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PDBsum entry 1oq7
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Oxidoreductase
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PDB id
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1oq7
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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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Azide and acetate complexes plus two iron-Depleted crystal structures of the di-Iron enzyme delta9 stearoyl-Acyl carrier protein desaturase. Implications for oxygen activation and catalytic intermediates.
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Authors
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M.Moche,
J.Shanklin,
A.Ghoshal,
Y.Lindqvist.
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Ref.
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J Biol Chem, 2003,
278,
25072-25080.
[DOI no: ]
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PubMed id
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Abstract
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Delta9 stearoyl-acyl carrier protein (ACP) desaturase is a mu-oxo-bridged
di-iron enzyme, which belongs to the structural class I of large helix bundle
proteins and that catalyzes the NADPH and O2-dependent formation of a cis-double
bond in stearoyl-ACP. The crystal structures of complexes with azide and
acetate, respectively, as well as the apoand single-iron forms of Delta9
stearoyl-ACP desaturase from Ricinus communis have been determined. In the azide
complex, the ligand forms a mu-1,3-bridge between the two iron ions in the
active site, replacing a loosely bound water molecule. The structure of the
acetate complex is similar, with acetate bridging the di-iron center in the same
orientation with respect to the di-iron center. However, in this complex, the
iron ligand Glu196 has changed its coordination mode from bidentate to
monodentate, the first crystallographic observation of a carboxylate shift in
Delta9 stearoyl-ACP desaturase. The two complexes are proposed to mimic a mu-1,2
peroxo intermediate present during catalytic turnover. There are striking
structural similarities between the di-iron center in the Delta9 stearoyl-ACP
desaturase-azide complex and in the reduced rubrerythrin-azide complex. This
suggests that Delta9 stearoyl-ACP desaturase might catalyze the formation of
water from exogenous hydrogen peroxide at a low rate. From the similarity in
iron center structure, we propose that the mu-oxo-bridge in oxidized desaturase
is bound to the di-iron center as in rubrerythrin and not as reported for the R2
subunit of ribonucleotide reductase and the hydroxylase subunit of methane
monooxygenase. The crystal structure of the one-iron depleted desaturase species
demonstrates that the affinities for the two iron ions comprising the di-iron
center are not equivalent, Fe1 being the higher affinity site and Fe2 being the
lower affinity site.
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Figure 6.
FIG. 6. Stereoview (a) and 2 F[o] - F[c] electron density
map contoured at 1  (b) of the apo form of
the desaturase di-iron center at 3.2-Å resolution. The
absence of iron ions introduces flexibility in the coordinating
residues of the original di-iron center.
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Figure 8.
FIG. 8. Comparison of acetate complexes of desaturase (A)
and methane monooxygenase hydroxylase (1MMO) (B). Hydrogen bonds
to iron ligands are indicated with dotted lines. Glu142 and
Asp228 in desaturase, corresponding to Asp143 and Asp242 in
MMOH, make hydrogen bonds to the histidine iron ligands.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2003,
278,
25072-25080)
copyright 2003.
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