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PDBsum entry 1cc9
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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 crystal structure of a reduced [nifese] hydrogenase provides an image of the activated catalytic center.
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Authors
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E.Garcin,
X.Vernede,
E.C.Hatchikian,
A.Volbeda,
M.Frey,
J.C.Fontecilla-Camps.
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Ref.
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Structure Fold Des, 1999,
7,
557-566.
[DOI no: ]
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PubMed id
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Abstract
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hydrogenases are metalloenzymes that catalyze the reaction
H2<-->2H+ + 2e-. They are generally heterodimeric, contain three iron-sulfur
clusters in their small subunit and a nickel-iron-containing active site in
their large subunit that includes a selenocysteine (SeCys) ligand. RESULTS: We
hydrogenase from Desulfomicrobium baculatum in its reduced, active form. A
comparison of active sites of the oxidized, as-prepared, Desulfovibrio gigas and
the reduced D. baculatum hydrogenases shows that in the reduced enzyme the
nickel-iron distance is 0.4 A shorter than in the oxidized enzyme. In addition,
the putative oxo ligand, detected in the as-prepared D. gigas enzyme, is absent
from the D. baculatum hydrogenase. We also observe higher-than-average
temperature factors for both the active site nickel-selenocysteine ligand and
the neighboring Glu18 residue, suggesting that both these moieties are involved
in proton transfer between the active site and the molecular surface. Other
hydrogenases are the presence of a third
cluster found in the D. gigas enzyme, and
a putative iron center that substitutes the magnesium ion that has already been
hydrogenases.
CONCLUSIONS: The heterolytic cleavage of molecular hydrogen seems to be mediated
by the nickel center and the selenocysteine residue. Beside modifying the
catalytic properties of the enzyme, the selenium ligand might protect the nickel
atom from oxidation. We conclude that the putative oxo ligand is a signature of
hydrogenases.
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Figure 6.
Figure 6. The environment of the putative hydrogen sulfide
molecule. Stereoview of the active site and the hydrogen sulfide
molecule. The distance between the iron of the active site and
the assigned hydrogen sulfide molecule, represented by a dotted
line, is 6.7 Å. The hydrogen sulfide molecule is
coordinated by residues Thr70L, Ala71L and Asn103L. This figure
was made using TURBO-FRODO [42].
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The above figure is
reprinted
by permission from Cell Press:
Structure Fold Des
(1999,
7,
557-566)
copyright 1999.
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