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PDBsum entry 1dop
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protein ligands metals Protein-protein interface(s) links
Photosynthetic reaction center PDB id
1dop

 

 

 

 

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Contents
Protein chains
151 a.a.
151 a.a.
Ligands
CLA ×4
PHO ×2
Metals
FE2
Theoretical model
PDB id:
1dop
Name: Photosynthetic reaction center
Title: Theoretical model of photosystem ii reaction center (core)
Structure: Photosystem ii reaction center. Chain: a, d. Fragment: core, residues 106 - 224 and 266 - 297 of the d1 protein and residues 106 - 224 and 263 - 294 of the d2 protein. Other_details: part of the d1 and d2 proteins with bound cofactors
Source: Spinacia oleracea. Spinach
Authors: B.Svensson,C.Etchebest,P.Tuffery,P.Van Kan,J.Smith, S.Styring
Key ref:
B.Svensson et al. (1996). A model for the photosystem II reaction center core including the structure of the primary donor P680. Biochemistry, 35, 14486-14502. PubMed id: 8931545 DOI: 10.1021/bi960764k
Date:
16-Oct-96     Release date:   15-May-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
P02955  (PSBA_SPIOL) - 
Protein chain
Pfam   ArchSchema ?
P06005  (PSBD_SPIOL) -  Photosystem II D2 protein
Seq:
Struc: 		353 a.a.
151 a.a.
Key:    PfamA domain  Secondary structure

 

 
DOI no: 10.1021/bi960764k Biochemistry 35:14486-14502 (1996)
PubMed id: 8931545  
 
 
A model for the photosystem II reaction center core including the structure of the primary donor P680.
B.Svensson, C.Etchebest, P.Tuffery, P.van Kan, J.Smith, S.Styring.
 
  ABSTRACT  
 
For a detailed understanding of the function of photosystem II (PSII), a molecular structure is needed. The crystal structure has not yet been determined, but the PSII reaction center proteins D1 and D2 show homology with the L and M subunits of the photosynthetic reaction center from purple bacteria. We have modeled important parts of the D1 and D2 proteins on the basis of the crystallographic structure of the reaction center from Rhodopseudomonas viridis. The model contains the central core of the PSII reaction center, including the protein regions for the transmembrane helices B, C, D, and E and loops B-C and C-D connecting the helices. In the model, four chlorophylls, two pheophytins, and the nonheme Fe2+ ion are included. We have applied techniques from computational chemistry that incorporate statistical data on side-chain rotameric states from known protein structure and that describe interactions within the model using an empirical potential energy function. The conformation of chlorophyll pigments in the model was optimized by using exciton interaction calculations in combination with potential energy calculations to find a solution that agrees with experimentally determined exciton interaction energies. The model is analyzed and compared with experimental results for the regions of P680, the redox active pheophytin, the acceptor side Fe2+, and the tyrosyl radicals TyrD and TyrZ. P680 is proposed to be a weakly coupled chlorophyll a pair which makes three hydrogen bonds with residues on the D1 and D2 proteins. In the model the redox-active pheophytin is hydrogen bonded to D1-Glu130 and possibly also to D1-Tyr126 and D1-Tyr147. TyrD is hydrogen bonded to D2-His190 and also interacts with D2-Gln165. TyrZ is bound in a hydrophilic environment which is partially constituted by D1-Gln165, D1-Asp170, D1-Glu189, and D1-His190. These polar residues are most likely involved in proton transfer from oxidized TyrZ or in metal binding.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20394099 T.Renger, and E.Schlodder (2010).
Primary photophysical processes in photosystem II: bridging the gap between crystal structure and optical spectra.
  Chemphyschem, 11, 1141-1153.  
18478701 A.Ben Fredj, Z.Ben Lakhdar, and M.F.Ruiz-López (2008).
The structure of chlorophyll a-water complexes: insights from quantum chemistry calculations.
  Chem Commun (Camb), (), 718-720.  
17492491 J.Kern, J.Biesiadka, B.Loll, W.Saenger, and A.Zouni (2007).
Structure of the Mn4-Ca cluster as derived from X-ray diffraction.
  Photosynth Res, 92, 389-405.  
16504567 T.M.Iverson (2006).
Evolution and unique bioenergetic mechanisms in oxygenic photosynthesis.
  Curr Opin Chem Biol, 10, 91.  
16307107 A.Telfer (2005).
Too much light? How beta-carotene protects the photosystem II reaction centre.
  Photochem Photobiol Sci, 4, 950-956.  
16121287 E.Krausz, J.L.Hughes, P.Smith, R.Pace, and S.Peterson Arsköld (2005).
Oxygen-evolving Photosystem II core complexes: a new paradigm based on the spectral identification of the charge-separating state, the primary acceptor and assignment of low-temperature fluorescence.
  Photochem Photobiol Sci, 4, 744-753.  
16049789 F.Vacha, J.Psencik, M.Kuty, M.Durchan, and P.Siffel (2005).
Evidence for localisation of accumulated chlorophyll cation on the D1-accessory chlorophyll in the reaction centre of photosystem II.
  Photosynth Res, 84, 297-302.  
16170631 M.K.Raval, B.Biswal, and U.C.Biswal (2005).
The mystery of oxygen evolution: analysis of structure and function of photosystem II, the water-plastoquinone oxido-reductase.
  Photosynth Res, 85, 267-293.  
14990494 M.Germano, C.C.Gradinaru, A.Y.Shkuropatov, I.H.van Stokkum, V.A.Shuvalov, J.P.Dekker, R.van Grondelle, and H.J.van Gorkom (2004).
Energy and electron transfer in photosystem II reaction centers with modified pheophytin composition.
  Biophys J, 86, 1664-1672.  
12221988 B.A.Diner, and F.Rappaport (2002).
Structure, dynamics, and energetics of the primary photochemistry of photosystem II of oxygenic photosynthesis.
  Annu Rev Plant Biol, 53, 551-580.  
11939798 C.Jeans, M.J.Schilstra, and D.R.Klug (2002).
The temperature dependence of P680(+) reduction in oxygen-evolving photosystem II.
  Biochemistry, 41, 5015-5023.  
12081503 F.Rappaport, M.Guergova-Kuras, P.J.Nixon, B.A.Diner, and J.Lavergne (2002).
Kinetics and pathways of charge recombination in photosystem II.
  Biochemistry, 41, 8518-8527.  
11980487 G.Bernát, F.Morvaridi, Y.Feyziyev, and S.Styring (2002).
pH dependence of the four individual transitions in the catalytic S-cycle during photosynthetic oxygen evolution.
  Biochemistry, 41, 5830-5843.  
11904453 J.Wang, D.Gosztola, S.V.Ruffle, C.Hemann, M.Seibert, M.R.Wasielewski, R.Hille, T.L.Gustafson, and R.T.Sayre (2002).
Functional asymmetry of photosystem II D1 and D2 peripheral chlorophyll mutants of Chlamydomonas reinhardtii.
  Proc Natl Acad Sci U S A, 99, 4091-4096.  
11478894 B.A.Diner, E.Schlodder, P.J.Nixon, W.J.Coleman, F.Rappaport, J.Lavergne, W.F.Vermaas, and D.A.Chisholm (2001).
Site-directed mutations at D1-His198 and D2-His197 of photosystem II in Synechocystis PCC 6803: sites of primary charge separation and cation and triplet stabilization.
  Biochemistry, 40, 9265-9281.  
11115631 B.A.Diner (2001).
Amino acid residues involved in the coordination and assembly of the manganese cluster of photosystem II. Proton-coupled electron transport of the redox-active tyrosines and its relationship to water oxidation.
  Biochim Biophys Acta, 1503, 147-163.  
11141071 C.A.Tracewell, A.Cua, D.H.Stewart, D.F.Bocian, and G.W.Brudvig (2001).
Characterization of carotenoid and chlorophyll photooxidation in photosystem II.
  Biochemistry, 40, 193-203.  
11115629 D.Kuzek, and R.J.Pace (2001).
Probing the Mn oxidation states in the OEC. Insights from spectroscopic, computational and kinetic data.
  Biochim Biophys Acta, 1503, 123-137.  
11115630 J.H.Nugent, A.M.Rich, and M.C.Evans (2001).
Photosynthetic water oxidation: towards a mechanism.
  Biochim Biophys Acta, 1503, 138-146.  
11340062 K.H.Rhee (2001).
Photosystem II: the solid structural era.
  Annu Rev Biophys Biomol Struct, 30, 307-328.  
11762431 P.Faller, R.J.Debus, K.Brettel, M.Sugiura, A.W.Rutherford, and A.Boussac (2001).
Rapid formation of the stable tyrosyl radical in photosystem II.
  Proc Natl Acad Sci U S A, 98, 14368-14373.  
11606198 R.Wiklund, G.F.Salih, P.Mäenpää, and C.Jansson (2001).
Engineering of the protein environment around the redox-active TyrZ in photosystem II. The role of F186 and P162 in the D1 protein of Synechocystis 6803.
  Eur J Biochem, 268, 5356-5364.  
11114911 S.Ermakova-Gerdes, Z.Yu, and W.Vermaas (2001).
Targeted random mutagenesis to identify functionally important residues in the D2 protein of photosystem II in Synechocystis sp. strain PCC 6803.
  J Bacteriol, 183, 145-154.  
10762245 A.T.Keilty, S.Y.Ermakova-Gerdes, and W.F.Vermaas (2000).
Probing the CD lumenal loop region of the D2 protein of photosystem II in Synechocystis sp. strain PCC 6803 by combinatorial mutagenesis.
  J Bacteriol, 182, 2453-2460.  
11087414 D.H.Stewart, P.J.Nixon, B.A.Diner, and G.W.Brudvig (2000).
Assignment of the Qy absorbance bands of photosystem II chromophores by low-temperature optical spectroscopy of wild-type and mutant reaction centers.
  Biochemistry, 39, 14583-14594.  
11101299 D.V.Vavilin, and W.F.Vermaas (2000).
Mutations in the CD-loop region of the D2 protein in Synechocystis sp. PCC 6803 modify charge recombination pathways in photosystem II in vivo.
  Biochemistry, 39, 14831-14838.  
10944191 J.Matysik, Alia, P.Gast, H.J.van Gorkom, A.J.Hoff, and H.J.de Groot (2000).
Photochemically induced nuclear spin polarization in reaction centers of photosystem II observed by 13C-solid-state NMR reveals a strongly asymmetric electronic structure of the P680(.+) primary donor chlorophyll.
  Proc Natl Acad Sci U S A, 97, 9865-9870.  
10841755 P.Geijer, Z.Deák, and S.Styring (2000).
Proton equilibria in the manganese cluster of photosystem II control the intensities of the S(0) and S(2) state g approximately 2 electron paramagnetic resonance signals.
  Biochemistry, 39, 6763-6772.  
10828940 R.J.Debus, K.A.Campbell, D.P.Pham, A.M.Hays, and R.D.Britt (2000).
Glutamate 189 of the D1 polypeptide modulates the magnetic and redox properties of the manganese cluster and tyrosine Y(Z) in photosystem II.
  Biochemistry, 39, 6275-6287.  
11087370 S.Vasil'ev, and D.Bruce (2000).
Picosecond time-resolved fluorescence studies on excitation energy transfer in a histidine 117 mutant of the D2 protein of photosystem II in Synechocystis 6803.
  Biochemistry, 39, 14211-14218.  
18726468 C.Zhang, H.Fan, L.Li, and T.Kuang (1999).
Theoretical study on primary reaction of photosynthetic bacteria.
  Sci China C Life Sci, 42, 155-161.  
10545195 D.V.Vavilin, S.Y.Ermakova-Gerdes, A.T.Keilty, and W.F.Vermaas (1999).
Tryptophan at position 181 of the D2 protein of photosystem II confers quenching of variable fluorescence of chlorophyll: implications for the mechanism of energy-dependent quenching.
  Biochemistry, 38, 14690-14696.  
10320334 G.Christen, A.Seeliger, and G.Renger (1999).
P680(+)* reduction kinetics and redox transition probability of the water oxidizing complex as a function of pH and H/D isotope exchange in spinach thylakoids.
  Biochemistry, 38, 6082-6092.  
10026289 G.Christen, and G.Renger (1999).
The role of hydrogen bonds for the multiphasic P680(+)* reduction by YZ in photosystem II with intact oxyen evolution capacity. Analysis of kinetic H/D isotope exchange effects.
  Biochemistry, 38, 2068-2077.  
9930986 M.Haumann, A.Mulkidjanian, and W.Junge (1999).
Tyrosine-Z in oxygen-evolving photosystem II: a hydrogen-bonded tyrosinate.
  Biochemistry, 38, 1258-1267.  
10200173 T.Noguchi, J.Kurreck, Y.Inoue, and G.Renger (1999).
Comparative FTIR analysis of the microenvironment of in cyanide-treated, high pH-treated and iron-depleted photosystem II membrane fragments.
  Biochemistry, 38, 4846-4852.  
10482786 Z.Deak, S.Peterson, P.Geijer, K.A.Ahrling, and S.Styring (1999).
Methanol modification of the electron paramagnetic resonance signals from the S(0) and S(2) states of the water-oxidizing complex of photosystem II
  Biochim Biophys Acta, 1412, 240-249.  
9698383 A.M.Hays, I.R.Vassiliev, J.H.Golbeck, and R.J.Debus (1998).
Role of D1-His190 in proton-coupled electron transfer reactions in photosystem II: a chemical complementation study.
  Biochemistry, 37, 11352-11365.  
9922161 B.A.Diner, D.A.Force, D.W.Randall, and R.D.Britt (1998).
Hydrogen bonding, solvent exchange, and coupled proton and electron transfer in the oxidation and reduction of redox-active tyrosine Y(Z) in Mn-depleted core complexes of photosystem II.
  Biochemistry, 37, 17931-17943.  
9692943 C.Berthomieu, R.Hienerwadel, A.Boussac, J.Breton, and B.A.Diner (1998).
Hydrogen bonding of redox-active tyrosine Z of photosystem II probed by FTIR difference spectroscopy.
  Biochemistry, 37, 10547-10554.  
9600929 E.J.Peterman, van Amerongen H, van Grondelle R, and J.P.Dekker (1998).
The nature of the excited state of the reaction center of photosystem II of green plants: A high-resolution fluorescence spectroscopy study.
  Proc Natl Acad Sci U S A, 95, 6128-6133.  
9760263 F.Mamedov, R.T.Sayre, and S.Styring (1998).
Involvement of histidine 190 on the D1 protein in electron/proton transfer reactions on the donor side of photosystem II.
  Biochemistry, 37, 14245-14256.  
9826610 J.Gallant, B.Desbat, D.Vaknin, and C.Salesse (1998).
Polarization-modulated infrared spectroscopy and x-ray reflectivity of photosystem II core complex at the gas-water interface.
  Biophys J, 75, 2888-2899.  
9784589 M.Hippler, K.Redding, and J.D.Rochaix (1998).
Chlamydomonas genetics, a tool for the study of bioenergetic pathways.
  Biochim Biophys Acta, 1367, 1.  
9772171 M.Hundelt, A.M.Hays, R.J.Debus, and W.Junge (1998).
Oxygenic photosystem II: the mutation D1-D61N in Synechocystis sp. PCC 6803 retards S-state transitions without affecting electron transfer from YZ to P680+.
  Biochemistry, 37, 14450-14456.  
9454606 R.Ahlbrink, M.Haumann, D.Cherepanov, O.Bögershausen, A.Mulkidjanian, and W.Junge (1998).
Function of tyrosine Z in water oxidation by photosystem II: electrostatical promotor instead of hydrogen abstractor.
  Biochemistry, 37, 1131-1142.  
9708993 S.Ermakova-Gerdes, and W.Vermaas (1998).
Mobility of the primary electron-accepting plastoquinone QA of photosystem II in a Synechocystis sp. PCC 6803 strain carrying mutations in the D2 protein.
  Biochemistry, 37, 11569-11578.  
9753448 T.Noguchi, T.Tomo, and Y.Inoue (1998).
Fourier transform infrared study of the cation radical of P680 in the photosystem II reaction center: evidence for charge delocalization on the chlorophyll dimer.
  Biochemistry, 37, 13614-13625.  
9648534 V.P.Shinkarev (1998).
The general kinetic model of electron transfer in photosynthetic reaction centers activated by multiple flashes.
  Photochem Photobiol, 67, 683-699.  
9220977 J.De Las Rivas, and J.Barber (1997).
Structure and thermal stability of photosystem II reaction centers studied by infrared spectroscopy.
  Biochemistry, 36, 8897-8903.  
9391172 V.P.McNamara, F.S.Sutterwala, H.B.Pakrasi, and J.Whitmarsh (1997).
Structural model of cytochrome b559 in photosystem II based on a mutant with genetically fused subunits.
  Proc Natl Acad Sci U S A, 94, 14173-14178.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.

 

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