1
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Doyle LM, Bienenmann RLM, Gericke R, Xu S, Farquhar ER, Que L, McDonald AR. Preparation and characterization of Mn IIMn III complexes with relevance to class Ib ribonucleotide reductases. J Inorg Biochem 2024; 257:112583. [PMID: 38733704 DOI: 10.1016/j.jinorgbio.2024.112583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 04/26/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024]
Abstract
The Mn2 complex [MnII2(TPDP)(O2CPh)2](BPh4) (1, TPDP = 1,3-bis(bis(pyridin-2-ylmethyl)amino)propan-2-ol, Ph =phenyl) was prepared and subsequently characterized via single-crystal X-ray diffraction, X-ray absorption, electronic absorption, and infrared spectroscopies, and mass spectrometry. 1 was prepared in order to explore its properties as a structural and functional mimic of class Ib ribonucleotide reductases (RNRs). 1 reacted with superoxide anion (O2•-) to generate a peroxido-MnIIMnIII complex, 2. The electronic absorption and electron paramagnetic resonance (EPR) spectra of 2 were similar to previously published peroxido-MnIIMnIII species. Furthermore, X-ray near edge absorption structure (XANES) studies indicated the conversion of a MnII2 core in 1 to a MnIIMnIII state in 2. Treatment of 2 with para-toluenesulfonic acid (p-TsOH) resulted in the conversion to a new MnIIMnIII species, 3, rather than causing O-O bond scission, as previously encountered. 3 was characterized using electronic absorption, EPR, and X-ray absorption spectroscopies. Unlike other reported peroxido-MnIIMnIII species, 3 was capable of oxidative O-H activation, mirroring the generation of tyrosyl radical in class Ib RNRs, however without accessing the MnIIIMnIV state.
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Affiliation(s)
- Lorna M Doyle
- School of Chemistry, Trinity College Dublin, The University of Dublin, College Green, Dublin 2, Ireland
| | - Roel L M Bienenmann
- School of Chemistry, Trinity College Dublin, The University of Dublin, College Green, Dublin 2, Ireland
| | - Robert Gericke
- School of Chemistry, Trinity College Dublin, The University of Dublin, College Green, Dublin 2, Ireland
| | - Shuangning Xu
- Department of Chemistry and Centre for Metals in Biocatalysis, University of Minnesota, Minneapolis, 55455 MN, United States
| | - Erik R Farquhar
- Case Western Reserve University Center for Synchrotron Biosciences, National Synchrotron Light Source II, Brookhaven National Laboratory Upton, NY, 11973 New York, United States
| | - Lawrence Que
- Department of Chemistry and Centre for Metals in Biocatalysis, University of Minnesota, Minneapolis, 55455 MN, United States
| | - Aidan R McDonald
- School of Chemistry, Trinity College Dublin, The University of Dublin, College Green, Dublin 2, Ireland.
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2
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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. [PMID: 38937148 DOI: 10.1021/acs.accounts.4c00231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [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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3
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Doyle L, Magherusan A, Xu S, Murphy K, Farquhar ER, Molton F, Duboc C, Que L, McDonald AR. Class Ib Ribonucleotide Reductases: Activation of a Peroxido-Mn IIMn III to Generate a Reactive Oxo-Mn IIIMn IV Oxidant. Inorg Chem 2024; 63:2194-2203. [PMID: 38231137 PMCID: PMC10828993 DOI: 10.1021/acs.inorgchem.3c04163] [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: 11/23/2023] [Revised: 12/18/2023] [Accepted: 12/22/2023] [Indexed: 01/18/2024]
Abstract
In the postulated catalytic cycle of class Ib Mn2 ribonucleotide reductases (RNRs), a MnII2 core is suggested to react with superoxide (O2·-) to generate peroxido-MnIIMnIII and oxo-MnIIIMnIV entities prior to proton-coupled electron transfer (PCET) oxidation of tyrosine. There is limited experimental support for this mechanism. We demonstrate that [MnII2(BPMP)(OAc)2](ClO4) (1, HBPMP = 2,6-bis[(bis(2 pyridylmethyl)amino)methyl]-4-methylphenol) was converted to peroxido-MnIIMnIII (2) in the presence of superoxide anion that converted to (μ-O)(μ-OH)MnIIIMnIV (3) via the addition of an H+-donor (p-TsOH) or (μ-O)2MnIIIMnIV (4) upon warming to room temperature. The physical properties of 3 and 4 were probed using UV-vis, EPR, X-ray absorption, and IR spectroscopies and mass spectrometry. Compounds 3 and 4 were capable of phenol oxidation to yield a phenoxyl radical via a concerted PCET oxidation, supporting the proposed mechanism of tyrosyl radical cofactor generation in RNRs. The synthetic models demonstrate that the postulated O2/Mn2/tyrosine activation mechanism in class Ib Mn2 RNRs is plausible and provides spectral insights into intermediates currently elusive in the native enzyme.
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Affiliation(s)
- Lorna Doyle
- School
of Chemistry, Trinity College Dublin, The
University of Dublin, College Green, Dublin 2, Ireland
| | - Adriana Magherusan
- School
of Chemistry, Trinity College Dublin, The
University of Dublin, College Green, Dublin 2, Ireland
| | - Shuangning Xu
- Department
of Chemistry and Centre for Metals in Biocatalysis, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Kayleigh Murphy
- School
of Chemistry, Trinity College Dublin, The
University of Dublin, College Green, Dublin 2, Ireland
| | - Erik R. Farquhar
- Case
Western Reserve University Center for Synchrotron Biosciences, National
Synchrotron Light Source II, Brookhaven
National Laboratory Upton, New
York 11973, United States
| | - Florian Molton
- CNRS
UMR 5250, DCM, Univ. Grenoble Alpes, Grenoble F-38000, France
| | - Carole Duboc
- CNRS
UMR 5250, DCM, Univ. Grenoble Alpes, Grenoble F-38000, France
| | - Lawrence Que
- Department
of Chemistry and Centre for Metals in Biocatalysis, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Aidan R. McDonald
- School
of Chemistry, Trinity College Dublin, The
University of Dublin, College Green, Dublin 2, Ireland
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4
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Grotemeyer EN, Parham JD, Jackson TA. Reaction landscape of a mononuclear Mn III-hydroxo complex with hydrogen peroxide. Dalton Trans 2023; 52:14350-14370. [PMID: 37767937 DOI: 10.1039/d3dt02672h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2023]
Abstract
Peroxomanganese species have been proposed as key intermediates in the catalytic cycles of both manganese enzymes and synthetic catalysts. However, many of these intermediates have yet to be observed. Here, we report the formation of a series of intermediates, each generated from the reaction of the mononuclear MnIII-hydroxo complex [MnIII(OH)(dpaq2Me)]+ with hydrogen peroxide under slightly different conditions. By changing the acidity of the reaction mixture and/or the quantity of hydrogen peroxide added, we are able to control which intermediate forms. Using a combination of electronic absorption, 1H NMR, EPR, and X-ray absorption spectroscopies, as well as density functional theory (DFT) and complete active space self-consistent field (CASSCF) calculations, we formulate these intermediates as the bis(μ-oxo)dimanganese(III,IV) complex [MnIIIMnIV(μ-O)2(dpaq2Me)2]+, the MnIII-hydroperoxo complex [MnIII(OOH)(dpaq2Me)]+, and the MnIII-peroxo complex [MnIII(O2)(dpaq2Me)]. The formation of the MnIII-hydroperoxo species from the reaction of a MnIII-hydroxo complex with hydrogen peroxide mimics an elementary reaction proposed for many synthetic manganese catalysts that activate hydrogen peroxide.
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Affiliation(s)
- Elizabeth N Grotemeyer
- The University of Kansas, Department of Chemistry and Center for Environmentally Beneficial Catalysis, 1567 Irving Hill Road, Lawrence, KS 66045, USA.
| | - Joshua D Parham
- The University of Kansas, Department of Chemistry and Center for Environmentally Beneficial Catalysis, 1567 Irving Hill Road, Lawrence, KS 66045, USA.
| | - Timothy A Jackson
- The University of Kansas, Department of Chemistry and Center for Environmentally Beneficial Catalysis, 1567 Irving Hill Road, Lawrence, KS 66045, USA.
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5
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Yuan F, Su B, Yu Y, Wang J. Study and design of amino acid-based radical enzymes using unnatural amino acids. RSC Chem Biol 2023; 4:431-446. [PMID: 37292061 PMCID: PMC10246556 DOI: 10.1039/d2cb00250g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 05/17/2023] [Indexed: 06/10/2023] Open
Abstract
Radical enzymes harness the power of reactive radical species by placing them in a protein scaffold, and they are capable of catalysing many important reactions. New native radical enzymes, especially those with amino acid-based radicals, in the category of non-heme iron enzymes (including ribonucleotide reductases), heme enzymes, copper enzymes, and FAD-radical enzymes have been discovered and characterized. We discussed recent research efforts to discover new native amino acid-based radical enzymes, and to study the roles of radicals in processes such as enzyme catalysis and electron transfer. Furthermore, design of radical enzymes in a small and simple scaffold not only allows us to study the radical in a well-controlled system and test our understanding of the native enzymes, but also allows us to create powerful enzymes. In the study and design of amino acid-based radical enzymes, the use of unnatural amino acids allows precise control of pKa values and reduction potentials of the residue, as well as probing the location of the radical through spectroscopic methods, making it a powerful research tool. Our understanding of amino acid-based radical enzymes will allow us to tailor them to create powerful catalysts and better therapeutics.
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Affiliation(s)
- Feiyan Yuan
- Institute of Biochemical Engineering, Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology Beijing 102488 China
| | - Binbin Su
- Institute of Biochemical Engineering, Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology Beijing 102488 China
| | - Yang Yu
- Institute of Biochemical Engineering, Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology Beijing 102488 China
| | - Jiangyun Wang
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences Beijing 100101 China
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6
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Battistella B, Lohmiller T, Cula B, Hildebrandt P, Kuhlmann U, Dau H, Mebs S, Ray K. A New Thiolate-Bound Dimanganese Cluster as a Structural and Functional Model for Class Ib Ribonucleotide Reductases. Angew Chem Int Ed Engl 2023; 62:e202217076. [PMID: 36583430 DOI: 10.1002/anie.202217076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 12/24/2022] [Accepted: 12/29/2022] [Indexed: 12/31/2022]
Abstract
In class Ib ribonucleotide reductases (RNRs) a dimanganese(II) cluster activates superoxide (O2 ⋅- ) rather than dioxygen (O2 ), to access a high valent MnIII -O2 -MnIV species, responsible for the oxidation of tyrosine to tyrosyl radical. In a biomimetic approach, we report the synthesis of a thiolate-bound dimanganese complex [MnII 2 (BPMT)(OAc)2 ](ClO)4 (BPMT=(2,6-bis{[bis(2-pyridylmethyl)amino]methyl}-4-methylthiophenolate) (1) and its reaction with O2 ⋅- to form a [(BPMT)MnO2 Mn]2+ complex 2. Resonance Raman investigation revealed the presence of an O-O bond in 2, while EPR analysis displayed a 16-line St =1/2 signal at g=2 typically associated with a MnIII MnIV core, as detected in class Ib RNRs. Unlike all other previously reported Mn-O2 -Mn complexes, generated by O2 ⋅- activation at Mn2 centers, 2 proved to be a capable electrophilic oxidant in aldehyde deformylation and phenol oxidation reactions, rendering it one of the best structural and functional models for class Ib RNRs.
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Affiliation(s)
- Beatrice Battistella
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
| | - Thomas Lohmiller
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany.,EPR4Energy Joint Lab, Department Spins in Energy Conversion and Quantum Information Science, Helmholtz Zentrum Berlin für Materialien und Energie GmbH, Albert-Einstein-Str. 16, 12489, Berlin, Germany
| | - Beatrice Cula
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
| | - Peter Hildebrandt
- Institut für Chemie, Fakultät II, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Uwe Kuhlmann
- Institut für Chemie, Fakultät II, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Holger Dau
- Institut für Physik, Freie Universität zu Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Stefan Mebs
- Institut für Physik, Freie Universität zu Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Kallol Ray
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
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7
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Kass D, Yao S, Krause KB, Corona T, Richter L, Braun T, Mebs S, Haumann M, Dau H, Lohmiller T, Limberg C, Drieß M, Ray K. Spectroscopic Properties of a Biologically Relevant [Fe 2 (μ-O) 2 ] Diamond Core Motif with a Short Iron-Iron Distance. Angew Chem Int Ed Engl 2023; 62:e202209437. [PMID: 36541062 DOI: 10.1002/anie.202209437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 12/05/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
Diiron cofactors in enzymes perform diverse challenging transformations. The structures of high valent intermediates (Q in methane monooxygenase and X in ribonucleotide reductase) are debated since Fe-Fe distances of 2.5-3.4 Å were attributed to "open" or "closed" cores with bridging or terminal oxido groups. We report the crystallographic and spectroscopic characterization of a FeIII 2 (μ-O)2 complex (2) with tetrahedral (4C) centres and short Fe-Fe distance (2.52 Å), persisting in organic solutions. 2 shows a large Fe K-pre-edge intensity, which is caused by the pronounced asymmetry at the TD FeIII centres due to the short Fe-μ-O bonds. A ≈2.5 Å Fe-Fe distance is unlikely for six-coordinate sites in Q or X, but for a Fe2 (μ-O)2 core containing four-coordinate (or by possible extension five-coordinate) iron centres there may be enough flexibility to accommodate a particularly short Fe-Fe separation with intense pre-edge transition. This finding may broaden the scope of models considered for the structure of high-valent diiron intermediates formed upon O2 activation in biology.
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Affiliation(s)
- Dustin Kass
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
| | - Shenglai Yao
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 115, 10623, Berlin, Germany
| | - Konstantin B Krause
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
| | - Teresa Corona
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
| | - Liza Richter
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
| | - Thomas Braun
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
| | - Stefan Mebs
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Michael Haumann
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Holger Dau
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Thomas Lohmiller
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany.,EPR4Energy Joint Lab, Department Spins in Energy Conversion and Quantum Information Science, Helmholtz Zentrum Berlin für Materialien und Energie GmbH, Albert-Einstein-Straße 16, 12489, Berlin, Germany
| | - Christian Limberg
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
| | - Matthias Drieß
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 115, 10623, Berlin, Germany
| | - Kallol Ray
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
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8
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Zou J, Yang L, Feng W. Mechanism of Radical Initiation and Transfer in Class Id Ribonucleotide Reductase Based on Density Functional Theory. Inorg Chem 2023; 62:2561-2575. [PMID: 36721875 DOI: 10.1021/acs.inorgchem.2c02926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Class Id ribonucleotide reductase (RNR) is a newly discovered enzyme, which employs the dimanganese cofactor in the superoxidized state (MnIII/MnIV) as the radical initiator. The dimanganese cofactor of class Id RNR in the reduced state (inactive) is clearly based on the crystal structure of the Fj-β subunit. However, the state of the dimanganese cofactor of class Id RNR in the oxidized state (active) is not known. The X-band EPR spectra have shown that the activated Fj-β subunit exists in two distinct complexes, 1 and 2. In this work, quantum mechanical/molecular mechanical calculations were carried out to study class Id RNR. First, we have determined that complex 2 contains a MnIII-(μ-oxo)2-MnIV cluster, and complex 1 contains a MnIII-(μ-hydroxo/μ-oxo)-MnIV cluster. Then, based on the determined dimanganese cofactors, the mechanism of radical initiation and transfer in class Id RNR is revealed. The MnIII-(μ-oxo)2-MnIV cluster in complex 2 has not enough reduction potential to initiate radical transfer directly. Instead, it needs to be monoprotonated into MnIII-(μ-hydroxo/μ-oxo)-MnIV (complex 1) before the radical transfer. The protonation state of μ-oxo can be regulated by changing the protein microenvironment, which is induced by the protein aggregation and separation of β subunits with α subunits. The radical transfer between the cluster of MnIII-(μ-hydroxo/μ-oxo)-MnIV and Trp30 in the radical-transfer chain of the Fj-β subunit (MnIII/MnIV ↔ His100 ↔ Asp194 ↔ Trp30 ↔ Arg99) is a water-mediated tri-proton-coupled electron transfer, which transfers proton from the ε-amino group of Lys71 to the carboxyl group of Glu97 via the water molecule Wat551 and the bridging μ-hydroxo ligand through a three-step reaction. This newly discovered proton-coupled electron-transfer mechanism in class Id RNR is different from those reported in the known Ia-Ic RNRs. The ε-amino group of Lys71, which serves as a proton donor, plays an important role in the radical transfer.
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Affiliation(s)
- Jinxin Zou
- Department of Biological Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Lu Yang
- Department of Biological Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Wei Feng
- Department of Biological Engineering, Beijing University of Chemical Technology, Beijing 100029, China
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9
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Čapek J, Večerek B. Why is manganese so valuable to bacterial pathogens? Front Cell Infect Microbiol 2023; 13:943390. [PMID: 36816586 PMCID: PMC9936198 DOI: 10.3389/fcimb.2023.943390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 01/04/2023] [Indexed: 02/05/2023] Open
Abstract
Apart from oxygenic photosynthesis, the extent of manganese utilization in bacteria varies from species to species and also appears to depend on external conditions. This observation is in striking contrast to iron, which is similar to manganese but essential for the vast majority of bacteria. To adequately explain the role of manganese in pathogens, we first present in this review that the accumulation of molecular oxygen in the Earth's atmosphere was a key event that linked manganese utilization to iron utilization and put pressure on the use of manganese in general. We devote a large part of our contribution to explanation of how molecular oxygen interferes with iron so that it enhances oxidative stress in cells, and how bacteria have learned to control the concentration of free iron in the cytosol. The functioning of iron in the presence of molecular oxygen serves as a springboard for a fundamental understanding of why manganese is so valued by bacterial pathogens. The bulk of this review addresses how manganese can replace iron in enzymes. Redox-active enzymes must cope with the higher redox potential of manganese compared to iron. Therefore, specific manganese-dependent isoenzymes have evolved that either lower the redox potential of the bound metal or use a stronger oxidant. In contrast, redox-inactive enzymes can exchange the metal directly within the individual active site, so no isoenzymes are required. It appears that in the physiological context, only redox-inactive mononuclear or dinuclear enzymes are capable of replacing iron with manganese within the same active site. In both cases, cytosolic conditions play an important role in the selection of the metal used. In conclusion, we summarize both well-characterized and less-studied mechanisms of the tug-of-war for manganese between host and pathogen.
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Affiliation(s)
- Jan Čapek
- *Correspondence: Jan Čapek, ; Branislav Večerek,
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10
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Wooldridge R, Stone S, Pedraza A, Ray WK, Helm RF, Allen KD. The Chlamydia trachomatis p-aminobenzoate synthase CADD is a manganese-dependent oxygenase that uses its own amino acid residues as substrates. FEBS Lett 2023; 597:557-572. [PMID: 36647787 DOI: 10.1002/1873-3468.14573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 12/28/2022] [Accepted: 01/02/2023] [Indexed: 01/18/2023]
Abstract
CADD (chlamydia protein associating with death domains) is a p-aminobenzoate (pAB) synthase involved in a noncanonical route for tetrahydrofolate biosynthesis in Chlamydia trachomatis. Although previously implicated to employ a diiron cofactor, here, we show that pAB synthesis by CADD requires manganese and the physiological cofactor is most likely a heterodinuclear Mn/Fe cluster. Isotope-labeling experiments revealed that the two oxygen atoms in the carboxylic acid portion of pAB are derived from molecular oxygen. Further, mass spectrometry-based proteomic analyses of CADD-derived peptides demonstrated a glycine substitution at Tyr27, providing strong evidence that this residue is sacrificed for pAB synthesis. Additionally, Lys152 was deaminated and oxidized to aminoadipic acid, supporting its proposed role as a sacrificial amino group donor.
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Affiliation(s)
| | - Spenser Stone
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA
| | - Andrew Pedraza
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA
| | - W Keith Ray
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA
| | - Richard F Helm
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA
| | - Kylie D Allen
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA
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11
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Yadav O, Ansari M, Ansari A. Electronic structures, bonding aspects and spectroscopic parameters of homo/hetero valent bridged dinuclear transition metal complexes. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 278:121331. [PMID: 35597159 DOI: 10.1016/j.saa.2022.121331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/25/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
Bridged dinuclear metal complexes have fascinated scientists worldwide, and remarkable success has been achieved to unravel the electronic structures, structure-function relationship, coordination environments, and fine mechanistic details of the enzymes owing to the repercussion of biomimetic studies carried out on dinuclear model systems. Molecular level study of these systems integrated with spectroscopic study helps in gaining deep insights about structural and electronic aspects of natural enzymatic systems. Considering the same, here first time we report DFT study on bridged non-heme metal complexes based on N-Et-HPTB ligand system containing homovalent (MIIMII); {[(MnII)2(O2CCH3)(N-Et-HPTB)]2+; Species I), [(FeII)2(O2CCH3)(N-Et-HPTB)]2+; Species II), [(CoII)2(O2CCH3)(N-Et-HPTB)]2+; Species III)} and heterovalent (MIIIMII): {[(MnIII)(MnII)(O2)(N-Et-HPTB)]2+; Species Ia) [(FeIII)(FeII)(O2)(N-Et-HPTB)]2+; Species IIa) and [(CoIII)(CoII)(O2)(N-Et-HPTB)]2+; Species IIIa)} dinuclear metal centres. Bridging oxygen bears a significant spin density which may prompt important chemical reactions involving activation of bonds like C-H/O-H/N-H etc. TD-DFT calculations for UV-Visible absorption have been carried out to further shed light on structural-functional and electronic structures of these dinuclear species. Studying these dinuclear species may be a good starting point for the study of active sites of the bimetallic centre of dinuclear enzymes and thus may serve as fascinating spectroscopic models. Further, FMO analysis, MEP mapping, and NBO calculations were employed to analyze bonding aspects predict theoretical reactivity behaviour and any kind of stabilizing interactions present in the reported species.
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Affiliation(s)
- Oval Yadav
- Department of Chemistry, Central University of Haryana, Mahendergarh 123031, India
| | - Mursaleem Ansari
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, Pawai 400076, India
| | - Azaj Ansari
- Department of Chemistry, Central University of Haryana, Mahendergarh 123031, India.
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12
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Self-sacrificial tyrosine cleavage by an Fe:Mn oxygenase for the biosynthesis of para-aminobenzoate in Chlamydia trachomatis. Proc Natl Acad Sci U S A 2022; 119:e2210908119. [PMID: 36122239 PMCID: PMC9522330 DOI: 10.1073/pnas.2210908119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chlamydia protein associating with death domains (CADD) is involved in the biosynthesis of para-aminobenzoate (pABA), an essential component of the folate cofactor that is required for the survival and proliferation of the human pathogen Chlamydia trachomatis. The pathway used by Chlamydiae for pABA synthesis differs from the canonical multi-enzyme pathway used by most bacteria that relies on chorismate as a metabolic precursor. Rather, recent work showed pABA formation by CADD derives from l-tyrosine. As a member of the emerging superfamily of heme oxygenase-like diiron oxidases (HDOs), CADD was proposed to use a diiron cofactor for catalysis. However, we report maximal pABA formation by CADD occurs upon the addition of both iron and manganese, which implicates a heterobimetallic Fe:Mn cluster is the catalytically active form. Isotopic labeling experiments and proteomics studies show that CADD generates pABA from a protein-derived tyrosine (Tyr27), a residue that is ∼14 Å from the dimetal site. We propose that this self-sacrificial reaction occurs through O2 activation by a probable Fe:Mn cluster through a radical relay mechanism that connects to the "substrate" Tyr, followed by amination and direct oxygen insertion. These results provide the molecular basis for pABA formation in C. trachomatis, which will inform the design of novel therapeutics.
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13
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John J, Aurelius O, Srinivas V, Saura P, Kim IS, Bhowmick A, Simon PS, Dasgupta M, Pham C, Gul S, Sutherlin KD, Aller P, Butryn A, Orville AM, Cheah MH, Owada S, Tono K, Fuller FD, Batyuk A, Brewster AS, Sauter NK, Yachandra VK, Yano J, Kaila VRI, Kern J, Lebrette H, Högbom M. Redox-controlled reorganization and flavin strain within the ribonucleotide reductase R2b-NrdI complex monitored by serial femtosecond crystallography. eLife 2022; 11:79226. [PMID: 36083619 PMCID: PMC9462851 DOI: 10.7554/elife.79226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Redox reactions are central to biochemistry and are both controlled by and induce protein structural changes. Here, we describe structural rearrangements and crosstalk within the Bacillus cereus ribonucleotide reductase R2b-NrdI complex, a di-metal carboxylate-flavoprotein system, as part of the mechanism generating the essential catalytic free radical of the enzyme. Femtosecond crystallography at an X-ray free electron laser was utilized to obtain structures at room temperature in defined redox states without suffering photoreduction. Together with density functional theory calculations, we show that the flavin is under steric strain in the R2b-NrdI protein complex, likely tuning its redox properties to promote superoxide generation. Moreover, a binding site in close vicinity to the expected flavin O2 interaction site is observed to be controlled by the redox state of the flavin and linked to the channel proposed to funnel the produced superoxide species from NrdI to the di-manganese site in protein R2b. These specific features are coupled to further structural changes around the R2b-NrdI interaction surface. The mechanistic implications for the control of reactive oxygen species and radical generation in protein R2b are discussed.
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Affiliation(s)
- Juliane John
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden
| | - Oskar Aurelius
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden.,MAX IV Laboratory, Lund University, Lund, Sweden
| | - Vivek Srinivas
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden
| | - Patricia Saura
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden
| | - In-Sik Kim
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Asmit Bhowmick
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Philipp S Simon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Medhanjali Dasgupta
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Cindy Pham
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Kyle D Sutherlin
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Pierre Aller
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, United Kingdom.,Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, United Kingdom
| | - Agata Butryn
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, United Kingdom.,Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, United Kingdom
| | - Allen M Orville
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, United Kingdom.,Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, United Kingdom
| | - Mun Hon Cheah
- Department of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, Uppsala, Sweden
| | - Shigeki Owada
- Japan Synchrotron Radiation Research Institute, Sayo-gun, Japan.,RIKEN SPring-8 Center, Sayo-gun, Japan
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, Sayo-gun, Japan.,RIKEN SPring-8 Center, Sayo-gun, Japan
| | - Franklin D Fuller
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - Alexander Batyuk
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - Aaron S Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Nicholas K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Vittal K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Ville R I Kaila
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Hugo Lebrette
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden
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14
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Sun S, He Z, Jiang P, Baral R, Pandelia ME. Metal Dependence and Functional Diversity of Type I Cas3 Nucleases. Biochemistry 2022; 61:327-338. [PMID: 35184547 DOI: 10.1021/acs.biochem.1c00779] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Type I CRISPR-Cas systems provide prokaryotes with protection from parasitic genetic elements by cleaving foreign DNA. In addition, they impact bacterial physiology by regulating pathogenicity and virulence, making them key players in adaptability and evolution. The signature nuclease Cas3 is a phosphodiesterase belonging to the HD-domain metalloprotein superfamily. By directing specific metal incorporation, we map a promiscuous metal ion cofactor profile for Cas3 from Thermobifida fusca (Tf). Tf Cas3 affords significant ssDNA cleavage with four homo-dimetal centers (Fe2+, Co2+, Mn2+, and Ni2+), while the diferrous form is the most active and likely biologically relevant in vivo. Electron paramagnetic resonance (EPR) spectroscopy and Mössbauer spectroscopy show that the diiron cofactor can access three redox forms, while the diferrous form can be readily obtained with mild reductants. We further employ EPR and Mössbauer on Fe-enriched proteins to establish that Cas3″ enzymes harbor a dinuclear cofactor, which was not previously confirmed. We demonstrate that the ancillary His ligand is critical for efficient ssDNA cleavage but not for diiron assembly or small molecule hydrolysis. We further explore the ability of Cas3 to hydrolyze cyclic mononucleotides and show that Tf Cas3 hydrolyzes 2'3'-cAMP with catalytic efficiency comparable to that of the conserved virulence factor A (CvfA), an HD-domain protein hydrolyzing 2'3'-cylic phosphodiester bonds at RNA 3'-termini. Because this CvfA activity is linked to virulence regulation, Cas3 may also utilize 2'3'-cAMP hydrolysis as a possible molecular route to control virulence.
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Affiliation(s)
- Sining Sun
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Zunyu He
- Yale University, New Haven, Connecticut 06520-8055, United States
| | - Paul Jiang
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Rishika Baral
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Maria-Eirini Pandelia
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02453, United States
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15
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Banerjee R, Srinivas V, Lebrette H. Ferritin-Like Proteins: A Conserved Core for a Myriad of Enzyme Complexes. Subcell Biochem 2022; 99:109-153. [PMID: 36151375 DOI: 10.1007/978-3-031-00793-4_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Ferritin-like proteins share a common fold, a four α-helix bundle core, often coordinating a pair of metal ions. Although conserved, the ferritin fold permits a diverse set of reactions, and is central in a multitude of macromolecular enzyme complexes. Here, we emphasize this diversity through three members of the ferritin-like superfamily: the soluble methane monooxygenase, the class I ribonucleotide reductase and the aldehyde deformylating oxygenase. They all rely on dinuclear metal cofactors to catalyze different challenging oxygen-dependent reactions through the formation of multi-protein complexes. Recent studies using cryo-electron microscopy, serial femtosecond crystallography at an X-ray free electron laser source, or single-crystal X-ray diffraction, have reported the structures of the active protein complexes, and revealed unprecedented insights into the molecular mechanisms of these three enzymes.
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Affiliation(s)
- Rahul Banerjee
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Vivek Srinivas
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Hugo Lebrette
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, UPS, Université de Toulouse, Toulouse, France.
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16
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Paramagnetic resonance investigation of mono- and di-manganese-containing systems in biochemistry. Methods Enzymol 2022; 666:315-372. [DOI: 10.1016/bs.mie.2022.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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17
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Smethurst DGJ, Shcherbik N. Interchangeable utilization of metals: New perspectives on the impacts of metal ions employed in ancient and extant biomolecules. J Biol Chem 2021; 297:101374. [PMID: 34732319 PMCID: PMC8633580 DOI: 10.1016/j.jbc.2021.101374] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 10/25/2021] [Accepted: 10/28/2021] [Indexed: 02/08/2023] Open
Abstract
Metal ions provide considerable functionality across biological systems, and their utilization within biomolecules has adapted through changes in the chemical environment to maintain the activity they facilitate. While ancient earth's atmosphere was rich in iron and manganese and low in oxygen, periods of atmospheric oxygenation significantly altered the availability of certain metal ions, resulting in ion replacement within biomolecules. This adaptation mechanism has given rise to the phenomenon of metal cofactor interchangeability, whereby contemporary proteins and nucleic acids interact with multiple metal ions interchangeably, with different coordinated metals influencing biological activity, stability, and toxic potential. The ability of extant organisms to adapt to fluctuating metal availability remains relevant in a number of crucial biomolecules, including the superoxide dismutases of the antioxidant defense systems and ribonucleotide reductases. These well-studied and ancient enzymes illustrate the potential for metal interchangeability and adaptive utilization. More recently, the ribosome has also been demonstrated to exhibit interchangeable interactions with metal ions with impacts on function, stability, and stress adaptation. Using these and other examples, here we review the biological significance of interchangeable metal ions from a new angle that combines both biochemical and evolutionary viewpoints. The geochemical pressures and chemical properties that underlie biological metal utilization are discussed in the context of their impact on modern disease states and treatments.
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Affiliation(s)
- Daniel G J Smethurst
- Department for Cell Biology and Neuroscience, School of Osteopathic Medicine, Rowan University, Stratford, New Jersey, USA.
| | - Natalia Shcherbik
- Department for Cell Biology and Neuroscience, School of Osteopathic Medicine, Rowan University, Stratford, New Jersey, USA.
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18
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Jayachandran M, Yoon J, Wu J, Cipurko D, Quon J, Makhlynets O. Mechanistic studies of the cofactor assembly in class Ib ribonucleotide reductases and protein affinity for MnII and FeII. Metallomics 2021; 13:6413552. [PMID: 34718709 DOI: 10.1093/mtomcs/mfab062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 10/21/2021] [Indexed: 11/14/2022]
Abstract
Ribonucleotide reductase (RNR) is an essential enzyme found in all organisms. The function of RNR is to catalyze the conversion of nucleotides to deoxynucleotides. RNRs rely on metallocofactors to oxidize a conserved cysteine in the active site of the enzyme into a thiyl radical, which then initiates nucleotide reduction. The proteins required for MnIII2-Y• cluster formation in class Ib RNRs are NrdF (β-subunit) and NrdI (flavodoxin). An oxidant is channeled from the FMN cofactor in NrdI to the dimanganese center in NrdF, where it oxidizes the dimanganese center and a tyrosyl radical (Y•) is formed. Both Streptococcus sanguinis and Escherichia coli MnII2-NrdF structures have a constriction in the channel immediately above the metal site. In E. coli, the constriction is formed by the side chain of S159, whereas in the S. sanguinis system it involves T158. This serine-to-threonine substitution was investigated using S. sanguinis and Streptococcus pneumoniae class Ib RNRs but it is also present in other pathogenic streptococci. Using stopped-flow kinetics, we investigate the role of this substitution in the mechanism of MnIII2-Y• cluster formation. In addition to different kinetics observed in the studied streptococci, we found that affinity constants of NrdF for MnII and FeII are about 1 µM and the previously reported preference for MnII could not be explained by affinity only.
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Affiliation(s)
- Megha Jayachandran
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Jennifer Yoon
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Jacky Wu
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Denis Cipurko
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Joyce Quon
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Olga Makhlynets
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
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19
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McLean JT, Benny A, Nolan MD, Swinand G, Scanlan EM. Cysteinyl radicals in chemical synthesis and in nature. Chem Soc Rev 2021; 50:10857-10894. [PMID: 34397045 DOI: 10.1039/d1cs00254f] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nature harnesses the unique properties of cysteinyl radical intermediates for a diverse range of essential biological transformations including DNA biosynthesis and repair, metabolism, and biological photochemistry. In parallel, the synthetic accessibility and redox chemistry of cysteinyl radicals renders them versatile reactive intermediates for use in a vast array of synthetic applications such as lipidation, glycosylation and fluorescent labelling of proteins, peptide macrocyclization and stapling, desulfurisation of peptides and proteins, and development of novel therapeutics. This review provides the reader with an overview of the role of cysteinyl radical intermediates in both chemical synthesis and biological systems, with a critical focus on mechanistic details. Direct insights from biological systems, where applied to chemical synthesis, are highlighted and potential avenues from nature which are yet to be explored synthetically are presented.
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Affiliation(s)
- Joshua T McLean
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Alby Benny
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Mark D Nolan
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Glenna Swinand
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Eoin M Scanlan
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
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20
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Shoor M, Gudim I, Hersleth HP, Hammerstad M. Thioredoxin reductase from Bacillus cereus exhibits distinct reduction and NADPH-binding properties. FEBS Open Bio 2021; 11:3019-3031. [PMID: 34492167 PMCID: PMC8564101 DOI: 10.1002/2211-5463.13289] [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: 08/10/2021] [Revised: 09/03/2021] [Accepted: 09/06/2021] [Indexed: 11/23/2022] Open
Abstract
Low‐molecular‐weight (low Mr) thioredoxin reductases (TrxRs) are homodimeric NADPH‐dependent dithiol flavoenzymes that reduce thioredoxins (Trxs) or Trx‐like proteins involved in the activation networks of enzymes, such as the bacterial class Ib ribonucleotide reductase (RNR). During the last few decades, TrxR‐like ferredoxin/flavodoxin NADP+ oxidoreductases (FNRs) have been discovered and characterized in several types of bacteria, including those not encoding the canonical plant‐type FNR. In Bacillus cereus, a TrxR‐like FNR has been shown to reduce the flavodoxin‐like protein NrdI in the activation of class Ib RNR. However, some species only encode TrxR and lack the homologous TrxR‐like FNR. Due to the structural similarity between TrxRs and TrxR‐like FNRs, as well as variations in their occurrence in different microorganisms, we hypothesized that low Mr TrxR may be able to replace TrxR‐like FNR in, for example, the reduction of NrdI. In this study, characterization of TrxR from B. cereus has revealed a weak FNR activity toward NrdI reduction. Additionally, the crystal structure shows that only one out of two binding sites of the B. cereus TrxR homodimer is occupied with NADPH, indicating a possible asymmetric co‐substrate binding in TrxR.
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Affiliation(s)
- Marita Shoor
- Department of Biosciences, Section for Biochemistry and Molecular Biology, University of Oslo, Norway
| | - Ingvild Gudim
- Department of Biosciences, Section for Biochemistry and Molecular Biology, University of Oslo, Norway
| | - Hans-Petter Hersleth
- Department of Biosciences, Section for Biochemistry and Molecular Biology, University of Oslo, Norway.,Department of Chemistry, Section for Chemical Life Sciences, University of Oslo, Norway
| | - Marta Hammerstad
- Department of Biosciences, Section for Biochemistry and Molecular Biology, University of Oslo, Norway
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21
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Ruskoski TB, Boal AK. The periodic table of ribonucleotide reductases. J Biol Chem 2021; 297:101137. [PMID: 34461093 PMCID: PMC8463856 DOI: 10.1016/j.jbc.2021.101137] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 08/20/2021] [Accepted: 08/26/2021] [Indexed: 12/30/2022] Open
Abstract
In most organisms, transition metal ions are necessary cofactors of ribonucleotide reductase (RNR), the enzyme responsible for biosynthesis of the 2'-deoxynucleotide building blocks of DNA. The metal ion generates an oxidant for an active site cysteine (Cys), yielding a thiyl radical that is necessary for initiation of catalysis in all RNRs. Class I enzymes, widespread in eukaryotes and aerobic microbes, share a common requirement for dioxygen in assembly of the active Cys oxidant and a unique quaternary structure, in which the metallo- or radical-cofactor is found in a separate subunit, β, from the catalytic α subunit. The first class I RNRs, the class Ia enzymes, discovered and characterized more than 30 years ago, were found to use a diiron(III)-tyrosyl-radical Cys oxidant. Although class Ia RNRs have historically served as the model for understanding enzyme mechanism and function, more recently, remarkably diverse bioinorganic and radical cofactors have been discovered in class I RNRs from pathogenic microbes. These enzymes use alternative transition metal ions, such as manganese, or posttranslationally installed tyrosyl radicals for initiation of ribonucleotide reduction. Here we summarize the recent progress in discovery and characterization of novel class I RNR radical-initiating cofactors, their mechanisms of assembly, and how they might function in the context of the active class I holoenzyme complex.
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Affiliation(s)
- Terry B Ruskoski
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Amie K Boal
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA.
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22
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Narulkar DD, Ansari A, Vardhaman AK, Harmalkar SS, Lingamallu G, Dhavale VM, Sankaralingam M, Das S, Kumar P, Dhuri SN. A side-on Mn(III)-peroxo supported by a non-heme pentadentate N 3Py 2 ligand: synthesis, characterization and reactivity studies. Dalton Trans 2021; 50:2824-2831. [PMID: 33533342 DOI: 10.1039/d0dt03706k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A mononuclear manganese(iii)-peroxo complex [MnIII(N3Py2)(O2)]+ (1a) bearing a non-heme N,N'-dimethyl-N-(2-(methyl(pyridin-2-ylmethyl)amino)ethyl)-N'-(pyridin-2-ylmethyl)ethane-1,2-diamine (N3Py2) ligand was synthesized by the reaction of [Mn(N3Py2)(H2O)](ClO4)2 (1) with hydrogen peroxide and triethylamine in CH3CN at 25 °C. The reactivity of 1a in aldehyde deformylation using 2-phenyl propionaldehyde (2-PPA) was studied and the reaction kinetics was monitored by UV-visible spectroscopy. A kinetic isotope effect (KIE) = 1.7 was obtained in the reaction of 1a with 2-PPA and α-[D1]-PPA, suggesting nucleophilic character of 1a. The activation parameters ΔH‡ and ΔS‡ were determined using the Eyring plot while Ea was obtained from the Arrhenius equation by performing the reaction between 288 and 303 K. Hammett constants (σp) of para-substituted benzaldehydes p-X-Ph-CHO (X = Cl, F, H, and Me) were linear with a slope (ρ) = 3.0. Computational study suggested that the side-on structure of 1a is more favored over the end-on structure and facilitates the reactivity of 1a.
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Affiliation(s)
- Dattaprasad D Narulkar
- School of Chemical Sciences, Goa University, Goa-403206, India. and Department of Chemistry, Dnyanprassarak Mandal's College and Research Centre, Assagao, Goa-403507, India
| | - Azaj Ansari
- Department of Chemistry, Central University of Haryana, Mahendergarh-123031, Haryana, India
| | - Anil Kumar Vardhaman
- Polymers & Functional Materials Division, CSIR-Indian Institute of Chemical Technology, Uppal Road, Tarnaka, Hyderabad-500007, India
| | | | - Giribabu Lingamallu
- Polymers & Functional Materials Division, CSIR-Indian Institute of Chemical Technology, Uppal Road, Tarnaka, Hyderabad-500007, India
| | - Vishal M Dhavale
- CSIR-Central Electrochemical Research Institute, CSIR Madras Complex, Taramani, Chennai-600 113, India
| | - Muniyandi Sankaralingam
- Bioinspired & Biomimetic Inorganic Chemistry Lab, Department of Chemistry, National Institute of Technology Calicut, Kozhikode, Kerala 673601, India
| | - Sandip Das
- Indian Institute of Science Education and Research (IISER), Tirupati-517507, India
| | - Pankaj Kumar
- Indian Institute of Science Education and Research (IISER), Tirupati-517507, India
| | - Sunder N Dhuri
- School of Chemical Sciences, Goa University, Goa-403206, India.
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Paul GC, Sarkar P, Sarmah A, Shaw P, Maity S, Mukherjee C. A combined experimental and theoretical study on a single, unsupported oxo-bridged Mn(III,III) dimer coordinated to two iminobenzosemiquinone π-radical anions. Dalton Trans 2021; 50:8768-8775. [PMID: 34085670 DOI: 10.1039/d1dt00489a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ligand H2LAP comprises a non-innocent 2-aminophenol unit and an innocent bis(pyridin-2-ylmethyl)amine unit. The ligand, upon reaction with an equivalent amount of Mn(ClO4)2·6H2O in the presence of Et3N under air in MeOH, provided a mono(oxo)-bridged dinuclear Mn2 complex ({[(LISQ)MnIII-O-MnIII(LISQ)][(ClO4)]2}; 1). X-ray crystal structure analysis of complex 1 revealed that in the dicationic unit, the physical oxidation state of each Mn ion was +III and the 2-aminophenol unit of ligand H2LAP was in its one-electron oxidized iminobenzosemiquinone form. 1H-NMR measurement of complex 1 confirmed that the complex acquired a diamagnetic ground state (St = 0). Thus, antiferromagnetic couplings among the paramagnetic centers were realized. The UV-Vis-NIR spectrum of complex 1 was consisted of ligand-to-metal charge-transfer transitions in the visible region, while ligand-to-metal and metal-to-ligand charge-transfer transitions were noticed in the near-infrared region due to the presence of iminobenzosemiquinone radical units. The cyclic voltammogram of the complex showed three one-electron oxidation waves and two one-electron reduction waves. While the first two oxidation processes were metal-based, the two successive reductions were ligand-centered. DFT-based theoretical studies confirmed the assignment.
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Affiliation(s)
- Ganesh Chandra Paul
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India. and Department of Chemistry, ICFAI Science School, ICFAI University Tripura, Agartala, 799210, Tripura(W), India
| | - Prasenjit Sarkar
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
| | - Amrit Sarmah
- Department of Molecular Modelling, Institute of Organic Chemistry and Biochemistry ASCR, v.v.i. Flemingovo nám. 2, CZ-166 10 Prague 6, Czech Republic and Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacký University Olomouc, 78371 Olomouc, Czech Republic
| | - Prantick Shaw
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
| | - Suvendu Maity
- Department of Chemistry, R. K. Mission Residential College, Narendrapur, Kolkata, 700103, India
| | - Chandan Mukherjee
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
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Premužić D, Hołyńska M, Ozarowski A, Pietzonka C, Roseborough A, Stoian SA. Model Dimeric Manganese(IV) Complexes Featuring Terminal Tris-hydroxotetraazaadamantane and Various Bridging Ligands. Inorg Chem 2020; 59:10768-10784. [PMID: 32687708 DOI: 10.1021/acs.inorgchem.0c01242] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
A series of model dinuclear manganese(IV) complexes of the general formula [(H3COH)(L')MnIV(μ-L)2MnIV(L')(HOCH3)] is presented. These compounds feature capping 4,6,10-trihydroxo-3,5,7-trimethyl-1,4,6,10-tetraazaadamantane ligands derived from a polydentate oxime compound (L'). The bridging ligands L include azide (1), methoxide (2), and oxalate (3) anions. The magnetic properties and high-field (HF) EPR spectra of 1-3 were studied in detail and revealed varying weak antiferromagnetic coupling and modest zero-field splitting (ZFS) of the local quartet spin sites. Our HF EPR studies provide insight into the dimer ZFS, including determination of the corresponding parameters by giant spin approach for methoxido-bridged complex 2. Furthermore, the physicochemical properties of 1-3 were studied using IR, UV-vis, and electrochemical (cyclic voltammetry) methods. Theoretical exchange coupling constants were obtained using broken-symmetry (BS) density functional theory (DFT). Computational estimates of the local quartet ground spins state ZFSs of 1-3 were obtained using coupled-perturbed (CP) DFT and complete active space self-consistent field (CASSCF) calculations with n-electron valence state perturbation theory (NEVPT2) corrections. We found that the CP DFT calculations which used the B3LYP functional and models derived experimental structures performed best in reproducing both the magnitude and the sign of the experimental D values. Moreover, our computational investigation of 1-3 suggests that we observe metals sites which have an increased +3 character and are supported by redox noninnocent 4,6,10-trihydroxo-3,5,7-trimethyl-1,4,6,10-tetraazaadamantane ligands. The latter conclusion is further corroborated by the observation that the free ligand can be readily oxidized to yield a NO-based radical.
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Affiliation(s)
- Dejan Premužić
- Fachbereich Chemie and Wissenschaftliches Zentrum für Materialwissenschaften(WZMW), Philipps-Universität Marburg Hans-Meerwein-Straße, Marburg D-35043, Germany
| | - Małgorzata Hołyńska
- Fachbereich Chemie and Wissenschaftliches Zentrum für Materialwissenschaften(WZMW), Philipps-Universität Marburg Hans-Meerwein-Straße, Marburg D-35043, Germany
| | - Andrew Ozarowski
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United States
| | - Clemens Pietzonka
- Fachbereich Chemie and Wissenschaftliches Zentrum für Materialwissenschaften(WZMW), Philipps-Universität Marburg Hans-Meerwein-Straße, Marburg D-35043, Germany
| | - Alexander Roseborough
- Department of Chemistry, University of Idaho, 875 Perimeter Drive, Moscow, Idaho 83844, United States
| | - Sebastian A Stoian
- Department of Chemistry, University of Idaho, 875 Perimeter Drive, Moscow, Idaho 83844, United States
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25
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Kim J, Park S, Go YK, Jin K, Kim Y, Nam KT, Kim SH. Probing the Structure and Binding Mode of EDTA on the Surface of Mn 3O 4 Nanoparticles for Water Oxidation by Advanced Electron Paramagnetic Resonance Spectroscopy. Inorg Chem 2020; 59:8846-8854. [PMID: 32501692 DOI: 10.1021/acs.inorgchem.0c00611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Identification of the surface structure of nanoparticles is important for understanding the catalytic mechanism and improving the properties of the particles. Here, we provide a detailed description of the coordination modes of ethylenediaminetetraacetate (EDTA) on Mn3O4 nanoparticles at the atomic level, as obtained by advanced electron paramagnetic resonance (EPR) spectroscopy. Binding of EDTA to Mn3O4 leads to dramatic changes in the EPR spectrum, with a 5-fold increase in the axial zero-field splitting parameter of Mn(II). This indicates significant changes in the coordination environment of the Mn(II) site; hence, the binding of EDTA causes a profound change in the electronic structure of the manganese site. Furthermore, the electron spin echo envelope modulation results reveal that two 14N atoms of EDTA are directly coordinated to the Mn site and a water molecule is coordinated to the surface of the nanoparticles. An Fourier transform infrared spectroscopy study shows that the Ca(II) ion is coordinated to the carboxylic ligands via the pseudobridging mode. The EPR spectroscopic results provide an atomic picture of surface-modified Mn3O4 nanoparticles for the first time. These results can enhance our understanding of the rational design of catalysts, for example, for the water oxidation reaction.
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Affiliation(s)
- Jin Kim
- Western Seoul Center, Korea Basic Science Institute (KBSI), Seoul 03759, Republic of Korea
| | - Sunghak Park
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Yoo Kyung Go
- Western Seoul Center, Korea Basic Science Institute (KBSI), Seoul 03759, Republic of Korea
| | - Kyoungsuk Jin
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Yujeong Kim
- Western Seoul Center, Korea Basic Science Institute (KBSI), Seoul 03759, Republic of Korea.,Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Ki Tae Nam
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Sun Hee Kim
- Western Seoul Center, Korea Basic Science Institute (KBSI), Seoul 03759, Republic of Korea.,Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
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26
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Grāve K, Griese JJ, Berggren G, Bennett MD, Högbom M. The Bacillus anthracis class Ib ribonucleotide reductase subunit NrdF intrinsically selects manganese over iron. J Biol Inorg Chem 2020; 25:571-582. [PMID: 32296998 PMCID: PMC7239806 DOI: 10.1007/s00775-020-01782-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 03/22/2020] [Indexed: 01/30/2023]
Abstract
Abstract Correct protein metallation in the complex mixture of the cell is a prerequisite for metalloprotein function. While some metals, such as Cu, are commonly chaperoned, specificity towards metals earlier in the Irving–Williams series is achieved through other means, the determinants of which are poorly understood. The dimetal carboxylate family of proteins provides an intriguing example, as different proteins, while sharing a common fold and the same 4-carboxylate 2-histidine coordination sphere, are known to require either a Fe/Fe, Mn/Fe or Mn/Mn cofactor for function. We previously showed that the R2lox proteins from this family spontaneously assemble the heterodinuclear Mn/Fe cofactor. Here we show that the class Ib ribonucleotide reductase R2 protein from Bacillus anthracis spontaneously assembles a Mn/Mn cofactor in vitro, under both aerobic and anoxic conditions, when the metal-free protein is subjected to incubation with MnII and FeII in equal concentrations. This observation provides an example of a protein scaffold intrinsically predisposed to defy the Irving–Williams series and supports the assumption that the Mn/Mn cofactor is the biologically relevant cofactor in vivo. Substitution of a second coordination sphere residue changes the spontaneous metallation of the protein to predominantly form a heterodinuclear Mn/Fe cofactor under aerobic conditions and a Mn/Mn metal center under anoxic conditions. Together, the results describe the intrinsic metal specificity of class Ib RNR and provide insight into control mechanisms for protein metallation. Graphical Abstract ![]()
Electronic supplementary material The online version of this article (10.1007/s00775-020-01782-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kristīne Grāve
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 10691, Stockholm, Sweden
| | - Julia J Griese
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 10691, Stockholm, Sweden.,Department of Cell and Molecular Biology, Uppsala University, BMC, Box 596, 75124, Uppsala, Sweden
| | - Gustav Berggren
- Department of Chemistry, Ångström Laboratory, Uppsala University, Lägerhyddsvägen 1, 75120, Uppsala, Sweden
| | - Matthew D Bennett
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 10691, Stockholm, Sweden
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 10691, Stockholm, Sweden.
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27
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28
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Kisgeropoulos EC, Griese JJ, Smith ZR, Branca RMM, Schneider CR, Högbom M, Shafaat HS. Key Structural Motifs Balance Metal Binding and Oxidative Reactivity in a Heterobimetallic Mn/Fe Protein. J Am Chem Soc 2020; 142:5338-5354. [PMID: 32062969 DOI: 10.1021/jacs.0c00333] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Heterobimetallic Mn/Fe proteins represent a new cofactor paradigm in bioinorganic chemistry and pose countless outstanding questions. The assembly of the active site defies common chemical convention by contradicting the Irving-Williams series, while the scope of reactivity remains unexplored. In this work, the assembly and C-H bond activation process in the Mn/Fe R2-like ligand-binding oxidase (R2lox) protein is investigated using a suite of biophysical techniques, including time-resolved optical spectroscopy, global kinetic modeling, X-ray crystallography, electron paramagnetic resonance spectroscopy, protein electrochemistry, and mass spectrometry. Selective metal binding is found to be under thermodynamic control, with the binding sites within the apo-protein exhibiting greater MnII affinity than FeII affinity. The comprehensive analysis of structure and reactivity of wild-type R2lox and targeted primary and secondary sphere mutants indicate that the efficiency of C-H bond activation directly correlates with the Mn/Fe cofactor reduction potentials and is inversely related to divalent metal binding affinity. These findings suggest the R2lox active site is precisely tuned for achieving both selective heterobimetallic binding and high levels of reactivity and offer a mechanism to examine the means by which proteins achieve appropriate metal incorporation.
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Affiliation(s)
| | - Julia J Griese
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.,Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
| | | | - Rui M M Branca
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, SE-171 21 Solna, Sweden
| | | | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
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29
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Kutin Y, Kositzki R, Branca RMM, Srinivas V, Lundin D, Haumann M, Högbom M, Cox N, Griese JJ. Chemical flexibility of heterobimetallic Mn/Fe cofactors: R2lox and R2c proteins. J Biol Chem 2019; 294:18372-18386. [PMID: 31591267 DOI: 10.1074/jbc.ra119.010570] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/04/2019] [Indexed: 11/06/2022] Open
Abstract
A heterobimetallic Mn/Fe cofactor is present in the R2 subunit of class Ic ribonucleotide reductases (R2c) and in R2-like ligand-binding oxidases (R2lox). Although the protein-derived metal ligands are the same in both groups of proteins, the connectivity of the two metal ions and the chemistry each cofactor performs are different: in R2c, a one-electron oxidant, the Mn/Fe dimer is linked by two oxygen bridges (μ-oxo/μ-hydroxo), whereas in R2lox, a two-electron oxidant, it is linked by a single oxygen bridge (μ-hydroxo) and a fatty acid ligand. Here, we identified a second coordination sphere residue that directs the divergent reactivity of the protein scaffold. We found that the residue that directly precedes the N-terminal carboxylate metal ligand is conserved as a glycine within the R2lox group but not in R2c. Substitution of the glycine with leucine converted the resting-state R2lox cofactor to an R2c-like cofactor, a μ-oxo/μ-hydroxo-bridged MnIII/FeIII dimer. This species has recently been observed as an intermediate of the oxygen activation reaction in WT R2lox, indicating that it is physiologically relevant. Cofactor maturation in R2c and R2lox therefore follows the same pathway, with structural and functional divergence of the two cofactor forms following oxygen activation. We also show that the leucine-substituted variant no longer functions as a two-electron oxidant. Our results reveal that the residue preceding the N-terminal metal ligand directs the cofactor's reactivity toward one- or two-electron redox chemistry, presumably by setting the protonation state of the bridging oxygens and thereby perturbing the redox potential of the Mn ion.
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Affiliation(s)
- Yury Kutin
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Ramona Kositzki
- Institut für Experimentalphysik, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Rui M M Branca
- Cancer Proteomics Mass Spectrometry, Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, Box 1031, SE-171 21 Solna, Sweden
| | - Vivek Srinivas
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Daniel Lundin
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Michael Haumann
- Institut für Experimentalphysik, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Nicholas Cox
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia.
| | - Julia J Griese
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden; Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden.
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30
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Yan Poon PC, Dedushko MA, Sun X, Yang G, Toledo S, Hayes EC, Johansen A, Piquette MC, Rees JA, Stoll S, Rybak-Akimova E, Kovacs JA. How Metal Ion Lewis Acidity and Steric Properties Influence the Barrier to Dioxygen Binding, Peroxo O-O Bond Cleavage, and Reactivity. J Am Chem Soc 2019; 141:15046-15057. [PMID: 31480847 DOI: 10.1021/jacs.9b04729] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Herein we quantitatively investigate how metal ion Lewis acidity and steric properties influence the kinetics and thermodynamics of dioxygen binding versus release from structurally analogous Mn-O2 complexes, as well as the barrier to Mn peroxo O-O bond cleavage, and the reactivity of Mn oxo intermediates. Previously we demonstrated that the steric and electronic properties of MnIII-OOR complexes containing N-heterocyclic (NAr) ligand scaffolds can have a dramatic influence on alkylperoxo O-O bond lengths and the barrier to alkylperoxo O-O bond cleavage. Herein, we examine the dioxygen reactivity of a new MnII complex containing a more electron-rich, less sterically demanding NAr ligand scaffold, and compare it with previously reported MnII complexes. Dioxygen binding is shown to be reversible with complexes containing the more electron-rich metal ions. The kinetic barrier to O2 binding and peroxo O-O bond cleavage is shown to correlate with redox potentials, as well as the steric properties of the supporting NAr ligands. The reaction landscape for the dioxygen chemistry of the more electron-rich complexes is shown to be relatively flat. A total of four intermediates, including a superoxo and peroxo species, are observed with the most electron-rich complex. Two new intermediates are shown to form following the peroxo, which are capable of cleaving strong X-H bonds. In the absence of a sacrificial H atom donor, solvent, or ligand, serves as a source of H atoms. With TEMPOH as sacrificial H atom donor, a deuterium isotope effect is observed (kH/kD = 3.5), implicating a hydrogen atom transfer (HAT) mechanism. With 1,4-cyclohexadiene, 0.5 equiv of benzene is produced prior to the formation of an EPR detected MnIIIMnIV bimetallic species, and 0.5 equiv after its formation.
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Affiliation(s)
- Penny Chaau Yan Poon
- Department of Chemistry , University of Washington , Campus Box 351700 , Seattle , Washington 98195-1700 , United States
| | - Maksym A Dedushko
- Department of Chemistry , University of Washington , Campus Box 351700 , Seattle , Washington 98195-1700 , United States
| | - Xianru Sun
- Department of Chemistry , Tufts University , 62 Talbot Avenue , Medford , Massachusetts 02155 , United States
| | - Guang Yang
- Department of Chemistry , Tufts University , 62 Talbot Avenue , Medford , Massachusetts 02155 , United States
| | - Santiago Toledo
- The Department of Chemistry , St. Edward's University , 3001 South Congress , Austin , Texas 78704-6489 , United States
| | - Ellen C Hayes
- Department of Chemistry , University of Washington , Campus Box 351700 , Seattle , Washington 98195-1700 , United States
| | - Audra Johansen
- Department of Chemistry , University of Washington , Campus Box 351700 , Seattle , Washington 98195-1700 , United States
| | - Marc C Piquette
- Department of Chemistry , Tufts University , 62 Talbot Avenue , Medford , Massachusetts 02155 , United States
| | - Julian A Rees
- Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Stefan Stoll
- Department of Chemistry , University of Washington , Campus Box 351700 , Seattle , Washington 98195-1700 , United States
| | - Elena Rybak-Akimova
- Department of Chemistry , Tufts University , 62 Talbot Avenue , Medford , Massachusetts 02155 , United States
| | - Julie A Kovacs
- Department of Chemistry , University of Washington , Campus Box 351700 , Seattle , Washington 98195-1700 , United States
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31
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Class Id ribonucleotide reductase utilizes a Mn 2(IV,III) cofactor and undergoes large conformational changes on metal loading. J Biol Inorg Chem 2019; 24:863-877. [PMID: 31414238 PMCID: PMC6754362 DOI: 10.1007/s00775-019-01697-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 08/02/2019] [Indexed: 12/15/2022]
Abstract
Outside of the photosynthetic machinery, high-valent manganese cofactors are rare in biology. It was proposed that a recently discovered subclass of ribonucleotide reductase (RNR), class Id, is dependent on a Mn2(IV,III) cofactor for catalysis. Class I RNRs consist of a substrate-binding component (NrdA) and a metal-containing radical-generating component (NrdB). Herein we utilize a combination of EPR spectroscopy and enzyme assays to underscore the enzymatic relevance of the Mn2(IV,III) cofactor in class Id NrdB from Facklamia ignava. Once formed, the Mn2(IV,III) cofactor confers enzyme activity that correlates well with cofactor quantity. Moreover, we present the X-ray structure of the apo- and aerobically Mn-loaded forms of the homologous class Id NrdB from Leeuwenhoekiella blandensis, revealing a dimanganese centre typical of the subclass, with a tyrosine residue maintained at distance from the metal centre and a lysine residue projected towards the metals. Structural comparison of the apo- and metal-loaded forms of the protein reveals a refolding of the loop containing the conserved lysine and an unusual shift in the orientation of helices within a monomer, leading to the opening of a channel towards the metal site. Such major conformational changes have not been observed in NrdB proteins before. Finally, in vitro reconstitution experiments reveal that the high-valent manganese cofactor is not formed spontaneously from oxygen, but can be generated from at least two different reduced oxygen species, i.e. H2O2 and superoxide (O 2 ·- ). Considering the observed differences in the efficiency of these two activating reagents, we propose that the physiologically relevant mechanism involves superoxide.
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32
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Grāve K, Lambert W, Berggren G, Griese JJ, Bennett MD, Logan DT, Högbom M. Redox-induced structural changes in the di-iron and di-manganese forms of Bacillus anthracis ribonucleotide reductase subunit NrdF suggest a mechanism for gating of radical access. J Biol Inorg Chem 2019; 24:849-861. [PMID: 31410573 PMCID: PMC6754363 DOI: 10.1007/s00775-019-01703-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 08/06/2019] [Indexed: 12/11/2022]
Abstract
Class Ib ribonucleotide reductases (RNR) utilize a di-nuclear manganese or iron cofactor for reduction of superoxide or molecular oxygen, respectively. This generates a stable tyrosyl radical (Y·) in the R2 subunit (NrdF), which is further used for ribonucleotide reduction in the R1 subunit of RNR. Here, we report high-resolution crystal structures of Bacillus anthracis NrdF in the metal-free form (1.51 Å) and in complex with manganese (MnII/MnII, 1.30 Å). We also report three structures of the protein in complex with iron, either prepared anaerobically (FeII/FeII form, 1.32 Å), or prepared aerobically in the photo-reduced FeII/FeII form (1.63 Å) and with the partially oxidized metallo-cofactor (1.46 Å). The structures reveal significant conformational dynamics, likely to be associated with the generation, stabilization, and transfer of the radical to the R1 subunit. Based on observed redox-dependent structural changes, we propose that the passage for the superoxide, linking the FMN cofactor of NrdI and the metal site in NrdF, is closed upon metal oxidation, blocking access to the metal and radical sites. In addition, we describe the structural mechanics likely to be involved in this process.
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Affiliation(s)
- Kristīne Grāve
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 10691, Stockholm, Sweden
| | - Wietske Lambert
- PRA Health Sciences, Amerikaweg 18, 9407 TK, Assen, The Netherlands
| | - Gustav Berggren
- Department of Chemistry, Ångström Laboratory, Uppsala University, Lägerhyddsvägen 1, 75120, Uppsala, Sweden
| | - Julia J Griese
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 10691, Stockholm, Sweden.,Department of Cell and Molecular Biology, Uppsala University. BMC, Box 596, 75124, Uppsala, Sweden
| | - Matthew D Bennett
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 10691, Stockholm, Sweden
| | - Derek T Logan
- Department of Biochemistry and Structural Biology, Lund University, Box 124, 221 00, Lund, Sweden.
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 10691, Stockholm, Sweden.
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Formation of Unstable and very Reactive Chemical Species Catalyzed by Metalloenzymes: A Mechanistic Overview. Molecules 2019; 24:molecules24132462. [PMID: 31277490 PMCID: PMC6651669 DOI: 10.3390/molecules24132462] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 06/26/2019] [Accepted: 07/03/2019] [Indexed: 11/16/2022] Open
Abstract
Nature has tailored a wide range of metalloenzymes that play a vast array of functions in all living organisms and from which their survival and evolution depends on. These enzymes catalyze some of the most important biological processes in nature, such as photosynthesis, respiration, water oxidation, molecular oxygen reduction, and nitrogen fixation. They are also among the most proficient catalysts in terms of their activity, selectivity, and ability to operate at mild conditions of temperature, pH, and pressure. In the absence of these enzymes, these reactions would proceed very slowly, if at all, suggesting that these enzymes made the way for the emergence of life as we know today. In this review, the structure and catalytic mechanism of a selection of diverse metalloenzymes that are involved in the production of highly reactive and unstable species, such as hydroxide anions, hydrides, radical species, and superoxide molecules are analyzed. The formation of such reaction intermediates is very difficult to occur under biological conditions and only a rationalized selection of a particular metal ion, coordinated to a very specific group of ligands, and immersed in specific proteins allows these reactions to proceed. Interestingly, different metal coordination spheres can be used to produce the same reactive and unstable species, although through a different chemistry. A selection of hand-picked examples of different metalloenzymes illustrating this diversity is provided and the participation of different metal ions in similar reactions (but involving different mechanism) is discussed.
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Hammerstad M, Røhr ÅK, Hersleth H. A Research-inspired biochemistry laboratory module-combining expression, purification, crystallization, structure-solving, and characterization of a flavodoxin-like protein. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2019; 47:318-332. [PMID: 30742352 PMCID: PMC6594058 DOI: 10.1002/bmb.21218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 11/20/2018] [Accepted: 01/19/2019] [Indexed: 06/09/2023]
Abstract
Many laboratory courses consist of short and seemingly unconnected individual laboratory exercises. To increase the course consistency, relevance, and student engagement, we have developed a research-inspired and project-based module, "From Gene to Structure and Function". This 2.5-week full-day biochemistry and structural biology module covers protein expression, purification, structure solving, and characterization. The module is centered around the flavodoxin-like protein NrdI, involved in the activation of the bacterial ribonucleotide reductase enzyme system. Through an in-depth focus on one specific protein, the students will learn the basic laboratory skills needed in order to generate a broader knowledge and breadth within the field. With respect to generic skills, the students report their findings as a scientific article, with the aim to learn to present concise research results and write scientific papers. The current research-inspired project has the potential of being further developed into a more discovery-driven project and extended to include other molecular biological techniques or biochemical/biophysical characterizations. In student evaluations, this research-inspired laboratory course has received very high ratings and been highly appreciated, where the students have gained research experience for more independent future work in the laboratory. © 2019 The Authors. Biochemistry and Molecular Biology Education published by Wiley Periodicals, Inc. on behalf of International Union of Biochemistry and Molecular Biology, 47(3):318-332, 2019.
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Affiliation(s)
- Marta Hammerstad
- Department of Biosciences, Section for Biochemistry and Molecular BiologyUniversity of OsloNO‐0316 OsloNorway
| | - Åsmund K. Røhr
- Department of Chemistry, Biotechnology and Food ScienceNorwegian University of Life SciencesNO‐1432 ÅsNorway
| | - Hans‐Petter Hersleth
- Department of Biosciences, Section for Biochemistry and Molecular BiologyUniversity of OsloNO‐0316 OsloNorway
- Department of Chemistry, Section for Chemical Life SciencesUniversity of OsloNO‐0315 OsloNorway
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Rose HR, Maggiolo AO, McBride MJ, Palowitch GM, Pandelia ME, Davis KM, Yennawar NH, Boal AK. Structures of Class Id Ribonucleotide Reductase Catalytic Subunits Reveal a Minimal Architecture for Deoxynucleotide Biosynthesis. Biochemistry 2019; 58:1845-1860. [PMID: 30855138 PMCID: PMC6456427 DOI: 10.1021/acs.biochem.8b01252] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Class I ribonucleotide reductases (RNRs) share a common mechanism of nucleotide reduction in a catalytic α subunit. All RNRs initiate catalysis with a thiyl radical, generated in class I enzymes by a metallocofactor in a separate β subunit. Class Id RNRs use a simple mechanism of cofactor activation involving oxidation of a MnII2 cluster by free superoxide to yield a metal-based MnIIIMnIV oxidant. This simple cofactor assembly pathway suggests that class Id RNRs may be representative of the evolutionary precursors to more complex class Ia-c enzymes. X-ray crystal structures of two class Id α proteins from Flavobacterium johnsoniae ( Fj) and Actinobacillus ureae ( Au) reveal that this subunit is distinctly small. The enzyme completely lacks common N-terminal ATP-cone allosteric motifs that regulate overall activity, a process that normally occurs by dATP-induced formation of inhibitory quaternary structures to prevent productive β subunit association. Class Id RNR activity is insensitive to dATP in the Fj and Au enzymes evaluated here, as expected. However, the class Id α protein from Fj adopts higher-order structures, detected crystallographically and in solution. The Au enzyme does not exhibit these quaternary forms. Our study reveals structural similarity between bacterial class Id and eukaryotic class Ia α subunits in conservation of an internal auxiliary domain. Our findings with the Fj enzyme illustrate that nucleotide-independent higher-order quaternary structures can form in simple RNRs with truncated or missing allosteric motifs.
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Affiliation(s)
- Hannah R. Rose
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
| | - Ailiena O. Maggiolo
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
| | - Molly J. McBride
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
| | - Gavin M. Palowitch
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
| | | | - Katherine M. Davis
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
| | - Neela H. Yennawar
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Amie K. Boal
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
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Magherusan AM, Kal S, Nelis DN, Doyle LM, Farquhar ER, Que L, McDonald AR. A Mn II Mn III -Peroxide Complex Capable of Aldehyde Deformylation. Angew Chem Int Ed Engl 2019; 58:5718-5722. [PMID: 30830996 DOI: 10.1002/anie.201900717] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 02/27/2019] [Indexed: 11/07/2022]
Abstract
Ribonucleotide reductases (RNRs) are essential enzymes required for DNA synthesis. In class Ib Mn2 RNRs superoxide (O2 .- ) was postulated to react with the MnII 2 core to yield a MnII MnIII -peroxide moiety. The reactivity of complex 1 ([MnII 2 (O2 CCH3 )2 (BPMP)](ClO4 ), where HBPMP=2,6-bis{[(bis(2-pyridylmethyl)amino]methyl}-4-methylphenol) towards O2 .- was investigated at -90 °C, generating a metastable species, 2. The electronic absorption spectrum of 2 displayed features (λmax =440, 590 nm) characteristic of a MnII MnIII -peroxide species, representing just the second example of such. Electron paramagnetic resonance and X-ray absorption spectroscopies, and mass spectrometry supported the formulation of 2 as a MnII MnIII -peroxide complex. Unlike all other previously reported Mn2 -peroxides, which were unreactive, 2 proved to be a capable oxidant in aldehyde deformylation. Our studies provide insight into the mechanism of O2 -activation in Class Ib Mn2 RNRs, and the highly reactive intermediates in their catalytic cycle.
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Affiliation(s)
- Adriana M Magherusan
- School of Chemistry, Trinity College Dublin, The University of Dublin, College Green, Dublin 2, Ireland
| | - Subhasree Kal
- Department of Chemistry and Centre for Metals in Biocatalysis, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN, 55455, USA
| | - Daniel N Nelis
- School of Chemistry, Trinity College Dublin, The University of Dublin, College Green, Dublin 2, Ireland
| | - Lorna M Doyle
- School of Chemistry, Trinity College Dublin, The University of Dublin, College Green, Dublin 2, Ireland
| | - Erik R Farquhar
- Case Western Reserve University Centre for Synchrotron Biosciences, National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Lawrence Que
- Department of Chemistry and Centre for Metals in Biocatalysis, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN, 55455, USA
| | - Aidan R McDonald
- School of Chemistry, Trinity College Dublin, The University of Dublin, College Green, Dublin 2, Ireland
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Harrison AO, Moore RM, Polson SW, Wommack KE. Reannotation of the Ribonucleotide Reductase in a Cyanophage Reveals Life History Strategies Within the Virioplankton. Front Microbiol 2019; 10:134. [PMID: 30804913 PMCID: PMC6370689 DOI: 10.3389/fmicb.2019.00134] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 01/21/2019] [Indexed: 01/16/2023] Open
Abstract
Ribonucleotide reductases (RNRs) are ancient enzymes that catalyze the reduction of ribonucleotides to deoxyribonucleotides. They are required for virtually all cellular life and are prominent within viral genomes. RNRs share a common ancestor and must generate a protein radical for direct ribonucleotide reduction. The mechanisms by which RNRs produce radicals are diverse and divide RNRs into three major classes and several subclasses. The diversity of radical generation methods means that cellular organisms and viruses typically contain the RNR best-suited to the environmental conditions surrounding DNA replication. However, such diversity has also fostered high rates of RNR misannotation within subject sequence databases. These misannotations have resulted in incorrect translative presumptions of RNR biochemistry and have diminished the utility of this marker gene for ecological studies of viruses. We discovered a misannotation of the RNR gene within the Prochlorococcus phage P-SSP7 genome, which caused a chain of misannotations within commonly observed RNR genes from marine virioplankton communities. These RNRs are found in marine cyanopodo- and cyanosiphoviruses and are currently misannotated as Class II RNRs, which are O2-independent and require cofactor B12. In fact, these cyanoviral RNRs are Class I enzymes that are O2-dependent and may require a di-metal cofactor made of Fe, Mn, or a combination of the two metals. The discovery of an overlooked Class I β subunit in the P-SSP7 genome, together with phylogenetic analysis of the α and β subunits confirms that the RNR from P-SSP7 is a Class I RNR. Phylogenetic and conserved residue analyses also suggest that the P-SSP7 RNR may constitute a novel Class I subclass. The reannotation of the RNR clade represented by P-SSP7 means that most lytic cyanophage contain Class I RNRs, while their hosts, B12-producing Synechococcus and Prochlorococcus, contain Class II RNRs. By using a Class I RNR, cyanophage avoid a dependence on host-produced B12, a more effective strategy for a lytic virus. The discovery of a novel RNR β subunit within cyanopodoviruses also implies that some unknown viral genes may be familiar cellular genes that are too divergent for homology-based annotation methods to identify.
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Affiliation(s)
- Amelia O. Harrison
- School of Marine Science and Policy, University of Delaware, Newark, DE, United States
| | - Ryan M. Moore
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, United States
| | - Shawn W. Polson
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, United States
| | - K. Eric Wommack
- School of Marine Science and Policy, University of Delaware, Newark, DE, United States
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Griese JJ, Kositzki R, Haumann M, Högbom M. Assembly of a heterodinuclear Mn/Fe cofactor is coupled to tyrosine-valine ether cross-link formation in the R2-like ligand-binding oxidase. J Biol Inorg Chem 2019; 24:211-221. [PMID: 30689052 PMCID: PMC6399176 DOI: 10.1007/s00775-019-01639-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 01/18/2019] [Indexed: 11/28/2022]
Abstract
R2-like ligand-binding oxidases (R2lox) assemble a heterodinuclear Mn/Fe cofactor which performs reductive dioxygen (O2) activation, catalyzes formation of a tyrosine-valine ether cross-link in the protein scaffold, and binds a fatty acid in a putative substrate channel. We have previously shown that the N-terminal metal binding site 1 is unspecific for manganese or iron in the absence of O2, but prefers manganese in the presence of O2, whereas the C-terminal site 2 is specific for iron. Here, we analyze the effects of amino acid exchanges in the cofactor environment on cofactor assembly and metalation specificity using X-ray crystallography, X-ray absorption spectroscopy, and metal quantification. We find that exchange of either the cross-linking tyrosine or the valine, regardless of whether the mutation still allows cross-link formation or not, results in unspecific manganese or iron binding at site 1 both in the absence or presence of O2, while site 2 still prefers iron as in the wild-type. In contrast, a mutation that blocks binding of the fatty acid does not affect the metal specificity of either site under anoxic or aerobic conditions, and cross-link formation is still observed. All variants assemble a dinuclear trivalent metal cofactor in the aerobic resting state, independently of cross-link formation. These findings imply that the cross-link residues are required to achieve the preference for manganese in site 1 in the presence of O2. The metalation specificity, therefore, appears to be established during the redox reactions leading to cross-link formation.
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Affiliation(s)
- Julia J Griese
- Department of Biochemistry and Biophysics, Stockholm University, 106 91, Stockholm, Sweden. .,Department of Cell and Molecular Biology, Uppsala University, 751 24, Uppsala, Sweden.
| | - Ramona Kositzki
- Institut für Experimentalphysik, Freie Universität Berlin, 14195, Berlin, Germany
| | - Michael Haumann
- Institut für Experimentalphysik, Freie Universität Berlin, 14195, Berlin, Germany
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, 106 91, Stockholm, Sweden.
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Lee Y, Jackson TA. Ligand Influence on Structural Properties and Reactivity of Bis(μ-oxo)dimanganese(III,IV) Species and Comparison of Reactivity with Terminal MnIV
-oxo Complexes. ChemistrySelect 2018. [DOI: 10.1002/slct.201803668] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yuri Lee
- Department of Chemistry; The University of Kansas, 1567; Irving Hill Road Lawrence KS 66045 USA
| | - Timothy A. Jackson
- Department of Chemistry; The University of Kansas, 1567; Irving Hill Road Lawrence KS 66045 USA
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Srinivas V, Lebrette H, Lundin D, Kutin Y, Sahlin M, Lerche M, Eirich J, Branca RMM, Cox N, Sjöberg BM, Högbom M. Metal-free ribonucleotide reduction powered by a DOPA radical in Mycoplasma pathogens. Nature 2018; 563:416-420. [PMID: 30429545 PMCID: PMC6317698 DOI: 10.1038/s41586-018-0653-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 08/22/2018] [Indexed: 12/14/2022]
Abstract
Ribonucleotide reductase (RNR) catalyses the only known de novo pathway for the production of all four deoxyribonucleotides that are required for DNA synthesis1,2. It is essential for all organisms that use DNA as their genetic material and is a current drug target3,4. Since the discovery that iron is required for function in the aerobic, class I RNR found in all eukaryotes and many bacteria, a dinuclear metal site has been viewed as necessary to generate and stabilize the catalytic radical that is essential for RNR activity5-7. Here we describe a group of RNR proteins in Mollicutes-including Mycoplasma pathogens-that possess a metal-independent stable radical residing on a modified tyrosyl residue. Structural, biochemical and spectroscopic characterization reveal a stable 3,4-dihydroxyphenylalanine (DOPA) radical species that directly supports ribonucleotide reduction in vitro and in vivo. This observation overturns the presumed requirement for a dinuclear metal site in aerobic ribonucleotide reductase. The metal-independent radical requires new mechanisms for radical generation and stabilization, processes that are targeted by RNR inhibitors. It is possible that this RNR variant provides an advantage under metal starvation induced by the immune system. Organisms that encode this type of RNR-some of which are developing resistance to antibiotics-are involved in diseases of the respiratory, urinary and genital tracts. Further characterization of this RNR family and its mechanism of cofactor generation will provide insight into new enzymatic chemistry and be of value in devising strategies to combat the pathogens that utilize it. We propose that this RNR subclass is denoted class Ie.
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Affiliation(s)
- Vivek Srinivas
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
| | - Hugo Lebrette
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
| | - Daniel Lundin
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
| | - Yuri Kutin
- Max Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Mülheim an der Ruhr, Germany
| | - Margareta Sahlin
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
| | - Michael Lerche
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
| | - Jürgen Eirich
- Cancer Proteomics Mass Spectrometry, Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Solna, Sweden
| | - Rui M M Branca
- Cancer Proteomics Mass Spectrometry, Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Solna, Sweden
| | - Nicholas Cox
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Britt-Marie Sjöberg
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden.
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
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Rozman Grinberg I, Lundin D, Sahlin M, Crona M, Berggren G, Hofer A, Sjöberg BM. A glutaredoxin domain fused to the radical-generating subunit of ribonucleotide reductase (RNR) functions as an efficient RNR reductant. J Biol Chem 2018; 293:15889-15900. [PMID: 30166338 PMCID: PMC6187632 DOI: 10.1074/jbc.ra118.004991] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 08/27/2018] [Indexed: 01/08/2023] Open
Abstract
Class I ribonucleotide reductase (RNR) consists of a catalytic subunit (NrdA) and a radical-generating subunit (NrdB) that together catalyze reduction of ribonucleotides to their corresponding deoxyribonucleotides. NrdB from the firmicute Facklamia ignava is a unique fusion protein with N-terminal add-ons of a glutaredoxin (Grx) domain followed by an ATP-binding domain, the ATP cone. Grx, usually encoded separately from the RNR operon, is a known RNR reductant. We show that the fused Grx domain functions as an efficient reductant of the F. ignava class I RNR via the common dithiol mechanism and, interestingly, also via a monothiol mechanism, although less efficiently. To our knowledge, a Grx that uses both of these two reaction mechanisms has not previously been observed with a native substrate. The ATP cone is in most RNRs an N-terminal domain of the catalytic subunit. It is an allosteric on/off switch promoting ribonucleotide reduction in the presence of ATP and inhibiting RNR activity in the presence of dATP. We found that dATP bound to the ATP cone of F. ignava NrdB promotes formation of tetramers that cannot form active complexes with NrdA. The ATP cone bound two dATP molecules but only one ATP molecule. F. ignava NrdB contains the recently identified radical-generating cofactor MnIII/MnIV We show that NrdA from F. ignava can form a catalytically competent RNR with the MnIII/MnIV-containing NrdB from the flavobacterium Leeuwenhoekiella blandensis In conclusion, F. ignava NrdB is fused with a Grx functioning as an RNR reductant and an ATP cone serving as an on/off switch.
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Affiliation(s)
- Inna Rozman Grinberg
- From the Department of Biochemistry and Biophysics, Stockholm University SE-10691 Stockholm, Sweden
| | - Daniel Lundin
- From the Department of Biochemistry and Biophysics, Stockholm University SE-10691 Stockholm, Sweden
| | - Margareta Sahlin
- From the Department of Biochemistry and Biophysics, Stockholm University SE-10691 Stockholm, Sweden
| | - Mikael Crona
- From the Department of Biochemistry and Biophysics, Stockholm University SE-10691 Stockholm, Sweden
- the Swedish Orphan Biovitrum AB, SE-112 76 Stockholm, Sweden
| | - Gustav Berggren
- the Department of Chemistry, Uppsala University, SE-752 36 Uppsala, Sweden, and
| | - Anders Hofer
- the Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden
| | - Britt-Marie Sjöberg
- From the Department of Biochemistry and Biophysics, Stockholm University SE-10691 Stockholm, Sweden,
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Denler MC, Wijeratne GB, Rice DB, Colmer HE, Day VW, Jackson TA. Mn III-Peroxo adduct supported by a new tetradentate ligand shows acid-sensitive aldehyde deformylation reactivity. Dalton Trans 2018; 47:13442-13458. [PMID: 30183042 PMCID: PMC6176719 DOI: 10.1039/c8dt02300j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The new tetradentate L7BQ ligand (L7BQ = 1,4-di(quinoline-8-yl)-1,4-diazepane) has been synthesized and shown to support MnII and MnIII-peroxo complexes. X-ray crystallography of the [MnII(L7BQ)(OTf)2] complex shows a monomeric MnII center with the L7BQ ligand providing four donor nitrogen atoms in the equatorial field, with two triflate ions bound in the axial positions. When this species is treated with H2O2 and Et3N at -40 °C, a MnIII-peroxo adduct, [MnIII(O2)(L7BQ)]+ is formed. The formation of this new intermediate is supported by a variety of spectroscopic techniques, including electronic absorption, Mn K-edge X-ray absorption and electron paramagnetic resonance methods. Evaluation of extended X-ray absorption fine structure data for [MnIII(O2)(L7BQ)]+ resolved Mn-O bond distances of 1.85 Å, which are on the short end of those previously reported for crystallographically characterized MnIII-peroxo adducts. An analysis of the X-ray pre-edge region of [MnIII(O2)(L7BQ)]+ revealed a large pre-edge area of 20.8 units. Time-dependent density functional theory computations indicate that the pre-edge intensity is due to Mn 4p-3d mixing caused by geometric distortions from centrosymmetry induced by both the peroxo and L7BQ ligands. The reactivity of [MnIII(O2)(L7BQ)]+ towards aldehydes was assessed through reaction with cyclohexanecarboxaldehyde and 2-phenylpropionaldehyde. From these experiments, it was determined that [MnIII(O2)(L7BQ)]+ only reacts with aldehydes in the presence of acid. Specifically, the addition of cyclohexanecarboxylic acid to [MnIII(O2)(L7BQ)]+ converts the MnIII-peroxo adduct to a new intermediate that could be responsible for the observed aldehyde deformylation activity. These observations underscore the challenges in identifying the reactive metal species in aldehyde deformylation reactions.
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Affiliation(s)
- Melissa C Denler
- The University of Kansas, Department of Chemistry and Center for Environmentally Beneficial Catalysis, 1251 Wescoe Hall Drive, Lawrence, KS 66045, USA.
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Metal-free class Ie ribonucleotide reductase from pathogens initiates catalysis with a tyrosine-derived dihydroxyphenylalanine radical. Proc Natl Acad Sci U S A 2018; 115:10022-10027. [PMID: 30224458 PMCID: PMC6176560 DOI: 10.1073/pnas.1811993115] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Conversion of ribonucleotides to the 2′-deoxyribonucleotides required for DNA biosynthesis is catalyzed by ribonucleotide reductases (RNRs) via a free-radical mechanism. Known types of RNRs all depend on redox-active transition metals—manganese, iron, or cobalt—for radical initiation. Pathogenic bacteria are challenged by transition metal sequestration and infliction of oxidative stress by their hosts, and the deployment of multiple RNRs with different metal requirements and radical-initiating oxidants is a known bacterial countermeasure. A class I RNR from two bacterial pathogens completely lacks transition metals in its active state and uses a tyrosine-derived dihydroxyphenylalanine radical as its initiator, embodying a novel tactic to combat transition metal- and oxidant-mediated innate immunity and reinforcing bacterial RNRs as potential antibiotic targets. All cells obtain 2′-deoxyribonucleotides for DNA synthesis through the activity of a ribonucleotide reductase (RNR). The class I RNRs found in humans and pathogenic bacteria differ in (i) use of Fe(II), Mn(II), or both for activation of the dinuclear-metallocofactor subunit, β; (ii) reaction of the reduced dimetal center with dioxygen or superoxide for this activation; (iii) requirement (or lack thereof) for a flavoprotein activase, NrdI, to provide the superoxide from O2; and (iv) use of either a stable tyrosyl radical or a high-valent dimetal cluster to initiate each turnover by oxidizing a cysteine residue in the α subunit to a radical (Cys•). The use of manganese by bacterial class I, subclass b-d RNRs, which contrasts with the exclusive use of iron by the eukaryotic Ia enzymes, appears to be a countermeasure of certain pathogens against iron deprivation imposed by their hosts. Here, we report a metal-free type of class I RNR (subclass e) from two human pathogens. The Cys• in its α subunit is generated by a stable, tyrosine-derived dihydroxyphenylalanine radical (DOPA•) in β. The three-electron oxidation producing DOPA• occurs in Escherichia coli only if the β is coexpressed with the NrdI activase encoded adjacently in the pathogen genome. The independence of this new RNR from transition metals, or the requirement for a single metal ion only transiently for activation, may afford the pathogens an even more potent countermeasure against transition metal-directed innate immunity.
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Syiemlieh I, Kumar A, Kurbah SD, Lal RA. Synthesis, characterization and structure assessment of mononuclear and binuclear low-spin manganese(II) complexes derived from oxaloyldihydrazones, 1,10-phenanthroline and 2,2′-bipyridine. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.04.043] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Parker MJ, Maggiolo AO, Thomas WC, Kim A, Meisburger SP, Ando N, Boal AK, Stubbe J. An endogenous dAMP ligand in Bacillus subtilis class Ib RNR promotes assembly of a noncanonical dimer for regulation by dATP. Proc Natl Acad Sci U S A 2018; 115:E4594-E4603. [PMID: 29712847 PMCID: PMC5960316 DOI: 10.1073/pnas.1800356115] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The high fidelity of DNA replication and repair is attributable, in part, to the allosteric regulation of ribonucleotide reductases (RNRs) that maintains proper deoxynucleotide pool sizes and ratios in vivo. In class Ia RNRs, ATP (stimulatory) and dATP (inhibitory) regulate activity by binding to the ATP-cone domain at the N terminus of the large α subunit and altering the enzyme's quaternary structure. Class Ib RNRs, in contrast, have a partial cone domain and have generally been found to be insensitive to dATP inhibition. An exception is the Bacillus subtilis Ib RNR, which we recently reported to be inhibited by physiological concentrations of dATP. Here, we demonstrate that the α subunit of this RNR contains tightly bound deoxyadenosine 5'-monophosphate (dAMP) in its N-terminal domain and that dATP inhibition of CDP reduction is enhanced by its presence. X-ray crystallography reveals a previously unobserved (noncanonical) α2 dimer with its entire interface composed of the partial N-terminal cone domains, each binding a dAMP molecule. Using small-angle X-ray scattering (SAXS), we show that this noncanonical α2 dimer is the predominant form of the dAMP-bound α in solution and further show that addition of dATP leads to the formation of larger oligomers. Based on this information, we propose a model to describe the mechanism by which the noncanonical α2 inhibits the activity of the B. subtilis Ib RNR in a dATP- and dAMP-dependent manner.
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Affiliation(s)
- Mackenzie J Parker
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Ailiena O Maggiolo
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
| | - William C Thomas
- Department of Chemistry, Princeton University, Princeton, NJ 08544
| | - Albert Kim
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | | | - Nozomi Ando
- Department of Chemistry, Princeton University, Princeton, NJ 08544;
| | - Amie K Boal
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802;
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
| | - JoAnne Stubbe
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139;
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
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Rose HR, Ghosh MK, Maggiolo AO, Pollock CJ, Blaesi EJ, Hajj V, Wei Y, Rajakovich LJ, Chang WC, Han Y, Hajj M, Krebs C, Silakov A, Pandelia ME, Bollinger JM, Boal AK. Structural Basis for Superoxide Activation of Flavobacterium johnsoniae Class I Ribonucleotide Reductase and for Radical Initiation by Its Dimanganese Cofactor. Biochemistry 2018; 57:2679-2693. [PMID: 29609464 DOI: 10.1021/acs.biochem.8b00247] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A ribonucleotide reductase (RNR) from Flavobacterium johnsoniae ( Fj) differs fundamentally from known (subclass a-c) class I RNRs, warranting its assignment to a new subclass, Id. Its β subunit shares with Ib counterparts the requirements for manganese(II) and superoxide (O2-) for activation, but it does not require the O2--supplying flavoprotein (NrdI) needed in Ib systems, instead scavenging the oxidant from solution. Although Fj β has tyrosine at the appropriate sequence position (Tyr 104), this residue is not oxidized to a radical upon activation, as occurs in the Ia/b proteins. Rather, Fj β directly deploys an oxidized dimanganese cofactor for radical initiation. In treatment with one-electron reductants, the cofactor can undergo cooperative three-electron reduction to the II/II state, in contrast to the quantitative univalent reduction to inactive "met" (III/III) forms seen with I(a-c) βs. This tendency makes Fj β unusually robust, as the II/II form can readily be reactivated. The structure of the protein rationalizes its distinctive traits. A distortion in a core helix of the ferritin-like architecture renders the active site unusually open, introduces a cavity near the cofactor, and positions a subclass-d-specific Lys residue to shepherd O2- to the Mn2II/II cluster. Relative to the positions of the radical tyrosines in the Ia/b proteins, the unreactive Tyr 104 of Fj β is held away from the cofactor by a hydrogen bond with a subclass-d-specific Thr residue. Structural comparisons, considered with its uniquely simple mode of activation, suggest that the Id protein might most closely resemble the primordial RNR-β.
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Affiliation(s)
| | | | | | | | | | | | - Yifeng Wei
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | | | | | | | | | | | | | - Maria-Eirini Pandelia
- Department of Biochemistry , Brandeis University , Waltham , Massachusetts 02454 , United States
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48
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Rozman Grinberg I, Lundin D, Hasan M, Crona M, Jonna VR, Loderer C, Sahlin M, Markova N, Borovok I, Berggren G, Hofer A, Logan DT, Sjöberg BM. Novel ATP-cone-driven allosteric regulation of ribonucleotide reductase via the radical-generating subunit. eLife 2018; 7:31529. [PMID: 29388911 PMCID: PMC5794259 DOI: 10.7554/elife.31529] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Accepted: 12/23/2017] [Indexed: 12/27/2022] Open
Abstract
Ribonucleotide reductases (RNRs) are key enzymes in DNA metabolism, with allosteric mechanisms controlling substrate specificity and overall activity. In RNRs, the activity master-switch, the ATP-cone, has been found exclusively in the catalytic subunit. In two class I RNR subclasses whose catalytic subunit lacks the ATP-cone, we discovered ATP-cones in the radical-generating subunit. The ATP-cone in the Leeuwenhoekiella blandensis radical-generating subunit regulates activity via quaternary structure induced by binding of nucleotides. ATP induces enzymatically competent dimers, whereas dATP induces non-productive tetramers, resulting in different holoenzymes. The tetramer forms by interactions between ATP-cones, shown by a 2.45 Å crystal structure. We also present evidence for an MnIIIMnIV metal center. In summary, lack of an ATP-cone domain in the catalytic subunit was compensated by transfer of the domain to the radical-generating subunit. To our knowledge, this represents the first observation of transfer of an allosteric domain between components of the same enzyme complex. When a cell copies its DNA, it uses four different building blocks called deoxyribonucleotides (dNTPs). These consist of one of the four ‘bases’ (A, T, C and G), which pair up to link the two strands of DNA in the double helix, bound to a sugar and a phosphate group. If the cell contains too little or too much of one of these building blocks, an incorrect base may be inserted into the DNA. This results in a mutation, which in bacteria can cause death, and in animals may lead to cancer. The enzyme that fabricates and carefully controls the amount of each dNTP building block inside a cell is called ribonucleotide reductase. Once there are enough building blocks in a cell the enzyme is turned off. A part of the enzyme called the ATP-cone acts as an on/off switch to control this activity. The ribonucleotide reductase consists of a large component and a small component. Until now, studies of the ATP-cone have found it only in the large component of the enzyme. However, when looking through a public database of sequence data, Rozman Grinberg et al. noticed that ribonucleotide reductases in some bacteria have their ATP-cone joined to the small component. Does this ATP-cone also control the amounts of dNTP building blocks inside cells and, if so, how? Rozman Grinberg et al. studied one such ATP-cone in a ribonucleotide reductase from a bacterium (named Leeuwenhoekiella blandensis) found in the Mediterranean Sea. This revealed that when the amount of dNTP building blocks reaches a certain limit, the ATP-cone turns off the enzyme. Examining the three-dimensional structure of the enzyme using a technique called X-ray crystallography revealed that when turned off, the enzyme’s small components are glued together in pairs. This prevents them from working. Rozman Grinberg et al. also discovered that this enzyme contains a new type of metal center with two manganese ions suggesting that a new reaction mechanism may operate in this class of ribonucleotide reductase. These findings support a theory that biological on/off switches can evolve rapidly. In addition to its evolutionary and biomedical interest, understanding how the ATP-cone works might help to improve the enzymes used in industrial processes.
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Affiliation(s)
- Inna Rozman Grinberg
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Daniel Lundin
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Mahmudul Hasan
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.,Department of Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | | | | | - Christoph Loderer
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Margareta Sahlin
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | | | - Ilya Borovok
- Department of Molecular Microbiology and Biotechnology, Tel-Aviv University, Tel Aviv-Yafo, Israel
| | - Gustav Berggren
- Department of Chemistry, Uppsala University, Uppsala, Sweden
| | - Anders Hofer
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Derek T Logan
- Department of Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | - Britt-Marie Sjöberg
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
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49
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Magherusan AM, Zhou A, Farquhar ER, García-Melchor M, Twamley B, Que L, McDonald AR. Mimicking Class I b Mn 2 -Ribonucleotide Reductase: A Mn II2 Complex and Its Reaction with Superoxide. Angew Chem Int Ed Engl 2017; 57:918-922. [PMID: 29165865 DOI: 10.1002/anie.201709806] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 11/02/2017] [Indexed: 02/05/2023]
Abstract
A fascinating discovery in the chemistry of ribonucleotide reductases (RNRs) has been the identification of a dimanganese (Mn2 ) active site in class I b RNRs that requires superoxide anion (O2.- ), rather than dioxygen (O2 ), to access a high-valent Mn2 oxidant. Complex 1 ([Mn2 (O2 CCH3 )(N-Et-HPTB)](ClO4 )2 , N-Et-HPTB=N,N,N',N'-tetrakis(2-(1-ethylbenzimidazolyl))-2-hydroxy-1,3-diaminopropane) was synthesised in high yield (90 %). 1 was reacted with O2.- at -40 °C resulting in the formation of a metastable species (2). 2 displayed electronic absorption features (λmax =460, 610 nm) typical of a Mn-peroxide species and a 29-line EPR signal typical of a MnII MnIII entity. Mn K-edge X-ray absorption near-edge spectroscopy (XANES) suggested a formal oxidation state change of MnII2 in 1 to MnII MnIII for 2. Electrospray ionisation mass spectrometry (ESI-MS) suggested 2 to be a MnII MnIII -peroxide complex. 2 was capable of oxidizing ferrocene and weak O-H bonds upon activation with proton donors. Our findings provide support for the postulated mechanism of O2.- activation at class I b Mn2 RNRs.
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Affiliation(s)
- Adriana M Magherusan
- School of Chemistry and CRANN/AMBER Nanoscience Institute, Trinity College Dublin, The University of Dublin, College Green, Dublin 2, Ireland
| | - Ang Zhou
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN, 55455, USA
| | - Erik R Farquhar
- Case Western Reserve University Center for Synchrotron Biosciences, National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Max García-Melchor
- School of Chemistry and CRANN/AMBER Nanoscience Institute, Trinity College Dublin, The University of Dublin, College Green, Dublin 2, Ireland
| | - Brendan Twamley
- School of Chemistry and CRANN/AMBER Nanoscience Institute, Trinity College Dublin, The University of Dublin, College Green, Dublin 2, Ireland
| | - Lawrence Que
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN, 55455, USA
| | - Aidan R McDonald
- School of Chemistry and CRANN/AMBER Nanoscience Institute, Trinity College Dublin, The University of Dublin, College Green, Dublin 2, Ireland
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50
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Magherusan AM, Zhou A, Farquhar ER, García-Melchor M, Twamley B, Que L, McDonald AR. Mimicking Class I b Mn2
-Ribonucleotide Reductase: A MnII
2
Complex and Its Reaction with Superoxide. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201709806] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Adriana M. Magherusan
- School of Chemistry and CRANN/AMBER Nanoscience Institute; Trinity College Dublin; The University of Dublin; College Green Dublin 2 Ireland
| | - Ang Zhou
- Department of Chemistry and Center for Metals in Biocatalysis; University of Minnesota; 207 Pleasant St. SE Minneapolis MN 55455 USA
| | - Erik R. Farquhar
- Case Western Reserve University Center for Synchrotron Biosciences; National Synchrotron Light Source II, Brookhaven National Laboratory; Upton NY 11973 USA
| | - Max García-Melchor
- School of Chemistry and CRANN/AMBER Nanoscience Institute; Trinity College Dublin; The University of Dublin; College Green Dublin 2 Ireland
| | - Brendan Twamley
- School of Chemistry and CRANN/AMBER Nanoscience Institute; Trinity College Dublin; The University of Dublin; College Green Dublin 2 Ireland
| | - Lawrence Que
- Department of Chemistry and Center for Metals in Biocatalysis; University of Minnesota; 207 Pleasant St. SE Minneapolis MN 55455 USA
| | - Aidan R. McDonald
- School of Chemistry and CRANN/AMBER Nanoscience Institute; Trinity College Dublin; The University of Dublin; College Green Dublin 2 Ireland
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