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PDBsum entry 2fyu
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Oxidoreductase
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PDB id
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2fyu
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Contents |
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446 a.a.
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423 a.a.
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378 a.a.
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241 a.a.
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196 a.a.
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106 a.a.
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75 a.a.
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64 a.a.
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57 a.a.
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60 a.a.
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53 a.a.
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References listed in PDB file
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Key reference
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Title
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Surface-Modulated motion switch: capture and release of iron-Sulfur protein in the cytochrome bc1 complex.
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Authors
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L.Esser,
X.Gong,
S.Yang,
L.Yu,
C.A.Yu,
D.Xia.
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Ref.
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Proc Natl Acad Sci U S A, 2006,
103,
13045-13050.
[DOI no: ]
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PubMed id
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Abstract
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In the cytochrome bc(1) complex, the swivel motion of the iron-sulfur protein
(ISP) between two redox sites constitutes a key component of the mechanism that
achieves the separation of the two electrons in a substrate molecule at the
quinol oxidation (Q(o)) site. The question remaining is how the motion of ISP is
controlled so that only one electron enters the thermodynamically favorable
chain via ISP. An analysis of eight structures of mitochondrial bc(1) with bound
Q(o) site inhibitors revealed that the presence of inhibitors causes a
bidirectional repositioning of the cd1 helix in the cytochrome b subunit. As the
cd1 helix forms a major part of the ISP binding crater, any positional shift of
this helix modulates the ability of cytochrome b to bind ISP. The analysis also
suggests a mechanism for reversal of the ISP fixation when the shape
complementarity is significantly reduced after a positional reorientation of the
reaction product quinone. The importance of shape complementarity in this
mechanism was confirmed by functional studies of bc(1) mutants and by a
structure determination of the bacterial form of bc(1). A mechanism for the high
fidelity of the bifurcated electron transfer is proposed.
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Figure 1.
Fig. 1. Prosthetic groups and subunit structures of the cyt
bc[1] complex. (A) Arrangement of prosthetic groups in the
dimeric bc[1] complex and illustration of the electron
bifurcation at the Q[o] site. The b[L], b[H], and c[1] heme
groups are shown as ball-and-stick models, and the [2Fe2S]
clusters are depicted as cpk models. Carbon atoms, black;
nitrogen, blue; oxygen, red; sulfur, yellow; iron, brown. The
Q[o] pockets near the IMS side of the membrane and the Q[i]
pockets near the matrix side are labeled and shaded in gray. Cyt
c is shown as a gray shaded oval. Distances between redox
centers are given on the left half of the diagram, and the redox
potential for each center is given on the right. The high- and
low-potential ET paths are depicted with red and green arrows,
respectively. Circles in pink and light green within the Q[o]
pockets are hypothesized distal-QH[2] and proximal-Q binding
sites, respectively. (B) Ribbon diagram of the dimeric cyt b,
cyt c[1], and ISP subunit in the mitochondrial bc[1] complex.
Two symmetry-related cyt b subunits are shown (green and light
green). The eight TM helices of cyt b are denoted with letters
A–H. Helices A–E form one bundle in which the two b-type
hemes (b[L] and b[H] in ball-and-stick models) reside; helices
F–H form the other bundle. The ISP subunit (yellow and red for
the symmetry pair) has an extrinsic soluble domain with a
[2Fe2S] cluster at its tip, connecting to a TM segment by a
flexible neck. The extrinsic domain of cyt c[1] (blue and
magenta for the symmetry pair) with its heme group is rigidly
attached to its TM helix. The locations for the two active sites
(Q[o] and Q[i]) per monomer in cyt b are labeled. The surface
depression in cyt b at the IMS side of the membrane is labeled
as the ISP-docking crater.
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Figure 3.
Fig. 3. Control of the ISP-ED motion switch and the
proposed mechanism for electron bifurcation at the Q[o] pocket.
The structural components necessary for the control of ISP
conformational switch are illustrated in this cartoon rendition
of the Q[o] pocket. The PEWY motif and cd1 helix in gray
represent a native (Rest) configuration. The ISP in yellow and
magenta are of oxidized and reduced form, respectively. The PEWY
in blue stands for the open configuration with a bound Q[o] site
inhibitor. The cd1 helix in red symbolizes the conformation
(On/+) in the presence of a Pf inhibitor occupying the distal
site (pink), and the cd1 helix in green shows the conformation
(Off/–) when a Pm inhibitor is taking the proximal site
(purple). Cyt c[1] and heme b[L] are also shown.
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