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Schleicher E, Rein S, Illarionov B, Lehmann A, Al Said T, Kacprzak S, Bittl R, Bacher A, Fischer M, Weber S. Selective 13C labelling reveals the electronic structure of flavocoenzyme radicals. Sci Rep 2021; 11:18234. [PMID: 34521887 PMCID: PMC8440535 DOI: 10.1038/s41598-021-97588-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 08/24/2021] [Indexed: 02/08/2023] Open
Abstract
Flavocoenzymes are nearly ubiquitous cofactors that are involved in the catalysis and regulation of a wide range of biological processes including some light-induced ones, such as the photolyase-mediated DNA repair, magnetoreception of migratory birds, and the blue-light driven phototropism in plants. One of the factors that enable versatile flavin-coenzyme biochemistry and biophysics is the fine-tuning of the cofactor's frontier orbital by interactions with the protein environment. Probing the singly-occupied molecular orbital (SOMO) of the intermediate radical state of flavins is therefore a prerequisite for a thorough understanding of the diverse functions of the flavoprotein family. This may be ultimately achieved by unravelling the hyperfine structure of a flavin by electron paramagnetic resonance. In this contribution we present a rigorous approach to obtaining a hyperfine map of the flavin's chromophoric 7,8-dimethyl isoalloxazine unit at an as yet unprecedented level of resolution and accuracy. We combine powerful high-microwave-frequency/high-magnetic-field electron-nuclear double resonance (ENDOR) with 13C isotopologue editing as well as spectral simulations and density functional theory calculations to measure and analyse 13C hyperfine couplings of the flavin cofactor in DNA photolyase. Our data will provide the basis for electronic structure considerations for a number of flavin radical intermediates occurring in blue-light photoreceptor proteins.
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Affiliation(s)
- Erik Schleicher
- grid.5963.9Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104 Freiburg, Germany
| | - Stephan Rein
- grid.5963.9Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104 Freiburg, Germany
| | - Boris Illarionov
- grid.9026.d0000 0001 2287 2617Institut für Lebensmittelchemie, Universität Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Ariane Lehmann
- grid.5963.9Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104 Freiburg, Germany
| | - Tarek Al Said
- grid.5963.9Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104 Freiburg, Germany
| | - Sylwia Kacprzak
- grid.5963.9Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104 Freiburg, Germany ,grid.423218.ePresent Address: Bruker BioSpin GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany
| | - Robert Bittl
- grid.14095.390000 0000 9116 4836Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Adelbert Bacher
- grid.6936.a0000000123222966Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Markus Fischer
- grid.9026.d0000 0001 2287 2617Institut für Lebensmittelchemie, Universität Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Stefan Weber
- grid.5963.9Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104 Freiburg, Germany
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Wörner J, Chen J, Bacher A, Weber S. Non-classical disproportionation revealed by photo-chemically induced dynamic nuclear polarization NMR. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:281-290. [PMID: 37904753 PMCID: PMC10539781 DOI: 10.5194/mr-2-281-2021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 04/07/2021] [Indexed: 11/01/2023]
Abstract
Photo-chemically induced dynamic nuclear polarization (photo-CIDNP) was used to observe the light-induced disproportionation reaction of 6,7,8-trimethyllumazine starting out from its triplet state to generate a pair of radicals comprising a one-electron reduced and a one-electron oxidized species. Our evidence is based on the measurement of two marker proton hyperfine couplings, A iso (H(6α )) and A iso (H(8α )), which we correlated to predictions from density functional theory. The ratio of these two hyperfine couplings is reversed in the oxidized and the reduced radical species. Observation of the dismutation reaction is facilitated by the exceptional C-H acidity of the methyl group at position 7 of 6,7,8-trimethyllumazine and the slow proton exchange associated with it, which leads to NMR-distinguishable anionic (TML- ) and neutral (TMLH) protonation forms.
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Affiliation(s)
- Jakob Wörner
- Institute of Physical Chemistry, Albert-Ludwigs-Universität
Freiburg, Freiburg, 79104, Germany
| | - Jing Chen
- Institute of Physical Chemistry, Albert-Ludwigs-Universität
Freiburg, Freiburg, 79104, Germany
| | - Adelbert Bacher
- Department of Chemistry, Technical University of Munich, Garching,
85748, Germany
| | - Stefan Weber
- Institute of Physical Chemistry, Albert-Ludwigs-Universität
Freiburg, Freiburg, 79104, Germany
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Nohr D, Weber S, Schleicher E. EPR spectroscopy on flavin radicals in flavoproteins. Methods Enzymol 2019; 620:251-275. [PMID: 31072489 DOI: 10.1016/bs.mie.2019.03.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Flavin semiquinone redox states are important intermediates in a broad variety of reactions catalyzed by flavoproteins. As paramagnetic states they can be favorably probed by EPR spectroscopy in all its flavors. This review summarizes recent results in the characterization of flavin radicals. On the one hand, flavin radical states, e.g., trapped as reaction intermediates, can be characterized using modern pulsed EPR methods to unravel their electronic structure and to gain information about the surrounding environment and its changes on protein action. On the other hand, short-lived intermediate flavin radical states generated, e.g., photochemically, can be followed by time-resolved EPR, which allows a direct tracking of flavin-dependent reactions with a temporal resolution reaching nanoseconds.
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Affiliation(s)
- Daniel Nohr
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Stefan Weber
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Erik Schleicher
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.
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Nohr D, Rodriguez R, Weber S, Schleicher E. How can EPR spectroscopy help to unravel molecular mechanisms of flavin-dependent photoreceptors? Front Mol Biosci 2015; 2:49. [PMID: 26389123 PMCID: PMC4555020 DOI: 10.3389/fmolb.2015.00049] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 08/10/2015] [Indexed: 11/25/2022] Open
Abstract
Electron paramagnetic resonance (EPR) spectroscopy is a well-established spectroscopic method for the examination of paramagnetic molecules. Proteins can contain paramagnetic moieties in form of stable cofactors, transiently formed intermediates, or spin labels artificially introduced to cysteine sites. The focus of this review is to evaluate potential scopes of application of EPR to the emerging field of optogenetics. The main objective for EPR spectroscopy in this context is to unravel the complex mechanisms of light-active proteins, from their primary photoreaction to downstream signal transduction. An overview of recent results from the family of flavin-containing, blue-light dependent photoreceptors is given. In detail, mechanistic similarities and differences are condensed from the three classes of flavoproteins, the cryptochromes, LOV (Light-oxygen-voltage), and BLUF (blue-light using FAD) domains. Additionally, a concept that includes spin-labeled proteins and examination using modern pulsed EPR is introduced, which allows for a precise mapping of light-induced conformational changes.
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Affiliation(s)
- Daniel Nohr
- Department of Physical Chemistry, Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg Freiburg, Germany
| | - Ryan Rodriguez
- Department of Physical Chemistry, Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg Freiburg, Germany
| | - Stefan Weber
- Department of Physical Chemistry, Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg Freiburg, Germany
| | - Erik Schleicher
- Department of Physical Chemistry, Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg Freiburg, Germany
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Kammler L, van Gastel M. Electronic structure of the lowest triplet state of flavin mononucleotide. J Phys Chem A 2012; 116:10090-8. [PMID: 22998491 DOI: 10.1021/jp305778v] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The electronic structure of flavin mononucleotide (FMN), an organic cofactor that plays a role in many important enzymatic reactions, has been investigated by electron paramagnetic resonance (EPR) spectroscopy, optical spectroscopy, and quantum chemistry. In particular, the triplet state of FMN, which is paramagnetic (total spin S = 1), allows an investigation of the zero field splitting parameters D and E, which are directly related to the two singly occupied molecular orbitals. Triplet EPR spectra and optical absorption spectra at different pH values in combination with time dependent density functional theory (TDDFT) reveal that the highest occupied orbital (HOMO) and lowest unoccupied orbital (LUMO) of FMN are largely unaffected by changes in the protonation state of FMN. Rather, the orbital structure of the lower lying doubly occupied orbitals changes dramatically. Additional EPR experiments have been carried out in the presence of AgNO(3), which allows the formation of an Ag-FMN triplet state with different zero field splitting parameters and population and depopulation rates. Addition of AgNO(3) only induces small changes in the optical spectrum, indicating that the Ag(+) ion only contributes to the zero field splitting by second order spin-orbit coupling and leaves the orbital structure unaffected. By a combination of the three employed methods, the observed bands in the UV/vis spectra of FMN at different pH values are assigned to electronic transitions.
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Affiliation(s)
- Lydia Kammler
- Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Wegelerstrasse 12, 53115, Bonn, Germany
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Maly T, Cui D, Griffin RG, Miller AF. 1H dynamic nuclear polarization based on an endogenous radical. J Phys Chem B 2012; 116:7055-65. [PMID: 22472179 DOI: 10.1021/jp300539j] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We demonstrate a 15-fold enhancement of solid-state NMR signals via dynamic nuclear polarization (DNP) based on a stable, naturally occurring radical in a protein: the flavin mononucleotide (FMN) semiquinone of flavodoxin. The line width of flavodoxin's EPR signal suggests that the dominant DNP mechanism is the solid effect, consistent with the field-dependent DNP enhancement profile. The magnitude of the enhancement as well as the bulk-polarization build-up time constant (τ(B)) with which it develops are dependent on the isotopic composition of the protein. Deuteration of the protein to 85% increased the nuclear longitudinal relaxation time T(1n) and τ(B) by factors of five and seven, respectively. Slowed dissipation of polarization can explain the 2-fold higher maximal enhancement than that obtained in proteated protein, based on the endogenous semiquinone. In contrast, the long τ(B) of TOTAPOL-based DNP in nonglassy samples was not accompanied by a similarly important long T(1n), and in this case the enhancement was greatly reduced. The low concentrations of radicals occurring naturally in biological systems limit the magnitude of DNP enhancement that is attainable by this means. However, our enhancement factors of up to 15 can nonetheless make an important difference to the feasibility of applying solid-state NMR to biochemical systems. We speculate that DNP based on endogenous radicals may facilitate MAS NMR characterization of biochemical complexes and even organelles, and could also serve as a source of additional structural and physiological information.
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Affiliation(s)
- Thorsten Maly
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Pauwels E, Declerck R, Verstraelen T, De Sterck B, Kay CWM, Van Speybroeck V, Waroquier M. Influence of Protein Environment on the Electron Paramagnetic Resonance Properties of Flavoprotein Radicals: A QM/MM Study. J Phys Chem B 2010; 114:16655-65. [DOI: 10.1021/jp109763t] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ewald Pauwels
- Center for Molecular Modeling, Ghent University, Technologiepark 903, B-9052 Zwijnaarde, Belgium QCMM - alliance Ghent-Brussels, Belgium, and Institute of Structural and Molecular Biology and London Centre for Nanotechnology, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Reinout Declerck
- Center for Molecular Modeling, Ghent University, Technologiepark 903, B-9052 Zwijnaarde, Belgium QCMM - alliance Ghent-Brussels, Belgium, and Institute of Structural and Molecular Biology and London Centre for Nanotechnology, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Toon Verstraelen
- Center for Molecular Modeling, Ghent University, Technologiepark 903, B-9052 Zwijnaarde, Belgium QCMM - alliance Ghent-Brussels, Belgium, and Institute of Structural and Molecular Biology and London Centre for Nanotechnology, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Bart De Sterck
- Center for Molecular Modeling, Ghent University, Technologiepark 903, B-9052 Zwijnaarde, Belgium QCMM - alliance Ghent-Brussels, Belgium, and Institute of Structural and Molecular Biology and London Centre for Nanotechnology, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Christopher W. M. Kay
- Center for Molecular Modeling, Ghent University, Technologiepark 903, B-9052 Zwijnaarde, Belgium QCMM - alliance Ghent-Brussels, Belgium, and Institute of Structural and Molecular Biology and London Centre for Nanotechnology, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Veronique Van Speybroeck
- Center for Molecular Modeling, Ghent University, Technologiepark 903, B-9052 Zwijnaarde, Belgium QCMM - alliance Ghent-Brussels, Belgium, and Institute of Structural and Molecular Biology and London Centre for Nanotechnology, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Michel Waroquier
- Center for Molecular Modeling, Ghent University, Technologiepark 903, B-9052 Zwijnaarde, Belgium QCMM - alliance Ghent-Brussels, Belgium, and Institute of Structural and Molecular Biology and London Centre for Nanotechnology, University College London, Gower Street, London WC1E 6BT, United Kingdom
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Stoll S, NejatyJahromy Y, Woodward JJ, Ozarowski A, Marletta MA, Britt RD. Nitric oxide synthase stabilizes the tetrahydrobiopterin cofactor radical by controlling its protonation state. J Am Chem Soc 2010; 132:11812-23. [PMID: 20669954 DOI: 10.1021/ja105372s] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Nitric oxide synthase (NOS), a homodimeric enzyme with a flavin reductase domain and a P450-type heme-containing oxygenase domain, catalyzes the formation of NO from L-arginine, NADPH, and O(2) in a two-step reaction sequence. In the first step, a tetrahydrobiopterin (H(4)B) cofactor bound near one of the heme propionate groups acts as an electron donor to the P450-type heme active site, yielding a one-electron oxidized radical that is subsequently re-reduced. In solution, H(4)B undergoes two-electron oxidation, showing that the enzyme significantly alters the proton- and electron-transfer properties of the cofactor. Multifrequency EPR and ENDOR spectroscopy were used to determine magnetic parameters, and from them the (de)protonation state of the H(4)B radical in the oxygenase domain dimer of inducible NO synthase that was trapped by rapid freeze quench. From 9.5 and 330-416 GHz EPR and from 34 GHz (1)H ENDOR spectroscopy, the g tensor of the radical and the hyperfine tensors of several N and H nuclei in the radical were obtained. Density functional theory calculations at the PBE0/EPR-II level for H(4)B radical models predict different spin density distributions and g and hyperfine tensors for different protonation states. Comparison of the predicted and experimental values leads to the conclusion that the radical is cationic H(4)B(*+), suggesting that NOS stabilizes this protonated form to utilize the cofactor in a unique dual one-electron redox role, where it can deliver an electron to the active site for reductive oxygen activation and also remove an electron from the active site to generate NO and not NO(-). The protein environment also prevents further oxidation and subsequent loss of function of the cofactor, thus enabling the enzyme to perform the unusual catalytic one-electron chemistry.
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Affiliation(s)
- Stefan Stoll
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, USA
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Schleicher E, Bittl R, Weber S. New roles of flavoproteins in molecular cell biology: Blue-light active flavoproteins studied by electron paramagnetic resonance. FEBS J 2009; 276:4290-303. [DOI: 10.1111/j.1742-4658.2009.07141.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Okafuji A, Schnegg A, Schleicher E, Möbius K, Weber S. G-tensors of the flavin adenine dinucleotide radicals in glucose oxidase: a comparative multifrequency electron paramagnetic resonance and electron-nuclear double resonance study. J Phys Chem B 2008; 112:3568-74. [PMID: 18302360 DOI: 10.1021/jp077170j] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The flavin adenine dinucleotide (FAD) cofactor of Aspergillus niger glucose oxidase (GO) in its anionic (FAD*-) and neutral (FADH*) radical form was investigated by electron paramagnetic resonance (EPR) at high microwave frequencies (93.9 and 360 GHz) and correspondingly high magnetic fields and by pulsed electron-nuclear double resonance (ENDOR) spectroscopy at 9.7 GHz. Because of the high spectral resolution of the frozen-solution continuous-wave EPR spectrum recorded at 360 GHz, the anisotropy of the g-tensor of FAD*- could be fully resolved. By least-squares fittings of spectral simulations to experimental data, the principal values of g have been established with high precision: gX=2.00429(3), gY=2.00389(3), gZ=2.00216(3) (X, Y, and Z are the principal axes of g) yielding giso=2.00345(3). The gY-component of FAD*- from GO is moderately shifted upon deprotonation of FADH*, rendering the g-tensor of FAD*- slightly more axially symmetric as compared to that of FADH*. In contrast, significantly altered proton hyperfine couplings were observed by ENDOR upon transforming the neutral FADH* radical into the anionic FAD*- radical by pH titration of GO. That the g-principal values of both protonation forms remain largely identical demonstrates the robustness of g against local changes in the electron-spin density distribution of flavins. Thus, in flavins, the g-tensor reflects more global changes in the electronic structure and, therefore, appears to be ideally suited to identify chemically different flavin radicals.
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Affiliation(s)
- Asako Okafuji
- Freie Universität Berlin, Fachbereich Physik, Institut für Experimentalphysik, Arnimallee 14, 14195 Berlin, Germany
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Weber S, Bittl R. Studies of Organic Protein Cofactors Using Electron Paramagnetic Resonance. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2007. [DOI: 10.1246/bcsj.80.2270] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Meissner B, Schleicher E, Weber S, Essen LO. The dodecin from Thermus thermophilus, a bifunctional cofactor storage protein. J Biol Chem 2007; 282:33142-54. [PMID: 17855371 DOI: 10.1074/jbc.m704951200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Dodecins are so far the smallest known flavoproteins (68-71 amino acids) and are most likely involved in prokaryotic flavin storage. The dodecin monomers adopt a simple betaalphabetabeta-fold and assemble to hollow sphere-like dodecameric complexes. Flavin binding by the dodecin from Thermus thermophilus showed a 1:1 stoichiometry and apparent dissociation constants in the submicromolar to nanomolar range as characterized by isothermal titration calorimetry and fluorescence titrations. The x-ray structures of the flavin-prebound and FMN-reconstituted state of the T. thermophilus dodecin revealed binding of FMN dimers in a novel si-si- rather than the re-re- orientation of their isoalloxazine moieties as found before in an archaeal dodecin. Electron paramagnetic resonance studies demonstrated that upon reduction the excess electron is localized only on one flavin, thus making dodecin-bound flavins highly refractory to redox chemistry. Besides FMN dimers, trimers of coenzyme A are additionally bound to this eubacterial dodecin along the 3-fold symmetry face II of the dodecin complex. Therefore, dodecins can act as bifunctional cofactor storage proteins that sequester catalytic cofactors in prokaryotes very efficiently in an aggregated and unreactive state.
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Affiliation(s)
- Britta Meissner
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Strasse, Marburg, Germany
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