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PDBsum entry 1v4b
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Oxidoreductase
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PDB id
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1v4b
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References listed in PDB file
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Key reference
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Title
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Three-Dimensional structure of azor from escherichia coli. An oxidereductase conserved in microorganisms.
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Authors
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K.Ito,
M.Nakanishi,
W.C.Lee,
H.Sasaki,
S.Zenno,
K.Saigo,
Y.Kitade,
M.Tanokura.
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Ref.
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J Biol Chem, 2006,
281,
20567-20576.
[DOI no: ]
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PubMed id
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Abstract
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The crystal structure of AzoR (azoreductase) has been determined in complex with
FMN for two different crystal forms at 1.8 and 2.2 A resolution. AzoR is an
oxidoreductase isolated from Escherichia coli as a protein responsible for the
degradation of azo compounds. This enzyme is an FMN-dependent NADH-azoreductase
and catalyzes the reductive cleavage of azo groups by a ping-pong mechanism. The
structure suggests that AzoR acts in a homodimeric state forming the two
identical catalytic sites to which both monomers contribute. The structure
revealed that each monomer of AzoR has a flavodoxin-like structure, without the
explicit overall amino acid sequence homology. Superposition of the structures
from the two different crystal forms revealed the conformational change and
suggested a mechanism for accommodating substrates of different size.
Furthermore, comparison of the active site structure with that of NQO1 complexed
with substrates provides clues to the possible substrate-binding mechanism of
AzoR.
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Figure 2.
FIGURE 2. Interactions between FMN and amino acid residues
in the active site. a, schematic diagram showing contacts of the
FMN cofactor to amino acid residues. Hydrogen bonds are shown as
broken green lines (red residue numbers) and van der Waals'
interactions by red shading (black residue numbers). Each atom
element is represented by a sphere of different colors with a
chemical symbol. b, SIGMAA-weighted 2mF[o] - DF[c] electron
density maps surrounding the FMN. The map was calculated using
the data of P4[2]2[1]2 crystal structure and is contoured at 1.2
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c, the electrostatic potential of AzoR is mapped onto the
solvent-accessible surface, as calculated with GRASP. The FMN
molecules shown in a and b are represented by a stick model,
with color coding identical to that in Fig. 1.
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Figure 5.
FIGURE 5. Comparison of the active site of AzoR with that
of NQO1. One active site is shown for each of AzoR (a) and rat
NQO1 (b) (Protein Data Bank accession code 1QRD). The flavin
cofactors, duroquinone, and the side chains of conserved amino
acid residues in both enzymes are represented by a stick model,
with carbon atoms in gray, oxygen atoms in red, nitrogen atoms
in blue, and phosphorous atoms in orange. The polypeptide
moieties of one subunit for each enzyme are drawn as C  traces
in yellow and green.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2006,
281,
20567-20576)
copyright 2006.
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