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PDBsum entry 2uxm
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Photosynthesis
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PDB id
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2uxm
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Contents |
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241 a.a.
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281 a.a.
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303 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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Ph modulates the quinone position in the photosynthetic reaction center from rhodobacter sphaeroides in the neutral and charge separated states.
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Authors
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J.Koepke,
E.M.Krammer,
A.R.Klingen,
P.Sebban,
G.M.Ullmann,
G.Fritzsch.
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Ref.
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J Mol Biol, 2007,
371,
396-409.
[DOI no: ]
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PubMed id
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Abstract
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The structure of the photosynthetic reaction-center from Rhodobacter sphaeroides
has been determined at four different pH values (6.5, 8.0, 9.0, 10.0) in the
neutral and in charge separated states. At pH 8.0, in the neutral state, we
obtain a resolution of 1.87 A, which is the best ever reported for the bacterial
reaction center protein. Our crystallographic data confirm the existence of two
different binding positions of the secondary quinone (QB). We observe a new
orientation of QB in its distal position, which shows no ring-flip compared to
the orientation in the proximal position. Datasets collected for the different
pH values show a pH-dependence of the population of the proximal position. The
new orientation of QB in the distal position and the pH-dependence could be
confirmed by continuum electrostatics calculations. Our calculations are in
agreement with the experimentally observed proton uptake upon charge separation.
The high resolution of our crystallographic data allows us to identify new water
molecules and external residues being involved in two previously described
hydrogen bond proton channels. These extended proton-transfer pathways, ending
at either of the two oxo-groups of QB in its proximal position, provide
additional evidence that ring-flipping is not required for complete protonation
of QB upon reduction.
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Figure 2.
Figure 2. (a) Electron density around the distal and proximal QB
positions in the structure of this work (pH 8, dark-adapted state; PDB
entry 2j8c). The 0.2 and the 1σ levels of the
density are depicted in blue and magenta wireframes, respectively. The
models for the distal (orange) and the proximal (yellow) positions are
shown as stick model. The two head-groups are tilted out of the image
plane by about ±15°.
(b) Superposition of the two QB positions, color-coded in
yellow, orange, and red, respectively, with the structures from
Stowell et al. (PDB entries 1aig and 1aij) of the same state and at the same pH,
shown in red. Hydrogen bonds to neighboring protein atoms are
indicated by broken green lines, with their length given in
Å.
(c) Schematic drawing of the QB movement. Distal
position in black, hypothetical intermediate position in green, and
proximal QB position in blue. Hydrogen bonds to the distal
position are color-coded orange, to the intermediate position in red,
and to the proximal QB position in magenta. The length of
the total QB movement and the
Cα–Cα distance are indicated
by arrows.
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Figure 6.
Figure 6. Proton-uptake upon reduction of Q[B] as calculated
using the program GMCT. The total proton-uptake is shown by a
continuous line and experimental values (taken from Tandori et
al.^22) by black crosses with error bars. The contribution of
Asp L213 (broken line) and the protonation of the semiquinone
(dotted line) are shown additionally. The dash-dot line
describes the proton uptake by the rest of the protein.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2007,
371,
396-409)
copyright 2007.
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