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PDBsum entry 1ubh
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Oxidoreductase
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PDB id
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1ubh
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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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Structural studies of the carbon monoxide complex of [nife]hydrogenase from desulfovibrio vulgaris miyazaki f: suggestion for the initial activation site for dihydrogen.
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Authors
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H.Ogata,
Y.Mizoguchi,
N.Mizuno,
K.Miki,
S.Adachi,
N.Yasuoka,
T.Yagi,
O.Yamauchi,
S.Hirota,
Y.Higuchi.
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Ref.
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J Am Chem Soc, 2002,
124,
11628-11635.
[DOI no: ]
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PubMed id
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Abstract
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The carbon monoxide complex of [NiFe]hydrogenase from Desulfovibrio vulgaris
Miyazaki F has been characterized by X-ray crystallography and absorption and
resonance Raman spectroscopy. Nine crystal structures of the [NiFe]hydrogenase
in the CO-bound and CO-liberated forms were determined at 1.2-1.4 A resolution.
The exogenously added CO was assigned to be bound to the Ni atom at the Ni-Fe
active site. The CO was not replaced with H(2) in the dark at 100 K, but was
liberated by illumination with a strong white light. The Ni-C distances and
Ni-C-O angles were about 1.77 A and 160 degrees, respectively, except for one
case (1.72 A and 135 degrees ), in which an additional electron density peak
between the CO and Sgamma(Cys546) was recognized. Distinct changes were observed
in the electron density distribution of the Ni and Sgamma(Cys546) atoms between
the CO-bound and CO-liberated structures for all the crystals tested. The novel
structural features found near the Ni and Sgamma(Cys546) atoms suggest that
these two atoms at the Ni-Fe active site play a role during the initial
H(2)-binding process. Anaerobic addition of CO to dithionite-reduced
[NiFe]hydrogenase led to a new absorption band at about 470 nm ( approximately
3000 M(-1)cm(-1)). Resonance Raman spectra (excitation at 476.5 nm) of the CO
complex revealed CO-isotope-sensitive bands at 375/393 and 430 cm(-1) (368 and
413 cm(-1) for (13)C(18)O). The frequencies and relative intensities of the
CO-related Raman bands indicated that the exogenous CO is bound to the Ni atom
with a bent Ni-C-O structure in solution, in agreement with the refined
structure determined by X-ray crystallography.
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