1
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Brunclik SA, Grotemeyer EN, Aghaei Z, Mian MR, Jackson TA. Investigating Ligand Sphere Perturbations on Mn III-Alkylperoxo Complexes. Molecules 2024; 29:1849. [PMID: 38675669 PMCID: PMC11053420 DOI: 10.3390/molecules29081849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
Manganese catalysts that activate hydrogen peroxide carry out several different hydrocarbon oxidation reactions with high stereoselectivity. The commonly proposed mechanism for these reactions involves a key manganese(III)-hydroperoxo intermediate, which decays via O-O bond heterolysis to generate a Mn(V)-oxo species that institutes substrate oxidation. Due to the scarcity of characterized MnIII-hydroperoxo complexes, MnIII-alkylperoxo complexes are employed to understand factors that affect the mechanism of the O-O cleavage. Herein, we report a series of novel complexes, including two room-temperature-stable MnIII-alkylperoxo species, supported by a new amide-containing pentadentate ligand (6Medpaq5NO2). We use a combination of spectroscopic methods and density functional theory computations to probe the effects of the electronic changes in the ligand sphere trans to the hydroxo and alkylperoxo units to thermal stability and reactivity. The structural characterizations for both MnII(OTf)(6Medpaq5NO2) and [MnIII(OH)(6Medpaq5NO2)](OTf) were obtained via single-crystal X-ray crystallography. A perturbation to the ligand sphere allowed for a marked increase in reactivity towards an organic substrate, a modest change in the distribution of the O-O cleavage products from homolytic and heterolytic pathways, and little change in thermal stability.
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Affiliation(s)
- Samuel A. Brunclik
- Department of Chemistry and Center for Environmentally Beneficial Catalysis, University of Kansas, Lawrence, KS 66045, USA; (S.A.B.); (E.N.G.); (Z.A.)
| | - Elizabeth N. Grotemeyer
- Department of Chemistry and Center for Environmentally Beneficial Catalysis, University of Kansas, Lawrence, KS 66045, USA; (S.A.B.); (E.N.G.); (Z.A.)
| | - Zahra Aghaei
- Department of Chemistry and Center for Environmentally Beneficial Catalysis, University of Kansas, Lawrence, KS 66045, USA; (S.A.B.); (E.N.G.); (Z.A.)
| | - Mohammad Rasel Mian
- Protein Structure and X-ray Crystallography Laboratory, University of Kansas, Lawrence, KS 66045, USA;
| | - Timothy A. Jackson
- Department of Chemistry and Center for Environmentally Beneficial Catalysis, University of Kansas, Lawrence, KS 66045, USA; (S.A.B.); (E.N.G.); (Z.A.)
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2
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Powell M, Rao G, Britt RD, Rittle J. Enzymatic Hydroxylation of Aliphatic C-H Bonds by a Mn/Fe Cofactor. J Am Chem Soc 2023; 145:16526-16537. [PMID: 37471626 PMCID: PMC10401708 DOI: 10.1021/jacs.3c03419] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Indexed: 07/22/2023]
Abstract
The aerobic oxidation of carbon-hydrogen (C-H) bonds in biology is currently known to be accomplished by a limited set of cofactors that typically include heme, nonheme iron, and copper. While manganese cofactors perform difficult oxidation reactions, including water oxidation within Photosystem II, they are generally not known to be used for C-H bond activation, and those that do catalyze this important reaction display limited intrinsic reactivity. Here we report that the 2-aminoisobutyric acid hydroxylase from Rhodococcus wratislaviensis, AibH1H2, requires manganese to functionalize a strong, aliphatic C-H bond (BDE = 100 kcal/mol). Structural and spectroscopic studies of this enzyme reveal a redox-active, heterobimetallic manganese-iron active site at the locus of O2 activation and substrate coordination. This result expands the known reactivity of biological manganese-iron cofactors, which was previously restricted to single-electron transfer or stoichiometric protein oxidation. Furthermore, the AibH1H2 cofactor is supported by a protein fold distinct from typical bimetallic oxygenases, and bioinformatic analyses identify related proteins abundant in microorganisms. This suggests that many uncharacterized monooxygenases may similarly require manganese to perform oxidative biochemical tasks.
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Affiliation(s)
- Magan
M. Powell
- Department
of Chemistry, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Guodong Rao
- Department
of Chemistry, University of California,
Davis, Davis, California 95616, United States
| | - R. David Britt
- Department
of Chemistry, University of California,
Davis, Davis, California 95616, United States
| | - Jonathan Rittle
- Department
of Chemistry, University of California,
Berkeley, Berkeley, California 94720, United States
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3
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Hammerstad M, Rugtveit AK, Dahlen S, Andersen HK, Hersleth HP. Functional Diversity of Homologous Oxidoreductases-Tuning of Substrate Specificity by a FAD-Stacking Residue for Iron Acquisition and Flavodoxin Reduction. Antioxidants (Basel) 2023; 12:1224. [PMID: 37371954 DOI: 10.3390/antiox12061224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023] Open
Abstract
Although bacterial thioredoxin reductase-like ferredoxin/flavodoxin NAD(P)+ oxidoreductases (FNRs) are similar in terms of primary sequences and structures, they participate in diverse biological processes by catalyzing a range of different redox reactions. Many of the reactions are critical for the growth, survival of, and infection by pathogens, and insight into the structural basis for substrate preference, specificity, and reaction kinetics is crucial for the detailed understanding of these redox pathways. Bacillus cereus (Bc) encodes three FNR paralogs, two of which have assigned distinct biological functions in bacillithiol disulfide reduction and flavodoxin (Fld) reduction. Bc FNR2, the endogenous reductase of the Fld-like protein NrdI, belongs to a distinct phylogenetic cluster of homologous oxidoreductases containing a conserved His residue stacking the FAD cofactor. In this study, we have assigned a function to FNR1, in which the His residue is replaced by a conserved Val, in the reduction of the heme-degrading monooxygenase IsdG, ultimately facilitating the release of iron in an important iron acquisition pathway. The Bc IsdG structure was solved, and IsdG-FNR1 interactions were proposed through protein-protein docking. Mutational studies and bioinformatics analyses confirmed the importance of the conserved FAD-stacking residues on the respective reaction rates, proposing a division of FNRs into four functionally unique sequence similarity clusters likely related to the nature of this residue.
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Affiliation(s)
- Marta Hammerstad
- Department of Biosciences, Section for Biochemistry and Molecular Biology, University of Oslo, P.O. Box 1066, Blindern, NO-0316 Oslo, Norway
| | - Anne Kristine Rugtveit
- Department of Biosciences, Section for Biochemistry and Molecular Biology, University of Oslo, P.O. Box 1066, Blindern, NO-0316 Oslo, Norway
| | - Sondov Dahlen
- Department of Biosciences, Section for Biochemistry and Molecular Biology, University of Oslo, P.O. Box 1066, Blindern, NO-0316 Oslo, Norway
| | - Hilde Kristin Andersen
- Department of Biosciences, Section for Biochemistry and Molecular Biology, University of Oslo, P.O. Box 1066, Blindern, NO-0316 Oslo, Norway
| | - Hans-Petter Hersleth
- Department of Biosciences, Section for Biochemistry and Molecular Biology, University of Oslo, P.O. Box 1066, Blindern, NO-0316 Oslo, Norway
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4
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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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5
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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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6
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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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7
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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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8
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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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9
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Morreale FE, Kleine S, Leodolter J, Junker S, Hoi DM, Ovchinnikov S, Okun A, Kley J, Kurzbauer R, Junk L, Guha S, Podlesainski D, Kazmaier U, Boehmelt G, Weinstabl H, Rumpel K, Schmiedel VM, Hartl M, Haselbach D, Meinhart A, Kaiser M, Clausen T. BacPROTACs mediate targeted protein degradation in bacteria. Cell 2022; 185:2338-2353.e18. [PMID: 35662409 PMCID: PMC9240326 DOI: 10.1016/j.cell.2022.05.009] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/15/2022] [Accepted: 05/10/2022] [Indexed: 12/14/2022]
Abstract
Hijacking the cellular protein degradation system offers unique opportunities for drug discovery, as exemplified by proteolysis-targeting chimeras. Despite their great promise for medical chemistry, so far, it has not been possible to reprogram the bacterial degradation machinery to interfere with microbial infections. Here, we develop small-molecule degraders, so-called BacPROTACs, that bind to the substrate receptor of the ClpC:ClpP protease, priming neo-substrates for degradation. In addition to their targeting function, BacPROTACs activate ClpC, transforming the resting unfoldase into its functional state. The induced higher-order oligomer was visualized by cryo-EM analysis, providing a structural snapshot of activated ClpC unfolding a protein substrate. Finally, drug susceptibility and degradation assays performed in mycobacteria demonstrate in vivo activity of BacPROTACs, allowing selective targeting of endogenous proteins via fusion to an established degron. In addition to guiding antibiotic discovery, the BacPROTAC technology presents a versatile research tool enabling the inducible degradation of bacterial proteins. BacPROTACs reprogram bacterial ClpCP proteases to degrade neo-substrates Substrate binding converts latent ClpC into active, higher-order complexes with ClpP Incorporation of cyclomarin as head group yields BacPROTACs active in mycobacteria BID can eliminate proteins of interest in vivo
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Affiliation(s)
- Francesca E Morreale
- Research Institute of Molecular Pathology, Vienna Biocenter, 1030 Vienna, Austria
| | - Stefan Kleine
- University of Duisburg-Essen, Center of Medical Biotechnology, Faculty of Biology, 45141 Essen, Germany
| | - Julia Leodolter
- Research Institute of Molecular Pathology, Vienna Biocenter, 1030 Vienna, Austria
| | - Sabryna Junker
- Research Institute of Molecular Pathology, Vienna Biocenter, 1030 Vienna, Austria
| | - David M Hoi
- Research Institute of Molecular Pathology, Vienna Biocenter, 1030 Vienna, Austria
| | - Stepan Ovchinnikov
- Research Institute of Molecular Pathology, Vienna Biocenter, 1030 Vienna, Austria
| | - Anastasia Okun
- Research Institute of Molecular Pathology, Vienna Biocenter, 1030 Vienna, Austria
| | - Juliane Kley
- Research Institute of Molecular Pathology, Vienna Biocenter, 1030 Vienna, Austria
| | - Robert Kurzbauer
- Research Institute of Molecular Pathology, Vienna Biocenter, 1030 Vienna, Austria
| | - Lukas Junk
- Saarland University, Organic Chemistry I, 66123 Saarbrücken, Germany
| | - Somraj Guha
- Saarland University, Organic Chemistry I, 66123 Saarbrücken, Germany
| | - David Podlesainski
- University of Duisburg-Essen, Center of Medical Biotechnology, Faculty of Biology, 45141 Essen, Germany
| | - Uli Kazmaier
- Saarland University, Organic Chemistry I, 66123 Saarbrücken, Germany
| | - Guido Boehmelt
- Boehringer Ingelheim RCV GmbH & Co KG, 1120 Vienna, Austria
| | | | - Klaus Rumpel
- Boehringer Ingelheim RCV GmbH & Co KG, 1120 Vienna, Austria
| | | | - Markus Hartl
- Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
| | - David Haselbach
- Research Institute of Molecular Pathology, Vienna Biocenter, 1030 Vienna, Austria
| | - Anton Meinhart
- Research Institute of Molecular Pathology, Vienna Biocenter, 1030 Vienna, Austria
| | - Markus Kaiser
- University of Duisburg-Essen, Center of Medical Biotechnology, Faculty of Biology, 45141 Essen, Germany.
| | - Tim Clausen
- Research Institute of Molecular Pathology, Vienna Biocenter, 1030 Vienna, Austria; Medical University of Vienna, 1030 Vienna, Austria.
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10
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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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11
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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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12
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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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13
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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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14
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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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15
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Downing AN, Coggins MK, Poon PCY, Kovacs JA. Influence of Thiolate versus Alkoxide Ligands on the Stability of Crystallographically Characterized Mn(III)-Alkylperoxo Complexes. J Am Chem Soc 2021; 143:6104-6113. [PMID: 33851827 DOI: 10.1021/jacs.0c13001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The work described herein demonstrates the exquisite control that the inner coordination sphere of metalloenzymes and transition-metal complexes can have on reactivity. We report one of few crystallographically characterized Mn-peroxo complexes and show that the tight correlations between metrical and spectroscopic parameters, established previously by our group for thiolate-ligated RS-Mn(III)-OOR complexes, can be extended to include an alkoxide-ligated RO-Mn(III)-OOR complex. We show that the alkoxide-ligated RO-Mn(III)-OOR complex is an order of magnitude more stable (t1/2298 K = 6730 s, kobs298 K = 1.03 × 10-4 s-1) than its thiolate-ligated RS-Mn(III)-OOR derivative (t1/2293 K = 249 s, k1293 K = 2.78 × 10-3 s-1). Electronic structure calculations provide insight regarding these differences in stability. The highest occupied orbital of the thiolate-ligated derivative possesses significant sulfur character and π-backdonation from the thiolate competes with π-backdonation from the peroxo π*(O-O). DFT-calculated Mulliken charges show that the Mn ion Lewis acidity of alkoxide-ligated RO-Mn(III)-OOR (+0.451) is greater than that of thiolate-ligated RS-Mn(III)-OOR (+0.306), thereby facilitating π-backdonation from the antibonding peroxo π*(O-O) orbital and increasing its stability. This helps to explain why the photosynthetic oxygen-evolving Mn complex, which catalyzes O-O bond formation as opposed to cleavage, incorporates O- and/or N-ligands as opposed to cysS-ligands.
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Affiliation(s)
- Alexandra N Downing
- The Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
| | - Michael K Coggins
- The Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
| | - Penny Chaau Yan Poon
- The Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
| | - Julie A Kovacs
- The Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
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16
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Overview of structurally homologous flavoprotein oxidoreductases containing the low M r thioredoxin reductase-like fold - A functionally diverse group. Arch Biochem Biophys 2021; 702:108826. [PMID: 33684359 DOI: 10.1016/j.abb.2021.108826] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/23/2021] [Accepted: 02/27/2021] [Indexed: 01/12/2023]
Abstract
Structural studies show that enzymes have a limited number of unique folds, although structurally related enzymes have evolved to perform a large variety of functions. In this review, we have focused on enzymes containing the low molecular weight thioredoxin reductase (low Mr TrxR) fold. This fold consists of two domains, both containing a three-layer ββα sandwich Rossmann-like fold, serving as flavin adenine dinucleotide (FAD) and, in most cases, pyridine nucleotide (NAD(P)H) binding-domains. Based on a search of the Protein Data Bank for all published structures containing the low Mr TrxR-like fold, we here present a comprehensive overview of enzymes with this structural architecture. These range from TrxR-like ferredoxin/flavodoxin NAD(P)+ oxidoreductases, through glutathione reductase, to NADH peroxidase. Some enzymes are solely composed of the low Mr TrxR-like fold, while others contain one or two additional domains. In this review, we give a detailed description of selected enzymes containing only the low Mr TrxR-like fold, however, catalyzing a diversity of chemical reactions. Our overview of this structurally similar, yet functionally distinct group of flavoprotein oxidoreductases highlights the fascinating and increasing number of studies describing the diversity among these enzymes, especially during the last decade(s).
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17
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Metalation: nature's challenge in bioinorganic chemistry. J Biol Inorg Chem 2020; 25:543-545. [PMID: 32333210 PMCID: PMC7239837 DOI: 10.1007/s00775-020-01790-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 04/20/2020] [Indexed: 12/28/2022]
Abstract
The association of proteins with metals, metalation, is challenging because the tightest binding metals are rarely the correct ones. Inside cells, correct metalation is enabled by controlled bioavailability plus extra mechanisms for tricky combinations such as iron and manganese.
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18
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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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19
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20
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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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21
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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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22
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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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23
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Emergence of metal selectivity and promiscuity in metalloenzymes. J Biol Inorg Chem 2019; 24:517-531. [DOI: 10.1007/s00775-019-01667-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 05/13/2019] [Indexed: 01/27/2023]
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24
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25
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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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26
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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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27
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Shova S, Vlad A, Cazacu M, Krzystek J, Ozarowski A, Malček M, Bucinsky L, Rapta P, Cano J, Telser J, Arion VB. Dinuclear manganese(iii) complexes with bioinspired coordination and variable linkers showing weak exchange effects: a synthetic, structural, spectroscopic and computation study. Dalton Trans 2019; 48:5909-5922. [DOI: 10.1039/c8dt04596h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
High-resolution HFEPR indicates weak exchange interactions between MnIII ions in agreement with DFT calculations.
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Affiliation(s)
- Sergiu Shova
- Inorganic Polymers Department
- “Petru Poni” Institute of Macromolecular Chemistry
- Iasi 700487
- Romania
| | - Angelica Vlad
- Inorganic Polymers Department
- “Petru Poni” Institute of Macromolecular Chemistry
- Iasi 700487
- Romania
| | - Maria Cazacu
- Inorganic Polymers Department
- “Petru Poni” Institute of Macromolecular Chemistry
- Iasi 700487
- Romania
| | - J. Krzystek
- National High Magnetic Field Laboratory
- Florida State University
- Tallahassee
- USA
| | - Andrew Ozarowski
- National High Magnetic Field Laboratory
- Florida State University
- Tallahassee
- USA
| | - Michal Malček
- Institute of Physical Chemistry and Chemical Physics
- Slovak University of Technology in Bratislava
- 81237 Bratislava
- Slovak Republic
| | - Lukas Bucinsky
- Institute of Physical Chemistry and Chemical Physics
- Slovak University of Technology in Bratislava
- 81237 Bratislava
- Slovak Republic
| | - Peter Rapta
- Institute of Physical Chemistry and Chemical Physics
- Slovak University of Technology in Bratislava
- 81237 Bratislava
- Slovak Republic
| | - Joan Cano
- Institut de Ciència Molecular
- Universitat de València
- 46980 Paterna
- Spain
| | - Joshua Telser
- Department of Biological
- Physical and Health Sciences
- Roosevelt University
- Chicago
- USA
| | - Vladimir B. Arion
- Institute of Inorganic Chemistry of the University of Vienna
- A1090 Vienna
- Austria
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28
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Griese JJ, Branca RMM, Srinivas V, Högbom M. Ether cross-link formation in the R2-like ligand-binding oxidase. J Biol Inorg Chem 2018; 23:879-886. [PMID: 29946980 PMCID: PMC6060897 DOI: 10.1007/s00775-018-1583-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 06/20/2018] [Indexed: 12/27/2022]
Abstract
R2-like ligand-binding oxidases contain a dinuclear metal cofactor which can consist either of two iron ions or one manganese and one iron ion, but the heterodinuclear Mn/Fe cofactor is the preferred assembly in the presence of MnII and FeII in vitro. We have previously shown that both types of cofactor are capable of catalyzing formation of a tyrosine–valine ether cross-link in the protein scaffold. Here we demonstrate that Mn/Fe centers catalyze cross-link formation more efficiently than Fe/Fe centers, indicating that the heterodinuclear cofactor is the biologically relevant one. We further explore the chemical potential of the Mn/Fe cofactor by introducing mutations at the cross-linking valine residue. We find that cross-link formation is possible also to the tertiary beta-carbon in an isoleucine, but not to the secondary beta-carbon or tertiary gamma-carbon in a leucine, nor to the primary beta-carbon of an alanine. These results illustrate that the reactivity of the cofactor is highly specific and directed.
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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.
| | - Rui M M Branca
- Cancer Proteomics Mass Spectrometry, Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Box 1031, 171 21, Solna, Sweden
| | - Vivek Srinivas
- Department of Biochemistry and Biophysics, Stockholm University, 106 91, Stockholm, Sweden
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, 106 91, Stockholm, Sweden.
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29
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Abstract
In response to microbial infection, the human host deploys metal-sequestering host-defense proteins, which reduce nutrient availability and thereby inhibit microbial growth and virulence. Calprotectin (CP) is an abundant antimicrobial protein released from neutrophils and epithelial cells at sites of infection. CP sequesters divalent first-row transition metal ions to limit the availability of essential metal nutrients in the extracellular space. While functional and clinical studies of CP have been pursued for decades, advances in our understanding of its biological coordination chemistry, which is central to its role in the host-microbe interaction, have been made in more recent years. In this review, we focus on the coordination chemistry of CP and highlight studies of its metal-binding properties and contributions to the metal-withholding innate immune response. Taken together, these recent studies inform our current model of how CP participates in metal homeostasis and immunity, and they provide a foundation for further investigations of a remarkable metal-chelating protein at the host-microbe interface and beyond.
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Affiliation(s)
- Emily M Zygiel
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Elizabeth M Nolan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
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30
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Basak T, Ghosh K, Gómez-García CJ, Chattopadhyay S. Synthesis, structure and magnetic characterization of a dinuclear and two mononuclear iron(III) complexes with N,O-donor Schiff base ligands. Polyhedron 2018. [DOI: 10.1016/j.poly.2017.12.040] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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31
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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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32
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Balamurugan M, Saravanan N, Ha H, Lee YH, Nam KT. Involvement of high-valent manganese-oxo intermediates in oxidation reactions: realisation in nature, nano and molecular systems. NANO CONVERGENCE 2018; 5:18. [PMID: 30101051 PMCID: PMC6061251 DOI: 10.1186/s40580-018-0150-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 06/19/2018] [Indexed: 05/12/2023]
Abstract
Manganese plays multiple role in many biological redox reactions in which it exists in different oxidation states from Mn(II) to Mn(IV). Among them the high-valent manganese-oxo intermediate plays important role in the activity of certain enzymes and lessons from the natural system provide inspiration for new developments of artificial systems for a sustainable energy supply and various organic conversions. This review describes recent advances and key lessons learned from the nature on high-valent Mn-oxo intermediates. Also we focus on the elemental science developed from the natural system, how the novel strategies are realised in nano particles and molecular sites at heterogeneous and homogeneous reaction conditions respectively. Finally, perspectives on the utilisation of the high-valent manganese-oxo species towards other organic reactions are proposed.
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Affiliation(s)
- Mani Balamurugan
- Department of Materials Science and Engineering, Seoul National University, Seoul, 151-744 South Korea
| | - Natarajan Saravanan
- Department of Materials Science and Engineering, Seoul National University, Seoul, 151-744 South Korea
| | - Heonjin Ha
- Department of Materials Science and Engineering, Seoul National University, Seoul, 151-744 South Korea
| | - Yoon Ho Lee
- Department of Materials Science and Engineering, Seoul National University, Seoul, 151-744 South Korea
| | - Ki Tae Nam
- Department of Materials Science and Engineering, Seoul National University, Seoul, 151-744 South Korea
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33
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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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34
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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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35
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Lee CM, Wu WY, Chiang MH, Bohle DS, Lee GH. Generation of a Mn(IV)–Peroxo or Mn(III)–Oxo–Mn(III) Species upon Oxygenation of Mono- and Binuclear Thiolate-Ligated Mn(II) Complexes. Inorg Chem 2017; 56:10559-10569. [DOI: 10.1021/acs.inorgchem.7b01513] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Chien-Ming Lee
- Department of Applied
Science, National Taitung University, Taitung 950, Taiwan
| | - Wun-Yan Wu
- Department of Applied
Science, National Taitung University, Taitung 950, Taiwan
| | | | - D. Scott Bohle
- Department
of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Gene-Hsiang Lee
- Instrumentation
Center, National Taiwan University, Taipei 107, Taiwan
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36
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Miller EK, Trivelas NE, Maugeri PT, Blaesi EJ, Shafaat HS. Time-Resolved Investigations of Heterobimetallic Cofactor Assembly in R2lox Reveal Distinct Mn/Fe Intermediates. Biochemistry 2017; 56:3369-3379. [PMID: 28574263 DOI: 10.1021/acs.biochem.7b00403] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The assembly mechanism of the Mn/Fe ligand-binding oxidases (R2lox), a family of proteins that are homologous to the nonheme diiron carboxylate enzymes, has been investigated using time-resolved techniques. Multiple heterobimetallic intermediates that exhibit unique spectral features, including visible absorption bands and exceptionally broad electron paramagnetic resonance signatures, are observed through optical and magnetic resonance spectroscopies. On the basis of comparison to known diiron species and model compounds, the spectra have been attributed to (μ-peroxo)-MnIII/FeIII and high-valent Mn/Fe species. Global spectral analysis coupled with isotopic substitution and kinetic modeling reveals elementary rate constants for the assembly of Mn/Fe R2lox under aerobic conditions. A complete reaction mechanism for cofactor maturation that is consistent with experimental data has been developed. These results suggest that the Mn/Fe cofactor can perform direct C-H bond abstraction, demonstrating the potential for potent chemical reactivity that remains unexplored.
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Affiliation(s)
| | | | | | - Elizabeth J Blaesi
- Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
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37
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Biological functions controlled by manganese redox changes in mononuclear Mn-dependent enzymes. Essays Biochem 2017; 61:259-270. [PMID: 28487402 DOI: 10.1042/ebc20160070] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 03/05/2017] [Accepted: 03/17/2017] [Indexed: 02/06/2023]
Abstract
Remarkably few enzymes are known to employ a mononuclear manganese ion that undergoes changes in redox state during catalysis. Many questions remain to be answered about the role of substrate binding and/or protein environment in modulating the redox properties of enzyme-bound Mn(II), the nature of the dioxygen species involved in the catalytic mechanism, and how these enzymes acquire Mn(II) given that many other metal ions in the cell form more stable protein complexes. Here, we summarize current knowledge concerning the structure and mechanism of five mononuclear manganese-dependent enzymes: superoxide dismutase, oxalate oxidase (OxOx), oxalate decarboxylase (OxDC), homoprotocatechuate 3,4-dioxygenase, and lipoxygenase (LOX). Spectroscopic measurements and/or computational studies suggest that Mn(III)/Mn(II) are the catalytically active oxidation states of the metal, and the importance of 'second-shell' hydrogen bonding interactions with metal ligands has been demonstrated for a number of examples. The ability of these enzymes to modulate the redox properties of the Mn(III)/Mn(II) couple, thereby allowing them to generate substrate-based radicals, appears essential for accessing diverse chemistries of fundamental importance to organisms in all branches of life.
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38
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Martinie RJ, Blaesi EJ, Krebs C, Bollinger JM, Silakov A, Pollock CJ. Evidence for a Di-μ-oxo Diamond Core in the Mn(IV)/Fe(IV) Activation Intermediate of Ribonucleotide Reductase from Chlamydia trachomatis. J Am Chem Soc 2017; 139:1950-1957. [PMID: 28075562 DOI: 10.1021/jacs.6b11563] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
High-valent iron and manganese complexes effect some of the most challenging biochemical reactions known, including hydrocarbon and water oxidations associated with the global carbon cycle and oxygenic photosynthesis, respectively. Their extreme reactivity presents an impediment to structural characterization, but their biological importance and potential chemical utility have, nevertheless, motivated extensive efforts toward that end. Several such intermediates accumulate during activation of class I ribonucleotide reductase (RNR) β subunits, which self-assemble dimetal cofactors with stable one-electron oxidants that serve to initiate the enzyme's free-radical mechanism. In the class I-c β subunit from Chlamydia trachomatis, a heterodinuclear Mn(II)/Fe(II) complex reacts with dioxygen to form a Mn(IV)/Fe(IV) intermediate, which undergoes reduction of the iron site to produce the active Mn(IV)/Fe(III) cofactor. Herein, we assess the structure of the Mn(IV)/Fe(IV) activation intermediate using Fe- and Mn-edge extended X-ray absorption fine structure (EXAFS) analysis and multifrequency pulse electron paramagnetic resonance (EPR) spectroscopy. The EXAFS results reveal a metal-metal vector of 2.74-2.75 Å and an intense light-atom (C/N/O) scattering interaction 1.8 Å from the Fe. Pulse EPR data reveal an exchangeable deuterium hyperfine coupling of strength |T| = 0.7 MHz, but no stronger couplings. The results suggest that the intermediate possesses a di-μ-oxo diamond core structure with a terminal hydroxide ligand to the Mn(IV).
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Affiliation(s)
- Ryan J Martinie
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Elizabeth J Blaesi
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Carsten Krebs
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - J Martin Bollinger
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Alexey Silakov
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Christopher J Pollock
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
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39
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Butterfield CN, Tebo BM. Substrate specificity and copper loading of the manganese-oxidizing multicopper oxidase Mnx from Bacillus sp. PL-12. Metallomics 2017; 9:183-191. [DOI: 10.1039/c6mt00239k] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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40
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Wise CE, Grant JL, Amaya JA, Ratigan SC, Hsieh CH, Manley OM, Makris TM. Divergent mechanisms of iron-containing enzymes for hydrocarbon biosynthesis. J Biol Inorg Chem 2016; 22:221-235. [DOI: 10.1007/s00775-016-1425-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 12/09/2016] [Indexed: 12/22/2022]
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41
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Lofstad M, Gudim I, Hammerstad M, Røhr ÅK, Hersleth HP. Activation of the Class Ib Ribonucleotide Reductase by a Flavodoxin Reductase in Bacillus cereus. Biochemistry 2016; 55:4998-5001. [DOI: 10.1021/acs.biochem.6b00699] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marie Lofstad
- Section
for Biochemistry and Molecular Biology, Department of Biosciences, University of Oslo, P.O.
Box 1066, Blindern, NO-0316 Oslo, Norway
| | - Ingvild Gudim
- Section
for Biochemistry and Molecular Biology, Department of Biosciences, University of Oslo, P.O.
Box 1066, Blindern, NO-0316 Oslo, Norway
| | - Marta Hammerstad
- Section
for Biochemistry and Molecular Biology, Department of Biosciences, University of Oslo, P.O.
Box 1066, Blindern, NO-0316 Oslo, Norway
| | - Åsmund Kjendseth Røhr
- Department
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Ås, Norway
| | - Hans-Petter Hersleth
- Section
for Biochemistry and Molecular Biology, Department of Biosciences, University of Oslo, P.O.
Box 1066, Blindern, NO-0316 Oslo, Norway
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42
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Preparation, structures and properties of manganese complexes containing amine–(amido or amidato)–phenolato type ligands. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2016.03.036] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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43
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Kutin Y, Srinivas V, Fritz M, Kositzki R, Shafaat HS, Birrell J, Bill E, Haumann M, Lubitz W, Högbom M, Griese JJ, Cox N. Divergent assembly mechanisms of the manganese/iron cofactors in R2lox and R2c proteins. J Inorg Biochem 2016; 162:164-177. [PMID: 27138102 DOI: 10.1016/j.jinorgbio.2016.04.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 04/04/2016] [Accepted: 04/12/2016] [Indexed: 01/22/2023]
Abstract
A manganese/iron cofactor which performs multi-electron oxidative chemistry is found in two classes of ferritin-like proteins, the small subunit (R2) of class Ic ribonucleotide reductase (R2c) and the R2-like ligand-binding oxidase (R2lox). It is unclear how a heterodimeric Mn/Fe metallocofactor is assembled in these two related proteins as opposed to a homodimeric Fe/Fe cofactor, especially considering the structural similarity and proximity of the two metal-binding sites in both protein scaffolds and the similar first coordination sphere ligand preferences of MnII and FeII. Using EPR and Mössbauer spectroscopies as well as X-ray anomalous dispersion, we examined metal loading and cofactor activation of both proteins in vitro (in solution). We find divergent cofactor assembly mechanisms for the two systems. In both cases, excess MnII promotes heterobimetallic cofactor assembly. In the absence of FeII, R2c cooperatively binds MnII at both metal sites, whereas R2lox does not readily bind MnII at either site. Heterometallic cofactor assembly is favored at substoichiometric FeII concentrations in R2lox. FeII and MnII likely bind to the protein in a stepwise fashion, with FeII binding to site 2 initiating cofactor assembly. In R2c, however, heterometallic assembly is presumably achieved by the displacement of MnII by FeII at site 2. The divergent metal loading mechanisms are correlated with the putative in vivo functions of R2c and R2lox, and most likely with the intracellular MnII/FeII concentrations in the host organisms from which they were isolated.
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Affiliation(s)
- Yuri Kutin
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Vivek Srinivas
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Matthieu Fritz
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Ramona Kositzki
- Institut für Experimentalphysik, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Hannah S Shafaat
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - James Birrell
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Eckhard Bill
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Michael Haumann
- Institut für Experimentalphysik, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden; Department of Chemistry, Stanford University, Stanford, CA 94305, United States.
| | - Julia J Griese
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.
| | - Nicholas Cox
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany; Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
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Restoration of growth by manganese in a mutant strain of Escherichia coli lacking most known iron and manganese uptake systems. Biometals 2016; 29:433-50. [PMID: 27003826 DOI: 10.1007/s10534-016-9927-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 03/14/2016] [Indexed: 10/22/2022]
Abstract
The interplay of manganese and iron homeostasis and oxidative stress in Escherichia coli can give important insights into survival of bacteria in the phagosome and under differing iron or manganese bioavailabilities. Here, we characterized a mutant strain devoid of all know iron/manganese-uptake systems relevant for growth in defined medium. Based on these results an exit strategy enabling the cell to cope with iron depletion and use of manganese as an alternative for iron could be shown. Such a strategy would also explain why E. coli harbors some iron- or manganese-dependent iso-enzymes such as superoxide dismutases or ribonucleotide reductases. The benefits for gaining a means for survival would be bought with the cost of less efficient metabolism as indicated in our experiments by lower cell densities with manganese than with iron. In addition, this strain was extremely sensitive to the metalloid gallium but this gallium toxicity can be alleviated by low concentrations of manganese.
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Griese JJ, Kositzki R, Schrapers P, Branca RMM, Nordström A, Lehtiö J, Haumann M, Högbom M. Structural Basis for Oxygen Activation at a Heterodinuclear Manganese/Iron Cofactor. J Biol Chem 2015; 290:25254-72. [PMID: 26324712 PMCID: PMC4646176 DOI: 10.1074/jbc.m115.675223] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Revised: 08/24/2015] [Indexed: 12/31/2022] Open
Abstract
Two recently discovered groups of prokaryotic di-metal carboxylate proteins harbor a heterodinuclear Mn/Fe cofactor. These are the class Ic ribonucleotide reductase R2 proteins and a group of oxidases that are found predominantly in pathogens and extremophiles, called R2-like ligand-binding oxidases (R2lox). We have recently shown that the Mn/Fe cofactor of R2lox self-assembles from Mn(II) and Fe(II) in vitro and catalyzes formation of a tyrosine-valine ether cross-link in the protein scaffold (Griese, J. J., Roos, K., Cox, N., Shafaat, H. S., Branca, R. M., Lehtiö, J., Gräslund, A., Lubitz, W., Siegbahn, P. E., and Högbom, M. (2013) Proc. Natl. Acad. Sci. U.S.A. 110, 17189-17194). Here, we present a detailed structural analysis of R2lox in the nonactivated, reduced, and oxidized resting Mn/Fe- and Fe/Fe-bound states, as well as the nonactivated Mn/Mn-bound state. X-ray crystallography and x-ray absorption spectroscopy demonstrate that the active site ligand configuration of R2lox is essentially the same regardless of cofactor composition. Both the Mn/Fe and the diiron cofactor activate oxygen and catalyze formation of the ether cross-link, whereas the dimanganese cluster does not. The structures delineate likely routes for gated oxygen and substrate access to the active site that are controlled by the redox state of the cofactor. These results suggest that oxygen activation proceeds via similar mechanisms at the Mn/Fe and Fe/Fe center and that R2lox proteins might utilize either cofactor in vivo based on metal availability.
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Affiliation(s)
- Julia J Griese
- From the Stockholm Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Ramona Kositzki
- the Institut für Experimentalphysik, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Peer Schrapers
- the Institut für Experimentalphysik, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Rui M M Branca
- the Cancer Proteomics Mass Spectrometry, Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Box 1031, SE-171 21 Solna, Sweden, and
| | - Anders Nordström
- the Department of Molecular Biology, Umeå University, SE-90187 Umeå, Sweden
| | - Janne Lehtiö
- the Cancer Proteomics Mass Spectrometry, Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Box 1031, SE-171 21 Solna, Sweden, and
| | - Michael Haumann
- the Institut für Experimentalphysik, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Martin Högbom
- From the Stockholm Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden,
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Rapatskiy L, Ames WM, Pérez-Navarro M, Savitsky A, Griese JJ, Weyhermüller T, Shafaat HS, Högbom M, Neese F, Pantazis DA, Cox N. Characterization of Oxygen Bridged Manganese Model Complexes Using Multifrequency 17O-Hyperfine EPR Spectroscopies and Density Functional Theory. J Phys Chem B 2015. [DOI: 10.1021/acs.jpcb.5b04614] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Leonid Rapatskiy
- Max-Planck Institute for Chemical Energy, Stiftstr. 34-36, Mülheim an der Ruhr, DE-45470 Germany
| | - William M. Ames
- Max-Planck Institute for Chemical Energy, Stiftstr. 34-36, Mülheim an der Ruhr, DE-45470 Germany
| | - Montserrat Pérez-Navarro
- Max-Planck Institute for Chemical Energy, Stiftstr. 34-36, Mülheim an der Ruhr, DE-45470 Germany
| | - Anton Savitsky
- Max-Planck Institute for Chemical Energy, Stiftstr. 34-36, Mülheim an der Ruhr, DE-45470 Germany
| | - Julia J. Griese
- Department
of Biochemistry and Biophysics, Stockholm University, Stockholm SE-106 91, Sweden
| | - Thomas Weyhermüller
- Max-Planck Institute for Chemical Energy, Stiftstr. 34-36, Mülheim an der Ruhr, DE-45470 Germany
| | - Hannah S. Shafaat
- Max-Planck Institute for Chemical Energy, Stiftstr. 34-36, Mülheim an der Ruhr, DE-45470 Germany
| | - Martin Högbom
- Department
of Biochemistry and Biophysics, Stockholm University, Stockholm SE-106 91, Sweden
| | - Frank Neese
- Max-Planck Institute for Chemical Energy, Stiftstr. 34-36, Mülheim an der Ruhr, DE-45470 Germany
| | - Dimitrios A. Pantazis
- Max-Planck Institute for Chemical Energy, Stiftstr. 34-36, Mülheim an der Ruhr, DE-45470 Germany
| | - Nicholas Cox
- Max-Planck Institute for Chemical Energy, Stiftstr. 34-36, Mülheim an der Ruhr, DE-45470 Germany
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Lundin D, Berggren G, Logan DT, Sjöberg BM. The origin and evolution of ribonucleotide reduction. Life (Basel) 2015; 5:604-36. [PMID: 25734234 PMCID: PMC4390871 DOI: 10.3390/life5010604] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 02/04/2015] [Accepted: 02/06/2015] [Indexed: 11/16/2022] Open
Abstract
Ribonucleotide reduction is the only pathway for de novo synthesis of deoxyribonucleotides in extant organisms. This chemically demanding reaction, which proceeds via a carbon-centered free radical, is catalyzed by ribonucleotide reductase (RNR). The mechanism has been deemed unlikely to be catalyzed by a ribozyme, creating an enigma regarding how the building blocks for DNA were synthesized at the transition from RNA- to DNA-encoded genomes. While it is entirely possible that a different pathway was later replaced with the modern mechanism, here we explore the evolutionary and biochemical limits for an origin of the mechanism in the RNA + protein world and suggest a model for a prototypical ribonucleotide reductase (protoRNR). From the protoRNR evolved the ancestor to modern RNRs, the urRNR, which diversified into the modern three classes. Since the initial radical generation differs between the three modern classes, it is difficult to establish how it was generated in the urRNR. Here we suggest a model that is similar to the B12-dependent mechanism in modern class II RNRs.
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Affiliation(s)
- Daniel Lundin
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, SE-106 91 Stockholm, Sweden.
| | - Gustav Berggren
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, SE-106 91 Stockholm, Sweden.
| | - Derek T Logan
- Department of Biochemistry and Structural Biology, Lund University, Box 124, SE-221 00 Lund, Sweden.
| | - Britt-Marie Sjöberg
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, SE-106 91 Stockholm, Sweden.
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Ganyecz Á, Csontos J, Nagy B, Kállay M. Theoretical and thermochemical network approaches to determine the heats of formation for HO2 and its ionic counterparts. J Phys Chem A 2015; 119:1164-76. [PMID: 25611209 DOI: 10.1021/jp5104643] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ádám Ganyecz
- MTA-BME Lendület Quantum Chemistry Research Group, Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics , P.O. Box 91, H-1521 Budapest, Hungary
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Hassan SS, Tiwari S, Guimarães LC, Jamal SB, Folador E, Sharma NB, de Castro Soares S, Almeida S, Ali A, Islam A, Póvoa FD, de Abreu VAC, Jain N, Bhattacharya A, Juneja L, Miyoshi A, Silva A, Barh D, Turjanski AG, Azevedo V, Ferreira RS. Proteome scale comparative modeling for conserved drug and vaccine targets identification in Corynebacterium pseudotuberculosis. BMC Genomics 2014; 15 Suppl 7:S3. [PMID: 25573232 PMCID: PMC4243142 DOI: 10.1186/1471-2164-15-s7-s3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Corynebacterium pseudotuberculosis (Cp) is a pathogenic bacterium that causes caseous lymphadenitis (CLA), ulcerative lymphangitis, mastitis, and edematous to a broad spectrum of hosts, including ruminants, thereby threatening economic and dairy industries worldwide. Currently there is no effective drug or vaccine available against Cp. To identify new targets, we adopted a novel integrative strategy, which began with the prediction of the modelome (tridimensional protein structures for the proteome of an organism, generated through comparative modeling) for 15 previously sequenced C. pseudotuberculosis strains. This pan-modelomics approach identified a set of 331 conserved proteins having 95-100% intra-species sequence similarity. Next, we combined subtractive proteomics and modelomics to reveal a set of 10 Cp proteins, which may be essential for the bacteria. Of these, 4 proteins (tcsR, mtrA, nrdI, and ispH) were essential and non-host homologs (considering man, horse, cow and sheep as hosts) and satisfied all criteria of being putative targets. Additionally, we subjected these 4 proteins to virtual screening of a drug-like compound library. In all cases, molecules predicted to form favorable interactions and which showed high complementarity to the target were found among the top ranking compounds. The remaining 6 essential proteins (adk, gapA, glyA, fumC, gnd, and aspA) have homologs in the host proteomes. Their active site cavities were compared to the respective cavities in host proteins. We propose that some of these proteins can be selectively targeted using structure-based drug design approaches (SBDD). Our results facilitate the selection of C. pseudotuberculosis putative proteins for developing broad-spectrum novel drugs and vaccines. A few of the targets identified here have been validated in other microorganisms, suggesting that our modelome strategy is effective and can also be applicable to other pathogens.
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50
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Berggren G, Duraffourg N, Sahlin M, Sjöberg BM. Semiquinone-induced maturation of Bacillus anthracis ribonucleotide reductase by a superoxide intermediate. J Biol Chem 2014; 289:31940-31949. [PMID: 25262022 DOI: 10.1074/jbc.m114.592535] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ribonucleotide reductases (RNRs) catalyze the conversion of ribonucleotides to deoxyribonucleotides, and represent the only de novo pathway to provide DNA building blocks. Three different classes of RNR are known, denoted I-III. Class I RNRs are heteromeric proteins built up by α and β subunits and are further divided into different subclasses, partly based on the metal content of the β-subunit. In subclass Ib RNR the β-subunit is denoted NrdF, and harbors a manganese-tyrosyl radical cofactor. The generation of this cofactor is dependent on a flavodoxin-like maturase denoted NrdI, responsible for the formation of an active oxygen species suggested to be either a superoxide or a hydroperoxide. Herein we report on the magnetic properties of the manganese-tyrosyl radical cofactor of Bacillus anthracis NrdF and the redox properties of B. anthracis NrdI. The tyrosyl radical in NrdF is stabilized through its interaction with a ferromagnetically coupled manganese dimer. Moreover, we show through a combination of redox titration and protein electrochemistry that in contrast to hitherto characterized NrdIs, the B. anthracis NrdI is stable in its semiquinone form (NrdIsq) with a difference in electrochemical potential of ∼110 mV between the hydroquinone and semiquinone state. The under anaerobic conditions stable NrdIsq is fully capable of generating the oxidized, tyrosyl radical-containing form of Mn-NrdF when exposed to oxygen. This latter observation strongly supports that a superoxide radical is involved in the maturation mechanism, and contradicts the participation of a peroxide species. Additionally, EPR spectra on whole cells revealed that a significant fraction of NrdI resides in its semiquinone form in vivo, underscoring that NrdIsq is catalytically relevant.
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Affiliation(s)
- Gustav Berggren
- Department of Biochemistry and Biophysics, Stockholm University SE-10691 Stockholm, Sweden and
| | - Nicolas Duraffourg
- Laboratoire de Chimie et Biologie des Métaux (UMR 5249), CEA-Grenoble, 17, rue des Martyrs, F-38057 Grenoble, France
| | - Margareta Sahlin
- Department of Biochemistry and Biophysics, Stockholm University SE-10691 Stockholm, Sweden and
| | - Britt-Marie Sjöberg
- Department of Biochemistry and Biophysics, Stockholm University SE-10691 Stockholm, Sweden and.
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