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PDBsum entry 1upd
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Electron transport
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PDB id
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1upd
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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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Molecular basis for redox-Bohr and cooperative effects in cytochrome c3 from desulfovibrio desulfuricans atcc 27774: crystallographic and modeling studies of oxidized and reduced high-Resolution structures at ph 7.6.
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Authors
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I.Bento,
P.M.Matias,
A.M.Baptista,
P.N.Da costa,
W.M.Van dongen,
L.M.Saraiva,
T.R.Schneider,
C.M.Soares,
M.A.Carrondo.
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Ref.
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Proteins, 2004,
54,
135-152.
[DOI no: ]
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PubMed id
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Abstract
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The tetraheme cytochrome c3 is a small metalloprotein with ca. 13,000 Da found
in sulfate-reducing bacteria, which is believed to act as a partner of
hydrogenase. The three-dimensional structure of the oxidized and reduced forms
of cytochrome c3 from Desulfovibrio desulfuricans ATCC 27774 at pH 7.6 were
determined using high-resolution X-ray crystallography and were compared with
the previously determined oxidized form at pH 4.0. Theoretical calculations were
performed with both structures, using continuum electrostatic calculations and
Monte Carlo sampling of protonation and redox states, in order to understand the
molecular basis of the redox-Bohr and cooperativity effects related to the
coupled transfer of electrons and protons. We were able to identify groups that
showed redox-linked conformational changes. In particular, Glu61, His76, and
propionate D of heme II showed important contributions to the
redox-cooperativity, whereas His76, propionate A of heme I, and propionate D of
heme IV were the key residues for the redox-Bohr effect. Upon reduction, an
important movement of the backbone region surrounding hemes I and II was also
identified, that, together with a few redox-linked conformational changes in
side-chain residues, results in a significant decrease in the solvent
accessibility of hemes I and II.
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Figure 2.
Figure 2. Stereoviews of heme II and its surroundings. a:
Oxidized form at pH 4.0; b: oxidized form at pH 7.6; c: reduced
form at pH 7.6.
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Figure 5.
Figure 5. Stereoview of heme I. a: Oxidized form at pH 4.0; b:
oxidized form at pH 7.6; c: reduced form at pH 7.6.
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The above figures are
reprinted
by permission from John Wiley & Sons, Inc.:
Proteins
(2004,
54,
135-152)
copyright 2004.
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Secondary reference #1
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Title
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Conformational component in the coupled transfer of multiple electrons and protons in a monomeric tetraheme cytochrome.
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Authors
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R.O.Louro,
I.Bento,
P.M.Matias,
T.Catarino,
A.M.Baptista,
C.M.Soares,
M.A.Carrondo,
D.L.Turner,
A.V.Xavier.
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Ref.
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J Biol Chem, 2001,
276,
44044-44051.
[DOI no: ]
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PubMed id
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Figure 3.
Fig. 3. Stereoview of heme I in all three redox forms.
The reduced form is blue; the oxidized form at pH 7.6 is yellow;
the oxidized form at pH 4.0 is red. Both in the reduced and
oxidized forms at pH 7.6, propionate A displays two alternative
side chain conformations. The figure was drawn with Molscript
(44) and Raster3D (45).
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Figure 4.
Fig. 4. Stereoview of the region surrounding heme II in
all three redox forms. The reduced form is blue; the oxidized
form at pH 7.6 is yellow; the oxidized form at pH 4.0 is red.
Propionate D of heme 2 and the side chains of Glu-61, Lys-75,
and His-76 are represented, and the differences observed between
both redox forms are discussed in the text.
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The above figures are
reproduced from the cited reference
with permission from the ASBMB
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Secondary reference #2
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Title
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Refinement of the three-Dimensional structures of cytochrome c3 from desulfovibrio vulgaris hildenborough at 1.67 angstroms resolution and from desulfovibrio desulfuricans atcc 27774 at 1.6 angstrom s resolution
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Authors
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P.Simoes,
P.M.Matias,
J.Morais,
K.Wilson,
Z.Dauter,
M.A.Carrondo.
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Ref.
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inorg chim acta, 1998,
273,
213.
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Secondary reference #3
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Title
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Structure of the tetraheme cytochrome from desulfovibrio desulfuricans atcc 27774: X-Ray diffraction and electron paramagnetic resonance studies.
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Authors
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J.Morais,
P.N.Palma,
C.Frazão,
J.Caldeira,
J.Legall,
I.Moura,
J.J.Moura,
M.A.Carrondo.
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Ref.
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Biochemistry, 1995,
34,
12830-12841.
[DOI no: ]
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PubMed id
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