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PDBsum entry 3prc
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Photosynthetic reaction center
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PDB id
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3prc
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Contents |
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332 a.a.
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273 a.a.
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323 a.a.
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258 a.a.
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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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The coupling of light-Induced electron transfer and proton uptake as derived from crystal structures of reaction centres from rhodopseudomonas viridis modified at the binding site of the secondary quinone, Qb.
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Authors
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C.R.Lancaster,
H.Michel.
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Ref.
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Structure, 1997,
5,
1339-1359.
[DOI no: ]
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PubMed id
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Abstract
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BACKGROUND: In a reaction of central importance to the energetics of
photosynthetic bacteria, light-induced electron transfer in the reaction centre
(RC) is coupled to the uptake of protons from the cytoplasm at the binding site
of the secondary quinone (QB). In the original structure of the RC from
Rhodopseudomonas viridis (PDB entry code 1PRC), the QB site was poorly defined
because in the standard RC crystals it was only approximately 30% occupied with
ubiquinone-9 (UQ9). We report here the structural characterization of the QB
site by crystallographic refinement of UQ9-depleted RCs and of complexes of the
RC either with ubiquinone-2 (UQ2) or the electron-transfer inhibitor
stigmatellin in the QB site. RESULTS: The structure of the RC complex with UQ2,
refined at 2.45 A resolution, constitutes the first crystallographically
reliably defined binding site for quinones from the bioenergetically important
quinone pool of biological, energy-transducing membranes. In the UQ9-depleted QB
site of the RC structure, refined at 2.4 A resolution, apparently five (and
possibly six) water molecules are bound instead of the ubiquinone head group,
and a detergent molecule binds in the region of the isoprenoid tail. All of the
protein-cofactor interactions implicated in the binding of the ubiquinone head
group are also implicated in the binding of the stigmatellin head group. In the
structure of the stigmatellin-RC complex, refined at 2.4 A resolution,
additional hydrogen bonds stabilize the binding of stigmatellin over that of
ubiquinone. The tentative position of UQ9 in the QB site in the original data
set (1PRC) was re-examined using the structure of the UQ9-depleted RC as a
reference. A modified QB site model, which exhibits greater similarity to the
distal ubiquinone-10 (UQ10) positioning in the structure of the RC from
Rhodobacter sphaeroides (PDB entry code 1PCR), is suggested as the dominant
binding site for native UQ9. CONCLUSIONS: The structures reported here can
provide models of quinone reduction cycle intermediates. The binding pattern
observed for the stigmatellin complex, where the ligand donates a hydrogen bond
to Ser L223 (where 'L' represents the L subunit of the RC), can be viewed as a
model for the stabilization of a monoprotonated reduced intermediate (QBH or
QBH-). The presence of Ser L223 in the QB site indicates that the QB site is not
optimized for QB binding, but for QB reduction to the quinol.
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Figure 3.
Figure 3. Comparison of the structure at the Q[B] site.
(a-c) The RC-UQ2 complex (in black) compared to the original
structure 1PRC [13] (in green). (d) The Q[B]-depleted RC (in
pink) compared to the RC-UQ2 complex (in black). (e,f) The
RC-stigmatellin complex (in orange) compared to that of the
RC-UQ2 complex (in black). Prospective hydrogen bonds are
represented as dashed lines. (Figure made with the program
MOLSCRIPT [96].)
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The above figure is
reprinted
by permission from Cell Press:
Structure
(1997,
5,
1339-1359)
copyright 1997.
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Secondary reference #1
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Title
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Refined crystal structures of reaction centres from rhodopseudomonas viridis in complexes with the herbicide atrazine and two chiral atrazine derivatives also lead to a new model of the bound carotenoid.
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Authors
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C.R.Lancaster,
H.Michel.
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Ref.
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J Mol Biol, 1999,
286,
883-898.
[DOI no: ]
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PubMed id
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Figure 4.
Figure 4. Comparison of triazine and quinone binding to the
Q[B] site (stereo views). Figures of three-dimensional molecular
structures without electron density were generated with
MolScript [Kraulis 1991]. (a) Stereo view; colour coding is as
follows: RC complex with ubiquinone-2 (2PRC, black), with
DG-420315 (7PRC, brown), with DG-420314 (6PRC, green), and with
atrazine (5PRC, blue). (b) Side view of (a)).
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Figure 5.
Figure 5. Hydrogen bonding interactions important for
atrazine binding to the RC. (a) Carbon atoms are shown in black,
nitrogen atoms in blue, oxygen in red, chlorine in green, and
hydrogen atoms in white. (b) Comparison to the distal (green,
1PRC[new]) and proximal (black, 2PRC) ubiquinone binding sites
[Lancaster and Michel 1997]. The structure of the atrazine
complex (5PRC) is shown in pink.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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Secondary reference #2
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Title
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Ubiquinone reduction and protonation in the reaction centre of rhodopseudomonas viridis: X-Ray structures and their functional implications
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Author
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C.R.D.Lancaster.
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Ref.
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biochim biophys acta, 1998,
1365,
143.
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Secondary reference #3
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Title
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Crystallographic refinement at 2.3 a resolution and refined model of the photosynthetic reaction centre from rhodopseudomonas viridis.
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Authors
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J.Deisenhofer,
O.Epp,
I.Sinning,
H.Michel.
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Ref.
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J Mol Biol, 1995,
246,
429-457.
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PubMed id
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Secondary reference #4
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Title
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The photosynthetic reaction center from the purple bacterium rhodopseudomonas viridis.
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Authors
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J.Deisenhofer,
H.Michel.
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Ref.
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Science, 1989,
245,
1463-1473.
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PubMed id
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Secondary reference #5
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Title
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Structure of the protein subunits in the photosynthetic reaction centre of rhodopseudomonas viridis at 3 angstroms resolution
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Authors
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J.Deisenhofer,
O.Epp,
K.Miki,
R.Huber,
H.Michel.
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Ref.
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nature, 1985,
318,
618.
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Secondary reference #6
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Title
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X-Ray structure analysis of a membrane protein complex. Electron density map at 3 a resolution and a model of the chromophores of the photosynthetic reaction center from rhodopseudomonas viridis.
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Authors
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J.Deisenhofer,
O.Epp,
K.Miki,
R.Huber,
H.Michel.
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Ref.
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J Mol Biol, 1984,
180,
385-398.
[DOI no: ]
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PubMed id
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Figure 3.
Fro. 3. Stereo draing of the special pair. The central local symmetry ais runs
between the BChl-bs. Ring numbers are indicated in one BChl-b. Phytyl chains are truncated.
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Figure 4.
FIG. 4. Stereo drawing of the prosthetic grups of the RC shwing 4 BChl-b (BC), 2 BPh-b (BP), 1
non-eine iron (Fe), 1 quinone (MQ) an heine grups (HE). The central local symmetry axis runs
vertically in the plane of the picture. The plane of the membane is assumed t be oriented
perpendicular to the central local symmetry axis, i.e. horizontal and perpendicular to the plane of th
picture. The dotted lines marked 0 and I indicate the presmed approximate outer and inner
membrane surfaces of the bacterial cell. The BChl-b, BPh-b, quinone and iron are lcated within th
cylindrical central part of the RC compex; te ~ 70 A diameter of the cylinder is perpendicular to th
local symmetry axis in the plane of the picture
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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Secondary reference #7
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Title
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Three-Dimensional crystals of a membrane protein complex. The photosynthetic reaction centre from rhodopseudomonas viridis.
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Author
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H.Michel.
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Ref.
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J Mol Biol, 1982,
158,
567-572.
[DOI no: ]
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PubMed id
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Figure 1.
IG:. 1. Elation profile of the molecular siev chromatograph step used for the isolation of thr
photosvnthetic reaction centrrs from tl. Gridis. I'hotosynthrtir membranes (I6 mg of protein/ml) were
solubil&d in 5''' f. w/v) S.K~dod~c?ildimet,h~lamine A-oxide. WI O,> (y/v) Sx3. 10 mwTris_ HCI (pH 7)
at room temprratre for 5 mill. After a clarifying spin (1OO,OOOg, 30 min). 09.5 ml of the supwnatant
was applird to a. TSK 3ooO SW column (LKH. (ZrLfelfing) and run nt 0.1 ml/in in 20 mM-sodium
phosphat,r (pH 7). 0.1 `)o (w/r) S,S-dodervldimc,th?aminr A-oxide, PI'',, (W/V) NaN,. The reaction
crntres form the prak arktad I%(`.
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The above figure is
reproduced from the cited reference
with permission from Elsevier
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