1
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Watanabe S, Noguchi T. Intermediate Formation via Proton Release during the Photoassembly of the Water-Oxidizing Mn 4CaO 5 Cluster in Photosystem II. J Phys Chem B 2024; 128:8145-8161. [PMID: 39148348 DOI: 10.1021/acs.jpcb.4c03768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
The early stages of the photoassembly of the water-oxidizing Mn4CaO5 cluster in spinach photosystem II (PSII) were monitored using rapid-scan time-resolved Fourier transform infrared (FTIR) spectroscopy. Carboxylate stretching and the amide I bands, which appeared upon the flash-induced oxidation of a Mn2+ ion, changed their features during the subsequent dark rearrangement process, indicating the relocation of the Mn3+ ion concomitant with protein conformational changes. Monitoring the isotope-edited FTIR signals of a Mes buffer estimated that nearly two protons are released upon the Mn2+ oxidation. Quantum chemical calculations for models of the Mn binding site suggested that the proton of a water ligand is transferred to D1-H332 through a hydrogen bond upon the Mn3+ formation and then released to the bulk as the Mn3+ shifts to bind to this histidine. Another Mn2+ ion may be inserted to form a binuclear Mn3+Mn2+ complex, whose structure was calculated to be stabilized by a μ-hydroxo bridge hydrogen-bonded with deprotonated D1-H337. Nearly one additional proton can thus be released from this histidine, assuming that it is mostly protonated before illumination. Alternatively, a proton could be released by further insertion of Ca2+, forming a Mn3+Mn2+Ca2+ complex with another hydroxo ligand connecting Ca2+ to the Mn3+Mn2+ complex.
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Affiliation(s)
- Shunya Watanabe
- Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Takumi Noguchi
- Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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2
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Flesher DA, Liu J, Wang J, Gisriel CJ, Yang KR, Batista VS, Debus RJ, Brudvig GW. Mutation-induced shift of the photosystem II active site reveals insight into conserved water channels. J Biol Chem 2024; 300:107475. [PMID: 38879008 PMCID: PMC11294709 DOI: 10.1016/j.jbc.2024.107475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 06/02/2024] [Accepted: 06/09/2024] [Indexed: 07/11/2024] Open
Abstract
Photosystem II (PSII) is the water-plastoquinone photo-oxidoreductase central to oxygenic photosynthesis. PSII has been extensively studied for its ability to catalyze light-driven water oxidation at a Mn4CaO5 cluster called the oxygen-evolving complex (OEC). Despite these efforts, the complete reaction mechanism for water oxidation by PSII is still heavily debated. Previous mutagenesis studies have investigated the roles of conserved amino acids, but these studies have lacked a direct structural basis that would allow for a more meaningful interpretation. Here, we report a 2.14-Å resolution cryo-EM structure of a PSII complex containing the substitution Asp170Glu on the D1 subunit. This mutation directly perturbs a bridging carboxylate ligand of the OEC, which alters the spectroscopic properties of the OEC without fully abolishing water oxidation. The structure reveals that the mutation shifts the position of the OEC within the active site without markedly distorting the Mn4CaO5 cluster metal-metal geometry, instead shifting the OEC as a rigid body. This shift disturbs the hydrogen-bonding network of structured waters near the OEC, causing disorder in the conserved water channels. This mutation-induced disorder appears consistent with previous FTIR spectroscopic data. We further show using quantum mechanics/molecular mechanics methods that the mutation-induced structural changes can affect the magnetic properties of the OEC by altering the axes of the Jahn-Teller distortion of the Mn(III) ion coordinated to D1-170. These results offer new perspectives on the conserved water channels, the rigid body property of the OEC, and the role of D1-Asp170 in the enzymatic water oxidation mechanism.
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Affiliation(s)
- David A Flesher
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Jinchan Liu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | | | - Ke R Yang
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
| | - Richard J Debus
- Department of Biochemistry, University of California, Riverside, California, USA.
| | - Gary W Brudvig
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA; Department of Chemistry, Yale University, New Haven, Connecticut, USA.
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3
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Noguchi T. Mechanism of Proton Transfer through the D1-E65/D2-E312 Gate during Photosynthetic Water Oxidation. J Phys Chem B 2024; 128:1866-1875. [PMID: 38364371 DOI: 10.1021/acs.jpcb.3c07787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2024]
Abstract
In photosystem II, the D1-E65/D2-E312 dyad in the Cl-1 channel has been proposed to play a pivotal role in proton transfer during water oxidation. However, the precise mechanism remains elusive. Here, the proton transfer mechanism within the Cl-1 channel was investigated using quantum mechanics/molecular mechanics calculations. The molecular vibration of the E65/E312 dyad and its deuteration effect revealed that the recently suggested stepwise proton transfer, i.e., initial proton release from the dyad followed by slow reprotonation, does not occur in the Cl-1 channel. Instead, proton transfer is proposed to take place via a conformational change at the E65/E312 dyad, acting as a gate. In its closed form, a proton is trapped within the dyad, preventing forward proton transfer. This closed form converts into the open form, where protonated D1-E65 provides a hydrogen bond to the water network, thereby facilitating fast Grotthuss-type proton transfer.
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Affiliation(s)
- Takumi Noguchi
- Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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Saito K, Nishio S, Ishikita H. Interplay of two low-barrier hydrogen bonds in long-distance proton-coupled electron transfer for water oxidation. PNAS NEXUS 2023; 2:pgad423. [PMID: 38130665 PMCID: PMC10733176 DOI: 10.1093/pnasnexus/pgad423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/20/2023] [Indexed: 12/23/2023]
Abstract
D1-Tyr161 (TyrZ) forms a low-barrier H-bond with D1-His190 and functions as a redox-active group in photosystem II. When oxidized to the radical form (TyrZ-O•), it accepts an electron from the oxygen-evolving Mn4CaO5 cluster, facilitating an increase in the oxidation state (Sn; n = 0-3). In this study, we investigated the mechanism of how TyrZ-O• drives proton-coupled electron transfer during the S2 to S3 transition using a quantum mechanical/molecular mechanical approach. In response to TyrZ-O• formation and subsequent loss of the low-barrier H-bond, the ligand water molecule at the Ca2+ site (W4) reorients away from TyrZ and donates an H-bond to D1-Glu189 at Mn4 of Mn4CaO5 together with an adjacent water molecule. The H-bond donation to the Mn4CaO5 cluster triggers the release of the proton from the lowest pKa site (W1 at Mn4) along the W1…D1-Asp61 low-barrier H-bond, leading to protonation of D1-Asp61. The interplay of the two low-barrier H-bonds, involving the Ca2+ interface and forming the extended Grotthuss-like network [TyrZ…D1-His190]-[Mn4CaO5]-[W1…D1-Asp61], rather than the direct electrostatic interaction, is likely a basis of the apparent long-distance interaction (11.4 Å) between TyrZ-O• formation and D1-Asp61 protonation.
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Affiliation(s)
- Keisuke Saito
- Department of Applied Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo 113-8654, Japan
- Research Center for Advanced Science and Technology, The University of Tokyo, Meguro-ku, Tokyo 153-8904, Japan
| | - Shunya Nishio
- Department of Applied Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Hiroshi Ishikita
- Department of Applied Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo 113-8654, Japan
- Research Center for Advanced Science and Technology, The University of Tokyo, Meguro-ku, Tokyo 153-8904, Japan
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5
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Matsubara T, Shimada Y, Kitajima-Ihara T, Nagao R, Noguchi T. Rapid-Scan Fourier Transform Infrared Monitoring of the Photoactivation Process in Cyanobacterial Photosystem II. J Phys Chem B 2023; 127:8150-8161. [PMID: 37718495 DOI: 10.1021/acs.jpcb.3c04325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
The catalytic site of photosynthetic water oxidation, the Mn4CaO5 cluster, in photosystem II (PSII) is known to be formed by a light-induced process called photoactivation. However, details of its molecular mechanism remain unresolved. In this study, we monitored the photoactivation process in cyanobacterial PSII using rapid-scan, time-resolved Fourier transform infrared (FTIR) spectroscopy. The Mn3+/Mn2+ FTIR difference spectra of PSII, in which D1-D170 was specifically 13C labeled, and PSII from the D1-D170A, D1-E189A, and D1-D342A mutants provide strong evidence that the initial Mn2+ is coordinated by D1-D170 and D1-E189. Protein conformational changes and relocation of photo-oxidized Mn3+ in the dark rearrangement process were detected as slow-phase signals in the amide I and carboxylate regions, whereas similar signals were not observed in D1-E189A PSII. It is thus proposed that relocation of Mn3+ via D1-E189 induces the conformational changes of the proteins to form proper Mn binding sites in the mature protein conformation.
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Affiliation(s)
- Takumi Matsubara
- Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Yuichiro Shimada
- Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Tomomi Kitajima-Ihara
- Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Ryo Nagao
- Faculty of Agriculture, Shizuoka University, Shizuoka 422-8529, Japan
| | - Takumi Noguchi
- Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
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Chakarawet K, Debus RJ, Britt RD. Mutation of a metal ligand stabilizes the high-spin form of the S 2 state in the O 2-producing Mn 4CaO 5 cluster of photosystem II. PHOTOSYNTHESIS RESEARCH 2023; 156:309-314. [PMID: 36653579 DOI: 10.1007/s11120-023-00998-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 01/09/2023] [Indexed: 05/23/2023]
Abstract
The residue D1-D170 bridges Mn4 with the Ca ion in the O2-evolving Mn4CaO5 cluster of Photosystem II. Recently, the D1-D170E mutation was shown to substantially alter the Sn+1-minus-Sn FTIR difference spectra [Debus RJ (2021) Biochemistry 60:3841-3855]. The mutation was proposed to alter the equilibrium between different Jahn-Teller conformers of the S1 state such that (i) a different S1 state conformer is stabilized in D1-D170E than in wild-type and (ii) the S1 to S2 transition in D1-D170E produces a high-spin form of the S2 state rather than the low-spin form that is produced in wild-type. In this study, we employed EPR spectroscopy to test if a high-spin form of the S2 state is formed preferentially in D1-D170E PSII. Our data show that illumination of dark-adapted D1-D170E PSII core complexes does indeed produce a high-spin form of the S2 state rather than the low-spin multiline form that is produced in wild-type. This observation provides further experimental support for a change in the equilibrium between S state conformers in both the S1 and S2 states in a site-directed mutant that retains substantial O2 evolving activity.
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Affiliation(s)
- Khetpakorn Chakarawet
- Department of Chemistry, University of California, Davis, CA, 95616, USA
- Department of Chemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Richard J Debus
- Department of Biochemistry, University of California, Riverside, CA, 92521, USA.
| | - R David Britt
- Department of Chemistry, University of California, Davis, CA, 95616, USA.
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Tamura H, Saito K, Nishio S, Ishikita H. Electron-Transfer Route in the Early Oxidation States of the Mn 4CaO 5 Cluster in Photosystem II. J Phys Chem B 2023; 127:205-211. [PMID: 36542840 PMCID: PMC9841979 DOI: 10.1021/acs.jpcb.2c08246] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/07/2022] [Indexed: 12/24/2022]
Abstract
The electron transfer from the oxygen-evolving Mn4CaO5 cluster to the electron acceptor D1-Tyr161 (TyrZ) is a prerequisite for water oxidation and O2 evolution. Here, we analyzed the electronic coupling in the rate-limiting electron-transfer transitions using a combined quantum mechanical/molecular mechanical/polarizable continuum model approach. In the S0 to S1 transition, the electronic coupling between the electron-donor Mn3(III) and TyrZ is small (2 meV). In contrast, the electronic coupling between the dangling Mn4(III) and TyrZ is significantly large (172 meV), which suggests that the electron transfer proceeds from Mn3(III) to TyrZ via Mn4(III). In the S1 to S2 transition, the electronic coupling between Mn4(III) and TyrZ is also larger (124 meV) than that between Mn1(III) and TyrZ (1 meV), which favors the formation of the open-cubane S2 conformation with Mn4(IV) over the formation of the closed-cubane S2 conformation with Mn1(IV). In the S0 to S1 and S1 to S2 transitions, the Mn4 d-orbital and the TyrZ π-orbital are hybridized via D1-Asp170, which suggests that D1-Asp170 commonly provides a dominant electron-transfer route.
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Affiliation(s)
- Hiroyuki Tamura
- Department
of Applied Chemistry, The University of
Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo113-8654, Japan
- Research
Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo153-8904, Japan
| | - Keisuke Saito
- Department
of Applied Chemistry, The University of
Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo113-8654, Japan
- Research
Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo153-8904, Japan
| | - Shunya Nishio
- Department
of Applied Chemistry, The University of
Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo113-8654, Japan
| | - Hiroshi Ishikita
- Department
of Applied Chemistry, The University of
Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo113-8654, Japan
- Research
Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo153-8904, Japan
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8
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Cyanophages as an important factor in the early evolution of oxygenic photosynthesis. Sci Rep 2022; 12:20581. [PMID: 36446879 PMCID: PMC9709159 DOI: 10.1038/s41598-022-24795-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 11/21/2022] [Indexed: 12/02/2022] Open
Abstract
Cyanophages are viruses that infect cyanobacteria. An interesting feature of many of them is the presence of psbA and psbD, genes that encode D1 and D2 proteins, respectively. The D1 and D2 are core proteins of the photosystem II (PSII) in cyanobacteria, algae and plants and influence the proper function of oxygenic photosynthesis (OP) in all oxyphototrophs on Earth. The frequent occurrence of psbA and psbD in cyanophages raises the question whether these genes coevolved with hosts during the early stages of cyanophage and cyanobacterial evolution, or whether they are direct descendants of genes adopted from the genomes of cyanobacterial hosts. The phylogeny of D1/D2 proteins encoded in the genomes of selected cyanophages and oxyphototrophs was reconstructed. In addition, common ancestral sequences of D1 and D2 proteins were predicted for cyanophages and oxyphototrophs. Based on this, the reconstruction of the 3D structures of D1 and D2 proteins was performed. In addition, the ratio of non-synonymous to synonymous (dN/dS) nucleotide substitutions in the coding sequences (CDSs) of psbA and psbD was determined. The results of the predicted spatial structures of the D1 and D2 proteins and purifying selection for the CDSs of psbA and psbD suggest that they belong to the ancient proteins, which may have formed the primordial PSII. It cannot be ruled out that they involved in water oxidation in cyanobacteria-like organisms at early stages of the evolution of life on Earth and coevolved with ancient cyanophages. The data are also discussed in the context of the origin of viruses.
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Shimada Y, Sugiyama A, Nagao R, Noguchi T. Role of D1-Glu65 in Proton Transfer during Photosynthetic Water Oxidation in Photosystem II. J Phys Chem B 2022; 126:8202-8213. [PMID: 36199221 DOI: 10.1021/acs.jpcb.2c05869] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Photosynthetic water oxidation takes place at the Mn4CaO5 cluster in photosystem II (PSII) through a light-driven cycle of five intermediates called S states (S0-S4). Although the PSII structures have shown the presence of several channels around the Mn4CaO5 cluster leading to the lumen, the pathways for proton release in the individual S-state transitions remain unidentified. Here, we studied the involvement of the so-called Cl channel in proton transfer during water oxidation by examining the effect of the mutation of D1-Glu65, a key residue in this channel, to Ala using Fourier transform infrared difference and time-resolved infrared spectroscopies together with thermoluminescence and delayed luminescence measurements. It was shown that the structure and the redox property of the catalytic site were little affected by the D1-Glu65Ala mutation. In the S2 → S3 transition, the efficiency was still high and the transition rate was only moderately retarded in the D1-Glu65Ala mutant. In contrast, the S3 → S0 transition was significantly inhibited by this mutation. These results suggest that proton transfer in the S2 → S3 transition occurs through multiple pathways including the Cl channel, whereas this channel likely serves as a single pathway for proton exit in the S3 → S0 transition.
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Affiliation(s)
- Yuichiro Shimada
- Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya464-8602, Japan
| | - Ayane Sugiyama
- Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya464-8602, Japan
| | - Ryo Nagao
- Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya464-8602, Japan.,Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-naka, Okayama700-8530, Japan
| | - Takumi Noguchi
- Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya464-8602, Japan
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