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PDBsum entry 1z48
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Oxidoreductase
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PDB id
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1z48
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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 1.3 a crystal structure of the flavoprotein yqjm reveals a novel class of old yellow enzymes.
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Authors
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K.Kitzing,
T.B.Fitzpatrick,
C.Wilken,
J.Sawa,
G.P.Bourenkov,
P.Macheroux,
T.Clausen.
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Ref.
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J Biol Chem, 2005,
280,
27904-27913.
[DOI no: ]
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PubMed id
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Abstract
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Here we report the crystal structure of YqjM, a homolog of Old Yellow Enzyme
(OYE) that is involved in the oxidative stress response of Bacillus subtilis. In
addition to the oxidized and reduced enzyme form, the structures of complexes
with p-hydroxybenzaldehyde and p-nitrophenol, respectively, were solved. As for
other OYE family members, YqjM folds into a (alpha/beta)8-barrel and has one
molecule of flavin mononucleotide bound non-covalently at the COOH termini of
the beta-sheet. Most of the interactions that control the electronic properties
of the flavin mononucleotide cofactor are conserved within the OYE family.
However, in contrast to all members of the OYE family characterized to date,
YqjM exhibits several unique structural features. For example, the enzyme exists
as a homotetramer that is assembled as a dimer of catalytically dependent
dimers. Moreover, the protein displays a shared active site architecture where
an arginine finger (Arg336) at the COOH terminus of one monomer extends into the
active site of the adjacent monomer and is directly involved in substrate
recognition. Another remarkable difference in the binding of the ligand in YqjM
is represented by the contribution of the NH2-terminal Tyr28 instead of a
COOH-terminal tyrosine in OYE and its homologs. The structural information led
to a specific data base search from which a new class of OYE oxidoreductases was
identified that exhibits a strict conservation of active site residues, which
are critical for this subfamily, most notably Cys26, Tyr28, Lys109, and Arg336.
Therefore, YqjM is the first representative of a new bacterial subfamily of OYE
homologs.
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Figure 3.
FIG. 3. The flavin binding site. A, stereo view of the
flavin binding site. The final 1.3 Å resolution 2F[o] -
F[c] map is contoured at 1.5  . The flavin and the
side chains of the amino acids are drawn in ball-and-stick mode,
with FMN in yellow and the residues from monomer A in gray and
from the neighboring monomer B in violet. B, schematic
illustration of the interaction of FMN with active site
residues. The thin red dotted lines illustrate hydrogen bonds.
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Figure 4.
FIG. 4. Electron density map of Cys26 and Tyr28 in the
active site. The 3F[o] - 2F[c] map is contoured at 1.2 . Amino
acids and FMN are presented as in Fig. 3.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2005,
280,
27904-27913)
copyright 2005.
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