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Britt RD, Rauchfuss TB, Rao G. The H-cluster of [FeFe] Hydrogenases: Its Enzymatic Synthesis and Parallel Inorganic Semisynthesis. Acc Chem Res 2024; 57:1941-1950. [PMID: 38937148 PMCID: PMC11256358 DOI: 10.1021/acs.accounts.4c00231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/12/2024] [Accepted: 06/14/2024] [Indexed: 06/29/2024]
Abstract
ConspectusNature's prototypical hydrogen-forming catalysts─hydrogenases─have attracted much attention because they catalyze hydrogen evolution at near zero overpotential and ambient conditions. Beyond any possible applications in the energy sphere, the hydrogenases feature complicated active sites, which implies novel biosynthetic pathways. In terms of the variety of cofactors, the [FeFe]-hydrogenase is among the most complex.For more than a decade, we have worked on the biosynthesis of the active site of [FeFe] hydrogenases. This site, the H-cluster, is a six-iron ensemble consisting of a [4Fe-4S]H cluster linked to a [2Fe]H cluster that is coordinated to CO, cyanide, and a unique organic azadithiolate ligand. Many years ago, three enzymes, namely, HydG, HydE, and HydF, were shown to be required for the biosynthesis and the in vitro maturation of [FeFe] hydrogenases. The structures of the maturases were determined crystallographically, but still little progress was made on the biosynthetic pathway. As described in this Account, the elucidation of the biosynthetic pathway began in earnest with the identification of a molecular iron-cysteinate complex produced within HydG.In this Account, we present our most recent progress toward the molecular mechanism of [2Fe]H biosynthesis using a collaborative approach involving cell-free biosynthesis, isotope and element-sensitive spectroscopies, as well as inorganic synthesis of purported biosynthetic intermediates. Our study starts from the radical SAM enzyme HydG that lyses tyrosine into CO and cyanide and forms an Fe(CO)2(CN)-containing species. Crystallographic identification of a unique auxiliary 5Fe-4S cluster in HydG leads to a proposed catalytic cycle in which a free cysteine-chelated "dangler" Fe serves as the platform for the stepwise formation of a [4Fe-4S][Fe(CO)(CN)(cysteinate)] intermediate, which releases the [Fe(CO)2(CN)(cysteinate)] product, Complex B. Since Complex B is unstable, we applied synthetic organometallic chemistry to make an analogue, syn-B, and showed that it fully replaces HydG in the in vitro maturation of the H-cluster. Syn-B serves as the substrate for the next radical SAM enzyme HydE, where the low-spin Fe(II) center is activated by 5'-dAdo• to form an adenosylated Fe(I) intermediate. We propose that this Fe(I) species strips the carbon backbone and dimerizes in HydE to form a [Fe2(SH)2(CO)4(CN)2]2- product. This mechanistic scenario is supported by the use of a synthetic version of this dimer complex, syn-dimer, which allows for the formation of active hydrogenase with only the HydF maturase. Further application of this semisynthesis strategy shows that an [Fe2(SCH2NH2)2(CO)4(CN)2]2- complex can activate the apo hydrogenase, marking it as the last biosynthetic intermediate en route to the H-cluster. This combined enzymatic and semisynthetic approach greatly accelerates our understanding of H-cluster biosynthesis. We anticipate additional mechanistic details regarding H-cluster biosynthesis to be gleaned, and this methodology may be further applied in the study of other complex metallocofactors.
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Affiliation(s)
- R. David Britt
- Department
of Chemistry, University of California,
Davis, Davis, California 95616, United
States
| | - Thomas B. Rauchfuss
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, Illinois 61820, United States
| | - Guodong Rao
- Department
of Chemistry, University of California,
Davis, Davis, California 95616, United
States
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Sirohiwal A, Neese F, Pantazis DA. Microsolvation of the Redox-Active Tyrosine-D in Photosystem II: Correlation of Energetics with EPR Spectroscopy and Oxidation-Induced Proton Transfer. J Am Chem Soc 2019; 141:3217-3231. [PMID: 30666866 PMCID: PMC6728127 DOI: 10.1021/jacs.8b13123] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Photosystem II (PSII) of oxygenic photosynthesis captures sunlight to drive the catalytic oxidation of water and the reduction of plastoquinone. Among the several redox-active cofactors that participate in intricate electron transfer pathways there are two tyrosine residues, YZ and YD. They are situated in symmetry-related electron transfer branches but have different environments and play distinct roles. YZ is the immediate oxidant of the oxygen-evolving Mn4CaO5 cluster, whereas YD serves regulatory and protective functions. The protonation states and hydrogen-bond network in the environment of YD remain debated, while the role of microsolvation in stabilizing different redox states of YD and facilitating oxidation or mediating deprotonation, as well the fate of the phenolic proton, is unclear. Here we present detailed structural models of YD and its environment using large-scale quantum mechanical models and all-atom molecular dynamics of a complete PSII monomer. The energetics of water distribution within a hydrophobic cavity adjacent to YD are shown to correlate directly with electron paramagnetic resonance (EPR) parameters such as the tyrosyl g-tensor, allowing us to map the correspondence between specific structural models and available experimental observations. EPR spectra obtained under different conditions are explained with respect to the mode of interaction of the proximal water with the tyrosyl radical and the position of the phenolic proton within the cavity. Our results revise previous models of the energetics and build a detailed view of the role of confined water in the oxidation and deprotonation of YD. Finally, the model of microsolvation developed in the present work rationalizes in a straightforward way the biphasic oxidation kinetics of YD, offering new structural insights regarding the function of the radical in biological photosynthesis.
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Affiliation(s)
- Abhishek Sirohiwal
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , 45470 Mülheim an der Ruhr , Germany
- Fakultät für Chemie und Biochemie , Ruhr-Universität Bochum , 44780 Bochum , Germany
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , 45470 Mülheim an der Ruhr , Germany
| | - Dimitrios A Pantazis
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , 45470 Mülheim an der Ruhr , Germany
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Retegan M, Cox N, Lubitz W, Neese F, Pantazis DA. The first tyrosyl radical intermediate formed in the S2-S3 transition of photosystem II. Phys Chem Chem Phys 2015; 16:11901-10. [PMID: 24760184 DOI: 10.1039/c4cp00696h] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The EPR "split signals" represent key intermediates of the S-state cycle where the redox active D1-Tyr161 (YZ) has been oxidized by the reaction center of the photosystem II enzyme to its tyrosyl radical form, but the successive oxidation of the Mn4CaO5 cluster has not yet occurred (SiYZ˙). Here we focus on the S2YZ˙ state, which is formed en route to the final metastable state of the catalyst, the S3 state, the state which immediately precedes O-O bond formation. Quantum chemical calculations demonstrate that both isomeric forms of the S2 state, the open and closed cubane isomers, can form states with an oxidized YZ˙ residue without prior deprotonation of the Mn4CaO5 cluster. The two forms are expected to lie close in energy and retain the electronic structure and magnetic topology of the corresponding S2 state of the inorganic core. As expected, tyrosine oxidation results in a proton shift towards His190. Analysis of the electronic rearrangements that occur upon formation of the tyrosyl radical suggests that a likely next step in the catalytic cycle is the deprotonation of a terminal water ligand (W1) of the Mn4CaO5 cluster. Diamagnetic metal ion substitution is used in our calculations to obtain the molecular g-tensor of YZ˙. It is known that the gx value is a sensitive probe not only of the extent of the proton shift between the tyrosine-histidine pair, but also of the polarization environment of the tyrosine, especially about the phenolic oxygen. It is shown for PSII that this environment is determined by the Ca(2+) ion, which locates two water molecules about the phenoxyl oxygen, indirectly modulating the oxidation potential of YZ.
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Affiliation(s)
- Marius Retegan
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-38, 45470 Mülheim an der Ruhr, Germany.
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Chatterjee R, Coates CS, Milikisiyants S, Lee CI, Wagner A, Poluektov OG, Lakshmi KV. High-Frequency Electron Nuclear Double-Resonance Spectroscopy Studies of the Mechanism of Proton-Coupled Electron Transfer at the Tyrosine-D Residue of Photosystem II. Biochemistry 2013; 52:4781-90. [DOI: 10.1021/bi3012093] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ruchira Chatterjee
- Department of Chemistry and
Chemical Biology and The Baruch ’60 Center for Biochemical
Solar Energy Research, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Christopher S. Coates
- Department of Chemistry and
Chemical Biology and The Baruch ’60 Center for Biochemical
Solar Energy Research, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Sergey Milikisiyants
- Department of Chemistry and
Chemical Biology and The Baruch ’60 Center for Biochemical
Solar Energy Research, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Cheng-I Lee
- Department of Life Science, National Chung Cheng University, 168 University Road,
Min-Hsiung, Chia-Yi 621, Taiwan
| | - Arlene Wagner
- Chemical Sciences and Engineering
Division, Argonne National Laboratory,
9700 South Cass Avenue, Argonne, Illinois 60439, United States
| | - Oleg G. Poluektov
- Chemical Sciences and Engineering
Division, Argonne National Laboratory,
9700 South Cass Avenue, Argonne, Illinois 60439, United States
| | - K. V. Lakshmi
- Department of Chemistry and
Chemical Biology and The Baruch ’60 Center for Biochemical
Solar Energy Research, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
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Tomter AB, Zoppellaro G, Schmitzberger F, Andersen NH, Barra AL, Engman H, Nordlund P, Andersson KK. HF-EPR, Raman, UV/VIS light spectroscopic, and DFT studies of the ribonucleotide reductase R2 tyrosyl radical from Epstein-Barr virus. PLoS One 2011; 6:e25022. [PMID: 21980375 PMCID: PMC3181257 DOI: 10.1371/journal.pone.0025022] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Accepted: 08/22/2011] [Indexed: 11/19/2022] Open
Abstract
Epstein-Barr virus (EBV) belongs to the gamma subfamily of herpes viruses, among the most common pathogenic viruses in humans worldwide. The viral ribonucleotide reductase small subunit (RNR R2) is involved in the biosynthesis of nucleotides, the DNA precursors necessary for viral replication, and is an important drug target for EBV. RNR R2 generates a stable tyrosyl radical required for enzymatic turnover. Here, the electronic and magnetic properties of the tyrosyl radical in EBV R2 have been determined by X-band and high-field/high-frequency electron paramagnetic resonance (EPR) spectroscopy recorded at cryogenic temperatures. The radical exhibits an unusually low g₁-tensor component at 2.0080, indicative of a positive charge in the vicinity of the radical. Consistent with these EPR results a relatively high C-O stretching frequency associated with the phenoxyl radical (at 1508 cm⁻¹) is observed with resonance Raman spectroscopy. In contrast to mouse R2, EBV R2 does not show a deuterium shift in the resonance Raman spectra. Thus, the presence of a water molecule as a hydrogen bond donor moiety could not be identified unequivocally. Theoretical simulations showed that a water molecule placed at a distance of 2.6 Å from the tyrosyl-oxygen does not result in a detectable deuterium shift in the calculated Raman spectra. UV/VIS light spectroscopic studies with metal chelators and tyrosyl radical scavengers are consistent with a more accessible dimetal binding/radical site and a lower affinity for Fe²⁺ in EBV R2 than in Escherichia coli R2. Comparison with previous studies of RNR R2s from mouse, bacteria, and herpes viruses, demonstrates that finely tuned electronic properties of the radical exist within the same RNR R2 Ia class.
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Affiliation(s)
- Ane B. Tomter
- Department of Molecular Biosciences, University of Oslo, Oslo, Norway
| | | | - Florian Schmitzberger
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Niels H. Andersen
- Department of Molecular Biosciences, University of Oslo, Oslo, Norway
| | - Anne-Laure Barra
- Laboratoire National des Champs Magnétiques Intenses, LNCMI-G, UPR 3228, CNRS, Grenoble, France
| | - Henrik Engman
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Pär Nordlund
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
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Matsuoka H, Shen JR, Kawamori A, Nishiyama K, Ohba Y, Yamauchi S. Proton-Coupled Electron-Transfer Processes in Photosystem II Probed by Highly Resolved g-Anisotropy of Redox-Active Tyrosine YZ. J Am Chem Soc 2011; 133:4655-60. [DOI: 10.1021/ja2000566] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hideto Matsuoka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira-2-1-1, Aobaku, Sendai 980-8577, Japan
| | - Jian-Ren Shen
- Graduate School of Natural Science and Technology, Department of Biology, Faculty of Science, Okayama University, Naka-Tsushima, Okayama 700-8530, Japan
| | - Asako Kawamori
- Agape-Kabutoyama Institute of Medicine, Kabutoyama-cho 54-3, Nishinomiya 662-0001, Japan
| | - Kei Nishiyama
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira-2-1-1, Aobaku, Sendai 980-8577, Japan
| | - Yasunori Ohba
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira-2-1-1, Aobaku, Sendai 980-8577, Japan
| | - Seigo Yamauchi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira-2-1-1, Aobaku, Sendai 980-8577, Japan
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Hart R, O'Malley PJ. A quantum mechanics/molecular mechanics study of the tyrosine residue, TyrD, of Photosystem II. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1797:250-4. [DOI: 10.1016/j.bbabio.2009.10.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2009] [Revised: 10/23/2009] [Accepted: 10/27/2009] [Indexed: 10/20/2022]
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Jenson DL, Barry BA. Proton-coupled electron transfer in photosystem II: proton inventory of a redox active tyrosine. J Am Chem Soc 2009; 131:10567-73. [PMID: 19586025 PMCID: PMC2846377 DOI: 10.1021/ja902896e] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Photosystem II (PSII) catalyzes the light driven oxidation of water and the reduction of plastoquinone. PSII is a multisubunit membrane protein; the D1 and D2 polypeptides form the heterodimeric core of the PSII complex. Water oxidation occurs at a manganese-containing oxygen evolving complex (OEC). PSII contains two redox active tyrosines, Y(Z) and Y(D), which form the neutral tyrosyl radicals, Y(z)(*) and Y(D)(*). Y(D) has been assigned as tyrosine 160 in the D2 polypeptide through isotopic labeling and site-directed mutagenesis. Whereas Y(D) is not directly involved in the oxidation of water, it has been implicated in the formation and stabilization of the OEC. PSII structures have shown Y(D) to be within hydrogen-bonding distance of histidine 189 in the D2 polypeptide. Spectroscopic studies have suggested that a proton is transferred between Y(D) and histidine 189 when Y(D) is oxidized and reduced. In our previous work, we used (2)H(2)O solvent exchange to demonstrate that the mechanism of Y(D) proton-coupled electron transfer (PCET) differs at high and low pH. In this article, we utilize the proton inventory technique to obtain more information concerning PCET mechanism at high pH. The hypercurvature of the proton inventory data provides evidence for the existence of multiple, proton-donation pathways to Y(D)(*). In addition, at least one of these pathways must involve the transfer of more than one proton.
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Affiliation(s)
- David L. Jenson
- School of Chemistry and Biochemistry and the Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Bridgette A. Barry
- School of Chemistry and Biochemistry and the Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332
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Svistunenko DA, Jones GA. Tyrosyl radicals in proteins: a comparison of empirical and density functional calculated EPR parameters. Phys Chem Chem Phys 2009; 11:6600-13. [DOI: 10.1039/b905522c] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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