Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9 Å

Tyrosine deprotonation and associated hydrogen bond rearrangements in a photosynthetic reaction center

Photosynthetic reaction centers from Blastochloris viridis possess Tyr-L162 located mid-way between the special pair chlorophyll (P) and the heme (heme3). While mutation of the tyrosine does not affect the kinetics of electron transfer from heme3 to P, recent time-resolved Laue diffraction studies reported displacement of Tyr-L162 in response to the formation of the photo-oxidized P(+•), implying a possible tyrosine deprotonation event. pK(a) values for Tyr-L162 were calculated using the corresponding crystal structures. Movement of deprotonated Tyr-L162 toward Thr-M185 was observed in P(+•) formation. It was associated with rearrangement of the H-bond network that proceeds to P via Thr-M185 and His-L168.

Psb27, a transiently associated protein, binds to the chlorophyll binding protein CP43 in photosystem II assembly intermediates

Photosystem II (PSII), a large multisubunit pigment-protein complex localized in the thylakoid membrane of cyanobacteria and chloroplasts, mediates light-driven evolution of oxygen from water. Recently, a high-resolution X-ray structure of the mature PSII complex has become available. Two PSII polypeptides, D1 and CP43, provide many of the ligands to an inorganic Mn(4)Ca center that is essential for water oxidation. Because of its unusual redox chemistry, PSII often undergoes degradation followed by stepwise assembly. Psb27, a small luminal polypeptide, functions as an important accessory factor in this elaborate assembly pathway. However, the structural location of Psb27 within PSII assembly intermediates has remained elusive. Here we report that Psb27 binds to CP43 in such assembly intermediates. We treated purified genetically tagged PSII assembly intermediate complexes from the cyanobacterium Synechocystis 6803 with chemical cross-linkers to examine intermolecular interactions between Psb27 and various PSII proteins. First, the water-soluble 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) was used to cross-link proteins with complementary charged groups in close association to one another. In the His27△ctpAPSII preparation, a 58-kDa cross-linked species containing Psb27 and CP43 was identified. This species was not formed in the HT3△ctpA△psb27PSII complex in which Psb27 was absent. Second, the homobifunctional thiol-cleavable cross-linker 3,3'-dithiobis(sulfosuccinimidylpropionate) (DTSSP) was used to reversibly cross-link Psb27 to CP43 in His27△ctpAPSII preparations, which allowed the use of liquid chromatography/tandem MS to map the cross-linking sites as Psb27K(63)↔CP43D(321) (trypsin) and CP43K(215)↔Psb27D(58)AGGLK(63)↔CP43D(321) (chymotrypsin), respectively. Our data suggest that Psb27 acts as an important regulatory protein during PSII assembly through specific interactions with the luminal domain of CP43.

Electrochemical and structural properties of a protein system designed to generate tyrosine Pourbaix diagrams

This report describes a model protein specifically tailored to electrochemically study the reduction potential of protein tyrosine radicals as a function of pH. The model system is based on the 67-residue α(3)Y three-helix bundle. α(3)Y contains a single buried tyrosine at position 32 and displays structural properties inherent to a protein. The present report presents differential pulse voltammograms obtained from α(3)Y at both acidic (pH 5.6) and alkaline (pH 8.3) conditions. The observed Faradaic response is uniquely associated with Y32, as shown by site-directed mutagenesis. This is the first time voltammetry is successfully applied to detect a redox-active tyrosine residing in a structured protein environment. Tyrosine is a proton-coupled electron-transfer cofactor making voltammetry-based pH titrations a central experimental approach. A second set of experiments was performed to demonstrate that pH-dependent studies can be conducted on the redox-active tyrosine without introducing large-scale structural changes in the protein scaffold. α(3)Y was re-engineered with the specific aim to place the imidazole group of a histidine close to the Y32 phenol ring. α(3)Y-K29H and α(3)Y-K36H each contain a histidine residue whose protonation perturbs the fluorescence of Y32. We show that these variants are stable and well-folded proteins whose helical content, tertiary structure, solution aggregation state, and solvent-sequestered position of Y32 remain pH insensitive across a range of at least 3-4 pH units. These results confirm that the local environment of Y32 can be altered and the resulting radical site studied by voltammetry over a broad pH range without interference from long-range structural effects.

Evolution of a divinyl chlorophyll-based photosystem in Prochlorococcus

Acquisition of new photosynthetic pigments has been a crucial process for the evolution of photosynthesis and photosynthetic organisms. In this process, pigment-binding proteins must evolve to fit new pigments. Prochlorococcus is a unique photosynthetic organism that uses divinyl chlorophyll (DVChl) instead of monovinyl chlorophyll. However, cyanobacterial mutants that accumulate DVChl immediately die even under medium-light conditions, suggesting that chlorophyll (Chl)-binding proteins had to evolve to fit to DVChl concurrently with Prochlorococcus evolution. To elucidate the coevolutionary process of Chl and Chl-binding proteins during the establishment of DVChl-based photosystems, we first compared the amino acid sequences of Chl-binding proteins in Prochlorococcus with those in other photosynthetic organisms. Two amino acid residues of the D1 protein, V205 and G282, are conserved in monovinyl chlorophyll-based photosystems; however, in Prochlorococcus, they are substituted with M205 and C282, respectively. According to the solved photosystem II structure, these amino acids are not involved in Chl binding. To mimic Prochlorococcus, V205 was mutated to M205 in the D1 protein from Synechocystis sp. PCC6803 and Synechocystis dvr mutant was transformed with this construct. Although these transgenic cells could not grow under high-light conditions, they acquired light tolerance and grew under medium-light conditions, whereas untransformed dvr mutants could not survive. Substitution of G282 for C282 contributed additional light tolerance, suggesting that the amino acid substitutions in the D1 protein played an essential role in the development of DVChl-based photosystems. Here, we discuss the coevolution of a photosynthetic pigment and its binding protein.

Effects of ammonia on the structure of the oxygen-evolving complex in photosystem II as revealed by light-induced FTIR difference spectroscopy

NH(3) is a structural analogue of substrate H(2)O and an inhibitor to the water oxidation reaction in photosystem II. To test whether or not NH(3) is able to replace substrate water molecules on the oxygen-evolving complex in photosystem II, we studied the effects of NH(3) on the high-frequency region (3750-3550 cm(-1)) of the S(2)Q(A)(-)/S(1)Q(A) FTIR difference spectra (pH 7.5 at 250 K), where OH stretch modes of weak hydrogen-bonded active water molecules occur. Our results showed that NH(3) did not replace the active water molecule on the oxygen-evolving complex that gave rise to the S(1) mode at ~3586 cm(-1) and the S(2) mode at ~3613 cm(-1) in the S(2)Q(A)(-)/S(1)Q(A) FTIR difference spectrum of PSII. In addition, our mid-frequency FTIR results showed a clear difference between pH 6.5 and 7.5 on the concentration dependence of the NH(4)Cl-induced upshift of the S(2) state carboxylate mode at 1365 cm(-1) in the S(2)Q(A)(-)/S(1)Q(A) spectra of NH(4)Cl-treated PSII samples. Our results provided strong evidence that NH(3) induced this upshift in the spectra of NH(4)Cl-treated PSII samples at 250 K. Moreover, our low-frequency FTIR results showed that the Mn-O-Mn cluster vibrational mode at 606 cm(-1) in the S(2)Q(A)(-)/S(1)Q(A) spectrum of the NaCl control PSII sample was diminished in those samples treated with NH(4)Cl. Our results suggest that NH(3) induced a significant alteration on the core structure of the Mn(4)CaO(5) cluster in PSII. The implication of our findings on the structure of the NH(3)-binding site on the OEC in PSII will be discussed.

Manganese-based Materials Inspired by Photosynthesis for Water-Splitting

In nature, the water-splitting reaction via photosynthesis driven by sunlight in plants, algae, and cyanobacteria stores the vast solar energy and provides vital oxygen to life on earth. The recent advances in elucidating the structures and functions of natural photosynthesis has provided firm framework and solid foundation in applying the knowledge to transform the carbon-based energy to renewable solar energy into our energy systems. In this review, inspired by photosynthesis robust photo water-splitting systems using manganese-containing materials including Mn-terpy dimer/titanium oxide, Mn-oxo tetramer/Nafion, and Mn-terpy oligomer/tungsten oxide, in solar fuel production are summarized and evaluated. Potential problems and future endeavors are also discussed.

Conservation of lipid functions in cytochrome bc complexes

Lipid binding sites and properties are compared in two sub-families of hetero-oligomeric membrane protein complexes known to have similar functions in order to gain further understanding of the role of lipid in the function, dynamics, and assembly of these complexes. Using the crystal structure information for both complexes, we compared the lipid binding properties of the cytochrome b(6)f and bc(1) complexes that function in photosynthetic and respiratory membrane energy transduction. Comparison of lipid and detergent binding sites in the b(6)f complex with those in bc(1) shows significant conservation of lipid positions. Seven lipid binding sites in the cyanobacterial b(6)f complex overlap three natural sites in the Chlamydomonas reinhardtii algal complex and four sites in the yeast mitochondrial bc(1) complex. The specific identity of lipids is different in b(6)f and bc(1) complexes: b(6)f contains sulfoquinovosyldiacylglycerol, phosphatidylglycerol, phosphatidylcholine, monogalactosyldiacylglycerol, and digalactosyldiacylglycerol, whereas cardiolipin, phosphatidylethanolamine, and phosphatidic acid are present in the yeast bc(1) complex. The lipidic chlorophyll a and β-carotene (β-car) in cyanobacterial b(6)f, as well as eicosane in C. reinhardtii, are unique to the b(6)f complex. Inferences of lipid binding sites and functions were supported by sequence, interatomic distance, and B-factor information on interacting lipid groups and coordinating amino acid residues. The lipid functions inferred in the b(6)f complex are as follows: (i) substitution of a transmembrane helix by a lipid and chlorin ring, (ii) lipid and β-car connection of peripheral and core domains, (iii) stabilization of the iron-sulfur protein transmembrane helix, (iv) n-side charge and polarity compensation, and (v) β-car-mediated super-complex with the photosystem I complex.

Towards models of the oxygen-evolving complex (OEC) of photosystem II: a Mn4Ca cluster of relevance to low oxidation states of the OEC

Synthetic access has been achieved into high oxidation state Mn/Ca chemistry with the 4 : 1 Mn : Ca stoichiometry of the oxygen-evolving complex (OEC) of plants and cyanobacteria; the anion of (Et(3)NH)(2)[Mn(III)(4)Ca(O(2)CPh)(4)(shi)(4)] has a square pyramidal metal topology and an S = 0 ground state.

Photosystem II, a growing complex: updates on newly discovered components and low molecular mass proteins

Photosystem II is a unique complex capable of absorbing light and splitting water. The complex has been thoroughly studied and to date there are more than 40 proteins identified, which bind to the complex either stably or transiently. Another special feature of this complex is the unusually high content of low molecular mass proteins that represent more than half of the proteins. In this review we summarize the recent findings on the low molecular mass proteins (<15kDa) and present an overview of the newly identified components as well. We have also performed co-expression analysis of the genes encoding PSII proteins to see if the low molecular mass proteins form a specific sub-group within the Photosystem II complex. Interestingly we found that the chloroplast-localized genes encoding PSII proteins display a different response to environmental and stress conditions compared to the nuclear localized genes. This article is part of a Special Issue entitled: Photosystem II.

Cytochrome b₅₅₉ and cyclic electron transfer within photosystem II

Cytochrome b₅₅₉ (Cyt b₅₅₉), β-carotene (Car), and chlorophyll (Chl) cofactors participate in the secondary electron-transfer pathways in photosystem II (PSII), which are believed to protect PSII from photodamage under conditions in which the primary electron-donation pathway leading to water oxidation is inhibited. Among these cofactors, Cyt b₅₅₉ is preferentially photooxidized under conditions in which the primary electron-donation pathway is blocked. When Cyt b₅₅₉ is preoxidized, the photooxidation of several of the 11 Car and 35 Chl molecules present per PSII is observed. In this review, the discovery of the secondary electron donors, their structures and electron-transfer properties, and progress in the characterization of the secondary electron-transfer pathways are discussed. This article is part of a Special Issue entitled: Photosystem II.

Ligation of D1-His332 and D1-Asp170 to the manganese cluster of photosystem II from Synechocystis assessed by multifrequency pulse EPR spectroscopy

Multifrequency electron spin-echo envelope modulation (ESEEM) spectroscopy is used to ascertain the nature of the bonding interactions of various active site amino acids with the Mn ions that compose the oxygen-evolving cluster (OEC) in photosystem II (PSII) from the cyanobacterium Synechocystis sp. PCC 6803 poised in the S(2) state. Spectra of natural isotopic abundance PSII ((14)N-PSII), uniformly (15)N-labeled PSII ((15)N-PSII), and (15)N-PSII containing (14)N-histidine ((14)N-His/(15)N-PSII) are compared. These complementary data sets allow for a precise determination of the spin Hamiltonian parameters of the postulated histidine nitrogen interaction with the Mn ions of the OEC. These results are compared to those from a similar study on PSII isolated from spinach. Upon mutation of His332 of the D1 polypeptide to a glutamate residue, all isotopically sensitive spectral features vanish. Additional K(a)- and Q-band ESEEM experiments on the D1-D170H site-directed mutant give no indication of new (14)N-based interactions.

Charge separation in photosystem II: a comparative and evolutionary overview

Our current understanding of the PSII reaction centre owes a great deal to comparisons to the simpler and better understood, purple bacterial reaction centre. Here we provide an overview of the similarities with a focus on charge separation and the electron acceptors. We go on to discuss some of the main differences between the two kinds of reaction centres that have been highlighted by the improving knowledge of PSII. We attempt to relate these differences to functional requirements of water splitting. Some are directly associated with that function, e.g. high oxidation potentials, while others are associated with regulation and protection against photodamage. The protective and regulatory functions are associated with the harsh chemistry performed during its normal function but also with requirements of the enzyme while it is undergoing assembly and repair. Key aspects of PSII reaction centre evolution are also addressed. This article is part of a Special Issue entitled: Photosystem II.

Structural and spectroscopic characterization of metastable thiolate-ligated manganese(III)-alkylperoxo species

Metastable Mn-peroxo species are proposed to form as key intermediates in biological oxidation reactions involving O(2) and C-H bond activation. The majority of these have yet to be spectroscopically characterized, and their inherent instability, in most cases, precludes structural characterization. Cysteinate-ligated metal-peroxos have been shown to form as reactive intermediates in both heme and nonheme iron enzymes. Herein we report the only examples of isolable Mn(III)-alkylperoxo species, and the first two examples of structurally characterized synthetic thiolate-ligated metal-peroxos. Spectroscopic data, including electronic absorption and IR spectra, and ESI mass spectra for (16)O vs (18)O-labeled metastable Mn(III)-OOR (R = (t)Bu, Cm) are discussed, as well as preliminary reactivity.

Proton coupled electron transfer and redox-active tyrosine Z in the photosynthetic oxygen-evolving complex

Proton coupled electron transfer (PCET) reactions play an essential role in many enzymatic processes. In PCET, redox-active tyrosines may be involved as intermediates when the oxidized phenolic side chain deprotonates. Photosystem II (PSII) is an excellent framework for studying PCET reactions, because it contains two redox-active tyrosines, YD and YZ, with different roles in catalysis. One of the redox-active tyrosines, YZ, is essential for oxygen evolution and is rapidly reduced by the manganese-catalytic site. In this report, we investigate the mechanism of YZ PCET in oxygen-evolving PSII. To isolate YZ(•) reactions, but retain the manganese-calcium cluster, low temperatures were used to block the oxidation of the metal cluster, high microwave powers were used to saturate the YD(•) EPR signal, and YZ(•) decay kinetics were measured with EPR spectroscopy. Analysis of the pH and solvent isotope dependence was performed. The rate of YZ(•) decay exhibited a significant solvent isotope effect, and the rate of recombination and the solvent isotope effect were pH independent from pH 5.0 to 7.5. These results are consistent with a rate-limiting, coupled proton electron transfer (CPET) reaction and are contrasted to results obtained for YD(•) decay kinetics at low pH. This effect may be mediated by an extensive hydrogen-bond network around YZ. These experiments imply that PCET reactions distinguish the two PSII redox-active tyrosines.

The extrinsic proteins of Photosystem II

In this review we examine the structure and function of the extrinsic proteins of Photosystem II. These proteins include PsbO, present in all oxygenic organisms, the PsbP and PsbQ proteins, which are found in higher plants and eukaryotic algae, and the PsbU, PsbV, CyanoQ, and CyanoP proteins, which are found in the cyanobacteria. These proteins serve to optimize oxygen evolution at physiological calcium and chloride concentrations. They also shield the Mn(4)CaO(5) cluster from exogenous reductants. Numerous biochemical, genetic and structural studies have been used to probe the structure and function of these proteins within the photosystem. We will discuss the most recent proposed functional roles for these components, their structures (as deduced from biochemical and X-ray crystallographic studies) and the locations of their proposed binding domains within the Photosystem II complex. This article is part of a Special Issue entitled: Photosystem II.

Structural models of the manganese complex of photosystem II and mechanistic implications

Photosynthetic water oxidation and O₂ formation are catalyzed by a Mn₄Ca complex bound to the proteins of photosystem II (PSII). The catalytic site, including the inorganic Mn₄CaO(n)H(x) core and its protein environment, is denoted as oxygen-evolving complex (OEC). Earlier and recent progress in the endeavor to elucidate the structure of the OEC is reviewed, with focus on recent results obtained by (i) X−ray spectroscopy (specifically by EXAFS analyses), and (ii) X-ray diffraction (XRD, protein crystallography). Very recently, an impressive resolution of 1.9Å has been achieved by XRD. Most likely however, all XRD data on the Mn₄CaO(n)H(x) core of the OEC are affected by X-ray induced modifications (radiation damage). Therefore and to address (important) details of the geometric and electronic structure of the OEC, a combined analysis of XRD and XAS data has been approached by several research groups. These efforts are reviewed and extended using an especially comprehensive approach. Taking into account XRD results on the protein environment of the inorganic core of the Mn complex, 12 alternative OEC models are considered and evaluated by quantitative comparison to (i) extended-range EXAFS data, (ii) polarized EXAFS of partially oriented PSII membrane particles, and (iii) polarized EXAFS of PSII crystals. We conclude that there is a class of OEC models that is in good agreement with both the recent crystallographic models and the XAS data. On these grounds, mechanistic implications for the O−O bond formation chemistry are discussed. This article is part of a Special Issue entitled: Photosystem II.

S1-state model of the O2-evolving complex of photosystem II

We introduce a quantum mechanics/molecular mechanics model of the oxygen-evolving complex of photosystem II in the S(1) Mn(4)(IV,III,IV,III) state, where Ca(2+) is bridged to manganese centers by the carboxylate moieties of D170 and A344 on the basis of the new X-ray diffraction (XRD) model recently reported at 1.9 Å resolution. The model is also consistent with high-resolution spectroscopic data, including polarized extended X-ray absorption fine structure data of oriented single crystals. Our results provide refined intermetallic distances within the Mn cluster and suggest that the XRD model most likely corresponds to a mixture of oxidation states, including species more reduced than those observed in the catalytic cycle of water splitting.

Structural-functional role of chloride in photosystem II

Chloride binding in photosystem II (PSII) is essential for photosynthetic water oxidation. However, the functional roles of chloride and possible binding sites, during oxygen evolution, remain controversial. This paper examines the functions of chloride based on its binding site revealed in the X-ray crystal structure of PSII at 1.9 Å resolution. We find that chloride depletion induces formation of a salt bridge between D2-K317 and D1-D61 that could suppress the transfer of protons to the lumen.

N-formylkynurenine as a marker of high light stress in photosynthesis

Photosystem II (PSII) is the membrane protein complex that catalyzes the photo-induced oxidation of water at a manganese-calcium active site. Light-dependent damage and repair occur in PSII under conditions of high light stress. The core reaction center complex is composed of the D1, D2, CP43, and CP47 intrinsic polypeptides. In this study, a new chromophore formed from the oxidative post-translational modification of tryptophan is identified in the CP43 subunit. Tandem mass spectrometry peptide sequencing is consistent with the oxidation of the CP43 tryptophan side chain, Trp-365, to produce N-formylkynurenine (NFK). Characterization with ultraviolet visible absorption and ultraviolet resonance Raman spectroscopy supports this assignment. An optical assay suggests that the yield of NFK increases 2-fold (2.2 ± 0.5) under high light illumination. A concomitant 2.4 ± 0.5-fold decrease is observed in the steady-state rate of oxygen evolution under the high light conditions. NFK is the product formed from reaction of tryptophan with singlet oxygen, which can be produced under high light stress in PSII. Reactive oxygen species reactions lead to oxidative damage of the reaction center, D1 protein turnover, and inhibition of electron transfer. Our results are consistent with a role for the CP43 NFK modification in photoinhibition.

Light-induced quinone reduction in photosystem II

The photosystem II core complex is the water:plastoquinone oxidoreductase of oxygenic photosynthesis situated in the thylakoid membrane of cyanobacteria, algae and plants. It catalyzes the light-induced transfer of electrons from water to plastoquinone accompanied by the net transport of protons from the cytoplasm (stroma) to the lumen, the production of molecular oxygen and the release of plastoquinol into the membrane phase. In this review, we outline our present knowledge about the "acceptor side" of the photosystem II core complex covering the reaction center with focus on the primary (Q(A)) and secondary (Q(B)) quinones situated around the non-heme iron with bound (bi)carbonate and a comparison with the reaction center of purple bacteria. Related topics addressed are quinone diffusion channels for plastoquinone/plastoquinol exchange, the newly discovered third quinone Q(C), the relevance of lipids, the interactions of quinones with the still enigmatic cytochrome b559 and the role of Q(A) in photoinhibition and photoprotection mechanisms. This article is part of a Special Issue entitled: Photosystem II.

The effects of redox-inactive metal ions on the activation of dioxygen: isolation and characterization of a heterobimetallic complex containing a Mn(III)-(μ-OH)-Ca(II) core

Rate enhancements for the reduction of dioxygen by a Mn(II) complex were observed in the presence of redox-inactive group 2 metal ions. The rate changes were correlated with an increase in the Lewis acidity of the group 2 metal ions. These studies led to the isolation of heterobimetallic complexes containing Mn(III)-(μ-OH)-M(II) cores (M(II) = Ca(II), Ba(II)) in which the hydroxo oxygen atom is derived from O(2). This type of core structure has relevance to the oxygen-evolving complex within photosystem II.

Molecular mechanisms of photodamage in the Photosystem II complex

Light induced damage of the photosynthetic apparatus is an important and highly complex phenomenon, which affects primarily the Photosystem II complex. Here the author summarizes the current state of understanding of the molecular mechanisms, which are involved in the light induced inactivation of Photosystem II electron transport together with the relevant mechanisms of photoprotection. Short wavelength ultraviolet radiation impairs primarily the Mn₄Ca catalytic site of the water oxidizing complex with additional effects on the quinone electron acceptors and tyrosine donors of PSII. The main mechanism of photodamage by visible light appears to be mediated by acceptor side modifications, which develop under conditions of excess excitation in which the capacity of light-independent photosynthetic processes limits the utilization of electrons produced in the initial photoreactions. This situation of excess excitation facilitates the reduction of intersystem electron carriers and Photosystem II acceptors, and thereby induces the formation of reactive oxygen species, especially singlet oxygen whose production is sensitized by triplet chlorophyll formation in the reaction center of Photosystem II. The highly reactive singlet oxygen and other reactive oxygen species, such as H₂O₂ and O₂⁻, which can also be formed in Photosystem II initiate damage of electron transport components and protein structure. In parallel with the excess excitation dependent mechanism of photodamage inactivation of the Mn₄Ca cluster by visible light may also occur, which impairs electron transfer through the Photosystem II complex and initiates further functional and structural damage of the reaction center via formation of highly oxidizing radicals, such as P 680(+) and Tyr-Z(+). However, the available data do not support the hypothesis that the Mn-dependent mechanism would be the exclusive or dominating pathway of photodamage in the visible spectral range. This article is part of a Special Issue entitled: Photosystem II.