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PDBsum entry 1fhh
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Electron transport
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PDB id
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1fhh
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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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Leucine 41 is a gate for water entry in the reduction of clostridium pasteurianum rubredoxin.
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Authors
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T.Min,
C.E.Ergenekan,
M.K.Eidsness,
T.Ichiye,
C.Kang.
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Ref.
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Protein Sci, 2001,
10,
613-621.
[DOI no: ]
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PubMed id
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Abstract
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Biological electron transfer is an efficient process even though the distances
between the redox moieties are often quite large. It is therefore of great
interest to gain an understanding of the physical basis of the rates and driving
forces of these reactions. The structural relaxation of the protein that occurs
upon change in redox state gives rise to the reorganizational energy, which is
important in the rates and the driving forces of the proteins involved. To
determine the structural relaxation in a redox protein, we have developed
methods to hold a redox protein in its final oxidation state during
crystallization while maintaining the same pH and salt conditions of the
crystallization of the protein in its initial oxidation state. Based on 1.5 A
resolution crystal structures and molecular dynamics simulations of oxidized and
reduced rubredoxins (Rd) from Clostridium pasteurianum (Cp), the structural
rearrangements upon reduction suggest specific mechanisms by which electron
transfer reactions of rubredoxin should be facilitated. First, expansion of the
[Fe-S] cluster and concomitant contraction of the NH...S hydrogen bonds lead to
greater electrostatic stabilization of the extra negative charge. Second, a
gating mechanism caused by the conformational change of Leucine 41, a nonpolar
side chain, allows transient penetration of water molecules, which greatly
increases the polarity of the redox site environment and also provides a source
of protons. Our method of producing crystals of Cp Rd from a reducing solution
leads to a distribution of water molecules not observed in the crystal structure
of the reduced Rd from Pyrococcus furiosus. How general this correlation is
among redox proteins must be determined in future work. The combination of our
high-resolution crystal structures and molecular dynamics simulations provides a
molecular picture of the structural rearrangement that occurs upon reduction in
Cp rubredoxin.
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Figure 2.
Fig. 2. The electron density map (2F0--Fc) around residue 41 for (a) the reduced form and (b) the oxidized form. In the reduced form,
there are two different conformations of Leu 41 side chain. When the side chain of Leu 41 is in the open conformation, a water molecule
(depicted by a star) can be placed in the electron density on the other side in hydrogen bonding distance of the S> atom of Cys 9.
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Figure 3.
Fig. 3. Local structure of the reduced form around Fe---S cluster and Leu 41 in its open conformation (open water gate). Placing the
side chain of Leu 41 away from Cys 9 S> allows the string of water molecules to approach the Cys 9 S>, with the first water forming
a hydrogen bond with Cys 9 S>.
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The above figures are
reprinted
from an Open Access publication published by the Protein Society:
Protein Sci
(2001,
10,
613-621)
copyright 2001.
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