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Contents |
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333 a.a.
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476 a.a.
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421 a.a.
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339 a.a.
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76 a.a.
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33 a.a.
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53 a.a.
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38 a.a.
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38 a.a.
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37 a.a.
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37 a.a.
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30 a.a.
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246 a.a.
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31 a.a.
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105 a.a.
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137 a.a.
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40 a.a.
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37 a.a.
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58 a.a.
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×2
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×72
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×4
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×4
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×2
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×14
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×2
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×4
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* Residue conservation analysis
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PDB id:
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| Name: |
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Photosynthesis
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Title:
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Architecture of the photosynthetic oxygen evolving center
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Structure:
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Photosystem q(b) protein. Chain: a, a. Synonym: 32 kda thylakoid membrane protein, photosystem ii protein d1. Photosystem ii core light harvesting protein. Chain: b, b. Photosystem ii cp43 protein. Chain: c, c. Photosystem ii reaction center d2 protein.
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Source:
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Thermosynechococcus elongatus. Organism_taxid: 146786. Organism_taxid: 146786
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Biol. unit:
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90mer (from
)
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Resolution:
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3.50Å
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R-factor:
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0.296
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R-free:
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0.342
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Authors:
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K.N.Ferreira,T.M.Iverson,K.Maghlaoui,J.Barber,S.Iwata
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Key ref:
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K.N.Ferreira
et al.
(2004).
Architecture of the photosynthetic oxygen-evolving center.
Science,
303,
1831-1838.
PubMed id:
DOI:
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Date:
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21-Jan-04
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Release date:
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24-Feb-04
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PROCHECK
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Headers
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References
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P0A444
(PSBA1_THEEB) -
Photosystem II protein D1 1 from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)
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Seq:
Struc:
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360 a.a.
333 a.a.
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Q8DIQ1
(PSBB_THEEB) -
Photosystem II CP47 reaction center protein from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)
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Seq:
Struc:
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510 a.a.
476 a.a.
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Q8DIF8
(PSBC_THEEB) -
Photosystem II CP43 reaction center protein from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)
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Seq:
Struc:
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461 a.a.
421 a.a.
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Q8CM25
(PSBD_THEEB) -
Photosystem II D2 protein from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)
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Seq:
Struc:
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352 a.a.
339 a.a.
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Q8DIP0
(PSBE_THEEB) -
Cytochrome b559 subunit alpha from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)
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Seq:
Struc:
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84 a.a.
76 a.a.
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Q8DIN9
(PSBF_THEEB) -
Cytochrome b559 subunit beta from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)
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Seq:
Struc:
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45 a.a.
33 a.a.
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Q8DJ43
(PSBH_THEEB) -
Photosystem II reaction center protein H from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)
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Seq:
Struc:
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66 a.a.
53 a.a.
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Q8DJZ6
(PSBI_THEEB) -
Photosystem II reaction center protein I from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)
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Seq:
Struc:
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38 a.a.
38 a.a.
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P59087
(PSBJ_THEEB) -
Photosystem II reaction center protein J from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)
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Seq:
Struc:
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40 a.a.
38 a.a.
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Q9F1K9
(PSBK_THEEB) -
Photosystem II reaction center protein K from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)
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Seq:
Struc:
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46 a.a.
37 a.a.
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Q8DIN8
(PSBL_THEEB) -
Photosystem II reaction center protein L from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)
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Seq:
Struc:
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37 a.a.
37 a.a.
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Q8DHA7
(PSBM_THEEB) -
Photosystem II reaction center protein M from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)
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Seq:
Struc:
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36 a.a.
30 a.a.
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P0A431
(PSBO_THEEB) -
Photosystem II extrinsic protein O from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)
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Seq:
Struc:
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272 a.a.
246 a.a.
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Q8DIQ0
(PSBT_THEEB) -
Photosystem II reaction center protein T from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)
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Seq:
Struc:
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32 a.a.
31 a.a.
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Q9F1L5
(PSBU_THEEB) -
Photosystem II extrinsic protein U from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)
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Seq:
Struc:
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134 a.a.
105 a.a.
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P0A386
(CY550_THEEB) -
Photosystem II extrinsic protein V from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)
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Seq:
Struc:
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163 a.a.
137 a.a.
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Q9F1R6
(PSBX_THEEB) -
Photosystem II reaction center protein X from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)
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Seq:
Struc:
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41 a.a.
40 a.a.
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 |
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| |
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DOI no:
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Science
303:1831-1838
(2004)
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PubMed id:
|
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|
|
|
|
| |
|
Architecture of the photosynthetic oxygen-evolving center.
|
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K.N.Ferreira,
T.M.Iverson,
K.Maghlaoui,
J.Barber,
S.Iwata.
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| |
ABSTRACT
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Photosynthesis uses light energy to drive the oxidation of water at an
oxygen-evolving catalytic site within photosystem II (PSII). We report the
structure of PSII of the cyanobacterium Thermosynechococcus elongatus at 3.5
angstrom resolution. We have assigned most of the amino acid residues of this
650-kilodalton dimeric multisubunit complex and refined the structure to reveal
its molecular architecture. Consequently, we are able to describe details of the
binding sites for cofactors and propose a structure of the oxygen-evolving
center (OEC). The data strongly suggest that the OEC contains a cubane-like
Mn3CaO4 cluster linked to a fourth Mn by a mono-micro-oxo bridge. The details of
the surrounding coordination sphere of the metal cluster and the implications
for a possible oxygen-evolving mechanism are discussed.
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Selected figure(s)
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Figure 1.
Fig. 1. Overall structure of PSII. (A) View of the PSII dimer
perpendicular to the membrane normal. Helices are represented as
cylinders with D1 in yellow; D2 in orange; CP47 in red; CP43 in
green; cyt b559 in wine red; PsbL, PsbM, and PsbT in medium
blue; and PsbH, PsbI, PsbJ, PsbK, PsbX, PsbZ, and the putative
PsbN in gray. The extrinsic proteins are PsbO in blue, PsbU in
magenta, and PsbV in cyan. Chlorophylls of the D1/D2 reaction
center are light green, pheophytins are blue, chlorophylls of
the antenna complexes are dark green, ß-carotenes are in
orange, hemes are in red, nonheme Fe is red, Q[A] and Q[B] are
purple. The oxygen-evolving center (OEC) is shown as the red
(oxygen atoms), magenta (Mn ions), and cyan (Ca^2+) balls. (B)
View of the PSII monomer along the membrane normal from the
lumenal side. A part of the other monomer in the dimmer is shown
to emphasize the region of monomer/monomer interaction along the
dotted line. The pseudo-twofold axis perpendicular to the
membrane plane passing through the nonheme Fe relates the
transmembrane helices of the D1/D2 heterodimer, the low
molecular subunits, PsbI and PsbX, and CP43 and CP47 as
emphasized by the black lines encircling these subunits.
Coloring is the same as in (A).
|
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Figure 2.
Fig. 2. Cofactors involved in electron transfer. (A) Electron
transfer cofactors shown perpendicular to the internal
pseudo-twofold. Coloring scheme is the same as in Fig. 1. The
phytol tails of the chlorophylls and pheophytins have been
removed for clarity. The side chains of Tyr[Z] (D1 Tyr161) and
D1 His190 are shown in yellow, and Tyr[D] (D2 Tyr160) and D2
His189 are in orange. The four chlorophylls comprising P680 are
in direct van der Waals contact, and other electron transfer
distances are given in Å. (B) The P680 dimer of
chlorophylls (P[D1] and P[D2]) and accessory Chls (Chl[D1] and
Chl[D2]). Coloring scheme is the same as in Fig. 1, except that
the protein main chain is depicted in light gray, whereas the
side-chain bonds and carbon atoms follow the coloring of the
protein subunits (D1, yellow; D2, orange). The histidine ligands
D1 His198 and D2 His197 are shown, as well as the redox-active
Tyr[Z]-D1 His190 and Tyr[D]-D2 His189 pairs. The view is down
the pseudo-twofold axis from the stromal side.
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The above figures are
reprinted
by permission from the AAAs:
Science
(2004,
303,
1831-1838)
copyright 2004.
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Figures were
selected
by the author.
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 |
 |
 |
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Literature references that cite this PDB file's key reference
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| |
PubMed id
|
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Reference
|
|
|
|
|
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A.R.Jaszewski,
S.Petrie,
R.J.Pace,
and
R.Stranger
(2011).
Toward the Assignment of the Manganese Oxidation Pattern in the Water-Oxidizing Complex of Photosystem II: A Time-Dependent DFT Study of XANES Energies.
|
| |
Chemistry,
17,
5699-5713.
|
|
|
|
|
|
|
A.Williamson,
B.Conlan,
W.Hillier,
and
T.Wydrzynski
(2011).
The evolution of Photosystem II: insights into the past and future.
|
| |
Photosynth Res,
107,
71-86.
|
|
|
|
|
|
|
C.M.Liu,
D.Q.Zhang,
and
D.B.Zhu
(2011).
Ring like octadecanuclear mixed-valence manganese cluster with a spin ground state of 20.
|
| |
Chem Asian J,
6,
74-77.
|
|
|
|
|
|
|
C.Pagliano,
F.Chimirri,
G.Saracco,
F.Marsano,
and
J.Barber
(2011).
One-step isolation and biochemical characterization of a highly active plant PSII monomeric core.
|
| |
Photosynth Res,
108,
33-46.
|
|
|
|
|
|
|
D.Wang,
H.Jiang,
X.Zong,
Q.Xu,
Y.Ma,
G.Li,
and
C.Li
(2011).
Crystal facet dependence of water oxidation on BiVO4 sheets under visible light irradiation.
|
| |
Chemistry,
17,
1275-1282.
|
|
|
|
|
|
|
G.Rea,
M.Lambreva,
F.Polticelli,
I.Bertalan,
A.Antonacci,
S.Pastorelli,
M.Damasso,
U.Johanningmeier,
and
M.T.Giardi
(2011).
Directed evolution and in silico analysis of reaction centre proteins reveal molecular signatures of photosynthesis adaptation to radiation pressure.
|
| |
PLoS One,
6,
e16216.
|
|
|
|
|
|
|
I.Vass
(2011).
Role of charge recombination processes in photodamage and photoprotection of the photosystem II complex.
|
| |
Physiol Plant,
142,
6.
|
|
|
|
|
|
|
J.G.García-Cerdán,
L.Kovács,
T.Tóth,
S.Kereïche,
E.Aseeva,
E.J.Boekema,
F.Mamedov,
C.Funk,
and
W.P.Schröder
(2011).
The PsbW protein stabilizes the supramolecular organization of photosystem II in higher plants.
|
| |
Plant J,
65,
368-381.
|
|
|
|
|
|
|
J.Nickelsen,
B.Rengstl,
A.Stengel,
M.Schottkowski,
J.Soll,
and
E.Ankele
(2011).
Biogenesis of the cyanobacterial thylakoid membrane system--an update.
|
| |
FEMS Microbiol Lett,
315,
1-5.
|
|
|
|
|
|
|
J.P.Allen,
and
J.C.Williams
(2011).
The evolutionary pathway from anoxygenic to oxygenic photosynthesis examined by comparison of the properties of photosystem II and bacterial reaction centers.
|
| |
Photosynth Res,
107,
59-69.
|
|
|
|
|
|
|
R.K.Seidler-Egdal,
A.Nielsen,
A.D.Bond,
M.J.Bjerrum,
and
C.J.McKenzie
(2011).
High turnover catalysis of water oxidation by Mn(II) complexes of monoanionic pentadentate ligands.
|
| |
Dalton Trans,
40,
3849-3858.
|
|
|
|
|
|
|
S.Banerjee,
M.Nandy,
S.Sen,
S.Mandal,
G.M.Rosair,
A.M.Slawin,
C.J.Gómez García,
J.M.Clemente-Juan,
E.Zangrando,
N.Guidolin,
and
S.Mitra
(2011).
Isolation of four new CoII/CoIII and NiII complexes with a pentadentate Schiff base ligand: syntheses, structural descriptions and magnetic studies.
|
| |
Dalton Trans,
40,
1652-1661.
|
|
|
|
|
|
|
S.Nayak,
H.P.Nayek,
S.Dehnen,
A.K.Powell,
and
J.Reedijk
(2011).
Trigonal propeller-shaped [Mn(III)3M(II)Na] complexes (M = Mn, Ca): structural and functional models for the dioxygen evolving centre of PSII.
|
| |
Dalton Trans,
40,
2699-2702.
|
|
|
|
|
|
|
V.I.Novoderezhkin,
E.Romero,
J.P.Dekker,
and
R.van Grondelle
(2011).
Multiple Charge-Separation Pathways in Photosystem II: Modeling of Transient Absorption Kinetics.
|
| |
Chemphyschem,
12,
681-688.
|
|
|
|
|
|
|
W.M.Sameera,
C.J.McKenzie,
and
J.E.McGrady
(2011).
On the mechanism of water oxidation by a bimetallic manganese catalyst: a density functional study.
|
| |
Dalton Trans,
40,
3859-3870.
|
|
|
|
|
|
|
Y.Guo,
J.Huang,
Y.Huang,
J.Wang,
and
Y.Yu
(2011).
Tetra-μ(2)-acetato-diaqua-bis-(μ(2)-2-{[1,3-dihy-droxy-2-(oxidometh-yl)propan-2-yl]imino-meth-yl}phenolato)trimanganese(II,III) acetonitrile disolvate dihydrate.
|
| |
Acta Crystallogr Sect E Struct Rep Online,
67,
m1098.
|
|
|
|
|
|
|
Y.Hou,
B.L.Abrams,
P.C.Vesborg,
M.E.Björketun,
K.Herbst,
L.Bech,
A.M.Setti,
C.D.Damsgaard,
T.Pedersen,
O.Hansen,
J.Rossmeisl,
S.Dahl,
J.K.Nørskov,
and
I.Chorkendorff
(2011).
Bioinspired molecular co-catalysts bonded to a silicon photocathode for solar hydrogen evolution.
|
| |
Nat Mater,
10,
434-438.
|
|
|
|
|
|
|
Y.Umena,
K.Kawakami,
J.R.Shen,
and
N.Kamiya
(2011).
Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9 Å.
|
| |
Nature,
473,
55-60.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
Y.Yang,
T.A.Ramelot,
J.R.Cort,
D.Wang,
C.Ciccosanti,
K.Hamilton,
R.Nair,
B.Rost,
T.B.Acton,
R.Xiao,
J.K.Everett,
G.T.Montelione,
and
M.A.Kennedy
(2011).
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