter,
E.L.Neidle,
D.M.Kurtz,
H.Eklund,
S.Ramaswamy.
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Ref.
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J Mol Biol, 2002,
318,
261-272.
[DOI no: ]
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PubMed id
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Abstract
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One of the major processes for aerobic biodegradation of aromatic compounds is
initiated by Rieske dioxygenases. Benzoate dioxygenase contains a reductase
component, BenC, that is responsible for the two-electron transfer from NADH via
FAD and an iron-sulfur cluster to the terminal oxygenase component. Here, we
present the structure of BenC from Acinetobacter sp. strain ADP1 at 1.5 A
resolution. BenC contains three domains, each binding a redox cofactor:
iron-sulfur, FAD and NADH, respectively. The [2Fe-2S] domain is similar to that
of plant ferredoxins, and the FAD and NADH domains are similar to members of the
ferredoxin:NADPH reductase superfamily. In phthalate dioxygenase reductase, the
only other Rieske dioxygenase reductase for which a crystal structure is
available, the ferredoxin-like and flavin binding domains are sequentially
reversed compared to BenC. The BenC structure shows significant differences in
the location of the ferredoxin domain relative to the other domains, compared to
phthalate dioxygenase reductase and other known systems containing these three
domains. In BenC, the ferredoxin domain interacts with both the flavin and
NAD(P)H domains. The iron-sulfur center and the flavin are about 9 A apart,
which allows a fast electron transfer. The BenC structure is the first
determined for a reductase from the class IB Rieske dioxygenases, whose
reductases transfer electrons directly to their oxygenase components. Based on
sequence similarities, a very similar structure was modeled for the class III
naphthalene dioxygenase reductase, which transfers electrons to an intermediary
ferredoxin, rather than the oxygenase component.
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Figure 3.
Figure 3. Stereo representation of the [2Fe-2S] center in
BenC. The center is connected to the protein via cysteine
residues 41, 46, 49 and 83, which ligate the two iron atoms as
well as by an intricate hydrogen bonding pattern, represented by
broken red lines, to the cysteine sulfur atoms and bridging
sulfides.
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Figure 4.
Figure 4. FAD binding in BenC. (a) The FAD-binding site is
situated between the FAD-binding domain, in yellow, and the
NADH-binding domain, in blue. The methyl groups of the
isoalloxazine ring are pointing towards the [2Fe-2S] center in
the ferredoxin-like domain. The FAD is represented inside a F[o]
-F[c] map, colored in green, contoured at 4×rms. The
picture was made with the program BOBSCRIPT
(http://www.strubi.ox.ac.uk/bobscript/). (b) A close-up of the
FAD molecule binding to the NADH and FAD binding domains of
BenC. There are five water molecules contributing to the
extensive hydrogen bonding holding the FAD in position. The
stacking interaction between Phe335 and the isoalloxazine ring
of the FAD can be seen at the bottom right of the Figure.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2002,
318,
261-272)
copyright 2002.
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