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Jaroch M, Sun G, Tsui HCT, Reed C, Sun J, Jörg M, Winkler ME, Rice KC, Dziergowska A, Stich TA, Dedon PC, Dos Santos PC, de Crécy-Lagard V. Alternate routes to mnm 5s 2U synthesis in Gram-positive bacteria. J Bacteriol 2024; 206:e0045223. [PMID: 38551342 PMCID: PMC11025329 DOI: 10.1128/jb.00452-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 03/09/2024] [Indexed: 04/09/2024] Open
Abstract
The wobble bases of tRNAs that decode split codons are often heavily modified. In bacteria, tRNAGlu, Gln, Asp contains a variety of xnm5s2U derivatives. The synthesis pathway for these modifications is complex and fully elucidated only in a handful of organisms, including the Gram-negative Escherichia coli K12 model. Despite the ubiquitous presence of mnm5s2U modification, genomic analysis shows the absence of mnmC orthologous genes, suggesting the occurrence of alternate biosynthetic schemes for the conversion of cmnm5s2U to mnm5s2U. Using a combination of comparative genomics and genetic studies, a member of the YtqA subgroup of the radical Sam superfamily was found to be involved in the synthesis of mnm5s2U in both Bacillus subtilis and Streptococcus mutans. This protein, renamed MnmL, is encoded in an operon with the recently discovered MnmM methylase involved in the methylation of the pathway intermediate nm5s2U into mnm5s2U in B. subtilis. Analysis of tRNA modifications of both S. mutans and Streptococcus pneumoniae shows that growth conditions and genetic backgrounds influence the ratios of pathway intermediates owing to regulatory loops that are not yet understood. The MnmLM pathway is widespread along the bacterial tree, with some phyla, such as Bacilli, relying exclusively on these two enzymes. Although mechanistic details of these newly discovered components are not fully resolved, the occurrence of fusion proteins, alternate arrangements of biosynthetic components, and loss of biosynthetic branches provide examples of biosynthetic diversity to retain a conserved tRNA modification in Nature.IMPORTANCEThe xnm5s2U modifications found in several tRNAs at the wobble base position are widespread in bacteria where they have an important role in decoding efficiency and accuracy. This work identifies a novel enzyme (MnmL) that is a member of a subgroup of the very versatile radical SAM superfamily and is involved in the synthesis of mnm5s2U in several Gram-positive bacteria, including human pathogens. This is another novel example of a non-orthologous displacement in the field of tRNA modification synthesis, showing how different solutions evolve to retain U34 tRNA modifications.
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Affiliation(s)
- Marshall Jaroch
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - Guangxin Sun
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Singapore-MIT Alliance for Research and Technology, CREATE Tower, Singapore
| | | | - Colbie Reed
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - Jingjing Sun
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Singapore-MIT Alliance for Research and Technology, CREATE Tower, Singapore
| | - Marko Jörg
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - Malcolm E. Winkler
- Department of Biology, Indiana University Bloomington, Bloomington, Indiana, USA
| | - Kelly C. Rice
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | | | - Troy A. Stich
- Department of Chemistry, Wake Forest University, Winston-Salem, North Carolina, USA
| | - Peter C. Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Singapore-MIT Alliance for Research and Technology, CREATE Tower, Singapore
| | | | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
- University of Florida Genetics Institute, Gainesville, Florida, USA
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2
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Jaroch M, Sun G, Tsui HCT, Reed C, Sun J, Jörg M, Winkler ME, Rice KC, Stich TA, Dedon PC, Dos Santos PC, de Crécy-Lagard V. Alternate routes to mnm 5 s 2 U synthesis in Gram-positive bacteria. bioRxiv 2023:2023.12.21.572861. [PMID: 38187551 PMCID: PMC10769405 DOI: 10.1101/2023.12.21.572861] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
The wobble bases of tRNAs that decode split codons are often heavily modified. In Bacteria tRNA Glu, Gln, Asp contain a variety of xnm 5 s 2 U derivatives. The synthesis pathway for these modifications is complex and fully elucidated only in a handful of organisms, including the Gram-negative Escherichia coli K12 model. Despite the ubiquitous presence of mnm 5 s 2 U modification, genomic analysis shows the absence of mnmC orthologous genes, suggesting the occurrence of alternate biosynthetic schemes for the installation of this modification. Using a combination of comparative genomics and genetic studies, a member of the YtqA subgroup of the Radical Sam superfamily was found to be involved in the synthesis of mnm 5 s 2 U in both Bacillus subtilis and Streptococcus mutans . This protein, renamed MnmL, is encoded in an operon with the recently discovered MnmM methylase involved in the methylation of the pathway intermediate nm 5 s 2 U into mnm 5 s 2 U in B. subtilis . Analysis of tRNA modifications of both S. mutans and Streptococcus pneumoniae shows that growth conditions and genetic backgrounds influence the ratios of pathways intermediates in regulatory loops that are not yet understood. The MnmLM pathway is widespread along the bacterial tree, with some phyla, such as Bacilli, relying exclusively on these two enzymes. The occurrence of fusion proteins, alternate arrangements of biosynthetic components, and loss of biosynthetic branches provide examples of biosynthetic diversity to retain a conserved tRNA modification in nature. Importance The xnm 5 s 2 U modifications found in several tRNAs at the wobble base position are widespread in Bacteria where they have an important role in decoding efficiency and accuracy. This work identifies a novel enzyme (MnmL) that is a member of a subgroup of the very versatile Radical SAM superfamily and is involved in the synthesis of mnm 5 s 2 U in several Gram-positive bacteria, including human pathogens. This is another novel example of a non-orthologous displacement in the field of tRNA modification synthesis, showing how different solutions evolve to retain U34 tRNA modifications.
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Thomas-Colwell J, Sookezian A, Kurtz DA, Kallick J, Henling LM, Stich TA, Hill MG, Hunter BM. Tuning Cobalt(II) Phosphine Complexes to be Axially Ambivalent. Inorg Chem 2022; 61:12625-12634. [PMID: 35920800 PMCID: PMC9387527 DOI: 10.1021/acs.inorgchem.2c01562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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We report the isolation and characterization of a series
of three
cobalt(II) bis(phosphine) complexes with varying numbers of coordinated
solvent ligands in the axial position. X-ray quality crystals of [Co(dppv)2][BF4]2(1), [Co(dppv)2(NCCH3)][BPh4]2(2), and [Co(dppv)2(NCCH3)2][BF4]2(3) (dppv = cis-1,2-bis(diphenylphosphino)ethylene) were grown under slightly different
conditions, and their structures were compared. This analysis revealed
multiple crystallization motifs for divalent cobalt(II) complexes
with the same set of phosphine ligands. Notably, the 4-coordinate
complex 1 is a rare example of a square-planar cobalt(II)
complex, the first crystallographically characterized square-planar
Co(II) complex containing only neutral, bidentate ligands. Characterization
of the different axial geometries via EPR and UV–visible spectroscopies
showed that there is a very shallow energy landscape for axial ligation.
Ligand field angular overlap model calculations support this conclusion,
and we provide a strategy for tuning other ligands to be axially labile
on a phosphine scaffold. This methodology is proposed to be used for
designing cobalt phosphine catalysts for a variety of oxidation and
reduction reactions. A
square-planar cobalt(II) complex featuring two chelating
diphosphine ligands was isolated with 0, 1, and 2 axial acetonitrile
ligands. AOM calculations, validated by EPR, suggest this “axial
ambivalence” results from the near degeneracy of the dx2 − y2/dz2 orbital energies, with a change in the parentage
of the SOMO upon axial ligation. The calculations additionally provide
a simple method of predicting square-planar ligand sets/geometries
tuned to bind axial substrates with varying s-donor strengths.
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Affiliation(s)
- Jack Thomas-Colwell
- Department of Chemistry, Occidental College, Los Angeles, California 90041, United States
| | - Arvin Sookezian
- Department of Chemistry, Occidental College, Los Angeles, California 90041, United States
| | - Daniel A Kurtz
- Rowland Institute at Harvard University, Cambridge, Massachusetts 02142, United States
| | - Jeremy Kallick
- Department of Chemistry, Occidental College, Los Angeles, California 90041, United States
| | - Lawrence M Henling
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Troy A Stich
- Department of Chemistry, Wake Forest University, Winston-Salem, North Carolina 27109, United States
| | - Michael G Hill
- Department of Chemistry, Occidental College, Los Angeles, California 90041, United States
| | - Bryan M Hunter
- Rowland Institute at Harvard University, Cambridge, Massachusetts 02142, United States
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Stich TA. Characterization of Paramagnetic Iron-Sulfur Clusters Using Electron Paramagnetic Resonance Spectroscopy. Methods Mol Biol 2021; 2353:259-280. [PMID: 34292554 DOI: 10.1007/978-1-0716-1605-5_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Continuous-wave (CW) electron paramagnetic resonance (EPR) spectroscopy is a powerful ally in characterizing the multitude of redox-active iron-sulfur cluster-containing ([Fe-S]) species present in biological samples. The technique detects only those clusters that are paramagnetic-having a nonzero total electron spin (S > 0)-thus, it can discriminate between clusters in different oxidation states. The low-temperature CW-EPR spectrum of an [Fe-S] yields the three magnetic g-values that serve as a fingerprint of its electronic structure. This chapter briefly describes the underlying theory that defines this electronic structure and provides a recipe for the acquisition and analysis of EPR spectra of [Fe-S] proteins.
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Affiliation(s)
- Troy A Stich
- Department of Chemistry, Wake Forest University, Winston-Salem, NC, USA.
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Sayler R, Stich TA, Joshi S, Cooper N, Shaw JT, Begley TP, Tantillo DJ, Britt RD. Trapping and Electron Paramagnetic Resonance Characterization of the 5'dAdo • Radical in a Radical S-Adenosyl Methionine Enzyme Reaction with a Non-Native Substrate. ACS Cent Sci 2019; 5:1777-1785. [PMID: 31807679 PMCID: PMC6891858 DOI: 10.1021/acscentsci.9b00706] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Indexed: 05/03/2023]
Abstract
S-Adenosyl methionine (SAM) is employed as a [4Fe-4S]-bound cofactor in the superfamily of radical SAM (rSAM) enzymes, in which one-electron reduction of the [4Fe-4S]-SAM moiety leads to homolytic cleavage of the S-adenosyl methionine to generate the 5'-deoxyadenosyl radical (5'dAdo•), a potent H-atom abstractor. HydG, a member of this rSAM family, uses the 5'dAdo• radical to lyse its substrate, tyrosine, producing CO and CN that bind to a unique Fe site of a second HydG Fe-S cluster, ultimately producing a mononuclear organometallic Fe-l-cysteine-(CO)2CN complex as an intermediate in the bioassembly of the catalytic H-cluster of [Fe-Fe] hydrogenase. Here we report the use of non-native tyrosine substrate analogues to further probe the initial radical chemistry of HydG. One such non-native substrate is 4-hydroxy phenyl propanoic acid (HPPA) which lacks the amino group of tyrosine, replacing the CαH-NH2 with a CH2 at the C2 position. Electron paramagnetic resonance (EPR) studies show the generation of a strong and relatively stable radical in the HydG reaction with natural abundance and 13C2-HPPA, with appreciable spin density localized at C2. These results led us to try parallel experiments with the more oxidized non-native substrate coumaric acid, which has a C2=C3 alkene substitution relative to HPPA's single bond. Interestingly, the HydG reaction with the cis-p-coumaric acid isomer led to the trapping of a new radical EPR signal, and EPR studies using cis-p-coumaric acid along with isotopically labeled SAM reveal that we have for the first time trapped and characterized the 5'dAdo• radical in an actual rSAM enzyme reaction, here by using this specific non-native substrate cis-p-coumaric acid. Density functional theory energetics calculations show that the cis-p-coumaric acid has approximately the same C-H bond dissociation free energy as 5'dAdo•, providing a possible explanation for our ability to trap an appreciable fraction of 5'dAdo• in this specific rSAM reaction. The radical's EPR line shape and its changes with SAM isotopic substitution are nearly identical to those of a 5'dAdo• radical recently generated by cryophotolysis of a prereduced [4Fe-4S]-SAM center in another rSAM enzyme, pyruvate formate-lyase activating enzyme, further supporting our assignment that we have indeed trapped and characterized the 5'dAdo• radical in a radical SAM enzymatic reaction by appropriate tuning of the relative radical free energies via the judicious selection of a non-native substrate.
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Affiliation(s)
- Richard
I. Sayler
- Department
of Chemistry, University of California,
Davis, Davis, California 95616, United States
| | - Troy A. Stich
- Department
of Chemistry, University of California,
Davis, Davis, California 95616, United States
| | - Sumedh Joshi
- Department
of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Nicole Cooper
- Department
of Chemistry, University of California,
Davis, Davis, California 95616, United States
| | - Jared T. Shaw
- Department
of Chemistry, University of California,
Davis, Davis, California 95616, United States
| | - Tadhg P. Begley
- Department
of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Dean J. Tantillo
- 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
- E-mail: . Phone: (530) 752
6377
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Rao G, Altman AB, Brown AC, Tao L, Stich TA, Arnold J, Britt RD. Metal Bonding with 3d and 6d Orbitals: An EPR and ENDOR Spectroscopic Investigation of Ti 3+-Al and Th 3+-Al Heterobimetallic Complexes. Inorg Chem 2019; 58:7978-7988. [PMID: 31185562 PMCID: PMC6584900 DOI: 10.1021/acs.inorgchem.9b00720] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Accessing covalent
bonding interactions between actinides and ligating atoms remains
a central problem in the field. Our current understanding of actinide
bonding is limited because of a paucity of diverse classes of compounds
and the lack of established models. We recently synthesized a thorium
(Th)–aluminum (Al) heterobimetallic molecule that represents
a new class of low-valent Th-containing compounds. To gain further
insight into this system and actinide–metal bonding more generally,
it is useful to study their underlying electronic structures. Here,
we report characterization by electron paramagnetic resonance (EPR)
and electron–nuclear double resonance (ENDOR) spectroscopy
of two heterobimetallic compounds: (i) a Cptt2ThH3AlCTMS3 [TMS = Si(CH3)3; Cptt = 1,3-di-tert-butylcyclopentadienyl]
complex with bridging hydrides and (ii) an actinide-free Cp2TiH3AlCTMS3 (Cp = cyclopentadienyl) analogue.
Analyses of the hyperfine interactions between the paramagnetic trivalent
metal centers and the surrounding magnetic nuclei, 1H and 27Al, yield spin distributions over both complexes. These results
show that while the bridging hydrides in the two complexes have similar
hyperfine couplings (aiso = −9.7
and −10.7 MHz, respectively), the spin density on the Al ion
in the Th3+ complex is ∼5-fold larger than that
in the titanium(3+) (Ti3+) analogue. This suggests a direct
orbital overlap between Th and Al, leading to a covalent interaction
between Th and Al. Our quantitative investigation by a pulse EPR technique
deepens our understanding of actinide bonding to main-group elements. The electronic structures of Ti3+−Al and Th3+−Al heterobimetallic complexes are probed by electron−nuclear
double resonance spectroscopy, revealing a much larger spin density
on the Al center in the latter and the presence of a covalent Th−Al
bonding interaction caused by the direct orbital overlap between Th
and Al.
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Affiliation(s)
- Guodong Rao
- Department of Chemistry , University of California at Davis , Davis , California 95616 , United States
| | - Alison B Altman
- Department of Chemistry , University of California at Berkeley , Berkeley , California 94720 , United States
| | - Alexandra C Brown
- Department of Chemistry , University of California at Berkeley , Berkeley , California 94720 , United States
| | - Lizhi Tao
- Department of Chemistry , University of California at Davis , Davis , California 95616 , United States
| | - Troy A Stich
- Department of Chemistry , University of California at Davis , Davis , California 95616 , United States
| | - John Arnold
- Department of Chemistry , University of California at Berkeley , Berkeley , California 94720 , United States
| | - R David Britt
- Department of Chemistry , University of California at Davis , Davis , California 95616 , United States
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7
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Lionetti D, Suseno S, Tsui EY, Lu L, Stich TA, Carsch KM, Nielsen RJ, Goddard WA, Britt RD, Agapie T. Effects of Lewis Acidic Metal Ions (M) on Oxygen-Atom Transfer Reactivity of Heterometallic Mn 3MO 4 Cubane and Fe 3MO(OH) and Mn 3MO(OH) Clusters. Inorg Chem 2019; 58:2336-2345. [PMID: 30730725 DOI: 10.1021/acs.inorgchem.8b02701] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The modulation of the reactivity of metal oxo species by redox inactive metals has attracted much interest due to the observation of redox inactive metal effects on processes involving electron transfer both in nature (the oxygen-evolving complex of Photosystem II) and in heterogeneous catalysis (mixed-metal oxides). Studies of small-molecule models of these systems have revealed numerous instances of effects of redox inactive metals on electron- and group-transfer reactivity. However, the heterometallic species directly involved in these transformations have rarely been structurally characterized and are often generated in situ. We have previously reported the preparation and structural characterization of multiple series of heterometallic clusters based on Mn3 and Fe3 cores and described the effects of Lewis acidity of the heterometal incorporated in these complexes on cluster reduction potential. To determine the effects of Lewis acidity of redox inactive metals on group transfer reactivity in structurally well-defined complexes, we studied [Mn3MO4], [Mn3MO(OH)], and [Fe3MO(OH)] clusters in oxygen atom transfer (OAT) reactions with phosphine substrates. The qualitative rate of OAT correlates with the Lewis acidity of the redox inactive metal, confirming that Lewis acidic metal centers can affect the chemical reactivity of metal oxo species by modulating cluster electronics.
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Affiliation(s)
| | | | | | - Luo Lu
- Department of Chemistry , University of California , Davis , California 95616 , United States
| | - Troy A Stich
- Department of Chemistry , University of California , Davis , California 95616 , United States
| | | | | | | | - R David Britt
- Department of Chemistry , University of California , Davis , California 95616 , United States
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8
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Armstrong BM, Sayler RI, Shupe BH, Stich TA, Britt RD, Franz AK. EPR Evidence for the Origin of Nonlinear Effects in an Enantioselective Cu(II)-Catalyzed Spiroannulation. ACS Catal 2018. [DOI: 10.1021/acscatal.8b03822] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Brittany M. Armstrong
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Richard I. Sayler
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Benjamin H. Shupe
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Troy A. Stich
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - R. David Britt
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Annaliese K. Franz
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
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Abstract
Biotin (vitamin B7) is an enzyme cofactor required by organisms from all branches of life but synthesized only in microbes and plants. In the final step of biotin biosynthesis, a radical S-adenosyl-l-methionine (SAM) enzyme, biotin synthase (BioB), converts the substrate dethiobiotin to biotin through the stepwise formation of two C-S bonds. Previous electron paramagnetic resonance (EPR) spectroscopic studies identified a semistable intermediate in the formation of the first C-S bond as 9-mercaptodethiobiotin linked to a paramagnetic [2Fe-2S] cluster through one of its bridging sulfides. Herein, we report orientation-selected pulse EPR spectroscopic results that reveal hyperfine interactions between the [2Fe-2S] cluster and a number of magnetic nuclei (e.g., 57Fe, 15N, 13C, and 2H) introduced in a site-specific manner via biosynthetic methods. Combining these results with quantum chemical modeling gives a structural model of the intermediate showing that C6, the target of the second hydrogen-atom abstraction, is now in close proximity to the nascent thioether sulfur and is ideally positioned for the second C-S bond forming event.
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Affiliation(s)
- Lizhi Tao
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Troy A. Stich
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Corey J. Fugate
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii 96822, United States
| | - Joseph T. Jarrett
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii 96822, United States
| | - R. David Britt
- Department of Chemistry, University of California, Davis, California 95616, United States
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10
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Gagnon DM, Stich TA, Mehta AP, Abdelwahed SH, Begley TP, Britt RD. An Aminoimidazole Radical Intermediate in the Anaerobic Biosynthesis of the 5,6-Dimethylbenzimidazole Ligand to Vitamin B12. J Am Chem Soc 2018; 140:12798-12807. [PMID: 30208703 DOI: 10.1021/jacs.8b05686] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Organisms that perform the de novo biosynthesis of cobalamin (vitamin B12) do so via unique pathways depending on the presence of oxygen in the environment. The anaerobic biosynthesis pathway of 5,6-dimethylbenzimidazole, the so-called "lower ligand" to the cobalt center, has been recently identified. This process begins with the conversion of 5-aminoimidazole ribotide (AIR) to 5-hydroxybenzimidazole (HBI) by the radical S-adenosyl-l-methionine (SAM) enzyme BzaF, also known as HBI synthase. In this work we report the characterization of a radical intermediate in the reaction of BzaF using electron paramagnetic resonance spectroscopy. Using various isotopologues of AIR, we extracted hyperfine parameters for a number of nuclei, allowing us to propose plausible chemical compositions and structures for this intermediate. Specifically, we find that an aminoimidazole radical is formed in close proximity to a fragment of the ribose ring. These findings induce the revision of past proposed mechanisms and illustrate the ability of radical SAM enzymes to tightly control the radical chemistry that they engender.
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Affiliation(s)
- Derek M Gagnon
- Department of Chemistry , University of California , Davis , California 95616 , United States
| | - Troy A Stich
- Department of Chemistry , University of California , Davis , California 95616 , United States
| | - Angad P Mehta
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Sameh H Abdelwahed
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Tadhg P Begley
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - R David Britt
- Department of Chemistry , University of California , Davis , California 95616 , United States
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11
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Tao L, Stich TA, Soldatova AV, Tebo BM, Spiro TG, Casey WH, Britt RD. Mn(III) species formed by the multi-copper oxidase MnxG investigated by electron paramagnetic resonance spectroscopy. J Biol Inorg Chem 2018; 23:1093-1104. [PMID: 29968177 DOI: 10.1007/s00775-018-1587-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 06/22/2018] [Indexed: 01/24/2023]
Abstract
The multi-copper oxidase (MCO) MnxG from marine Bacillus bacteria plays an essential role in geochemical cycling of manganese by oxidizing Mn2+(aq) to form manganese oxide minerals at rates that are three to five orders of magnitude faster than abiotic rates. The MCO MnxG protein is isolated as part of a multi-protein complex, denoted as Mnx, which includes one MnxG unit and a hexamer of MnxE3F3 subunit. During the oxidation of Mn2+(aq) catalyzed by the Mnx protein complex, an enzyme-bound Mn(III) species was trapped recently in the presence of pyrophosphate (PP) and analyzed using parallel-mode electron paramagnetic resonance (EPR) spectroscopy. Herein, we provide a full analysis of this enzyme-bound Mn(III) intermediate via temperature dependence studies and spectral simulations. This Mnx-bound Mn(III) species is characterized by a hyperfine-coupling value of A(55Mn) = 4.2 mT (corresponding to 120 MHz) and a negative zero-field splitting (ZFS) value of D = - 2.0 cm-1. These magnetic properties suggest that the Mnx-bound Mn(III) species could be either six-coordinate with a 5B1g ground state or square-pyramidal five-coordinate with a 5B1 ground state. In addition, as a control, Mn(III)PP is also analyzed by parallel-mode EPR spectroscopy. It exhibits distinctly different magnetic properties with a hyperfine-coupling value of A(55Mn) = 4.8 mT (corresponding to 140 MHz) and a negative ZFS value of D = - 2.5 cm-1. The different ZFS values suggest differences in ligand environment of Mnx-bound Mn(III) and aqueous Mn(III)PP species. These studies provide further insights into the mechanism of biological Mn2+(aq) oxidation.
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Affiliation(s)
- Lizhi Tao
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - Troy A Stich
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - Alexandra V Soldatova
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA, 98195, USA
| | - Bradley M Tebo
- Division of Environmental and Biomolecular Systems, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Thomas G Spiro
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA, 98195, USA
| | - William H Casey
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA, 95616, USA
- Department of Geology, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - R David Britt
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA, 95616, USA.
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12
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Barr I, Stich TA, Gizzi A, Grove T, Bonanno JB, Latham JA, Chung T, Wilmot CM, Britt RD, Almo SC, Klinman JP. X-ray and EPR Characterization of the Auxiliary Fe-S Clusters in the Radical SAM Enzyme PqqE. Biochemistry 2018; 57:1306-1315. [PMID: 29405700 PMCID: PMC5905707 DOI: 10.1021/acs.biochem.7b01097] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The Radical SAM (RS) enzyme PqqE catalyzes the first step in the biosynthesis of the bacterial cofactor pyrroloquinoline quinone, forming a new carbon-carbon bond between two side chains within the ribosomally synthesized peptide substrate PqqA. In addition to the active site RS 4Fe-4S cluster, PqqE is predicted to have two auxiliary Fe-S clusters, like the other members of the SPASM domain family. Here we identify these sites and examine their structure using a combination of X-ray crystallography and Mössbauer and electron paramagnetic resonance (EPR) spectroscopies. X-ray crystallography allows us to identify the ligands to each of the two auxiliary clusters at the C-terminal region of the protein. The auxiliary cluster nearest the RS site (AuxI) is in the form of a 2Fe-2S cluster ligated by four cysteines, an Fe-S center not seen previously in other SPASM domain proteins; this assignment is further supported by Mössbauer and EPR spectroscopies. The second, more remote cluster (AuxII) is a 4Fe-4S center that is ligated by three cysteine residues and one aspartate residue. In addition, we examined the roles these ligands play in catalysis by the RS and AuxII clusters using site-directed mutagenesis coupled with EPR spectroscopy. Lastly, we discuss the possible functional consequences that these unique AuxI and AuxII clusters may have in catalysis for PqqE and how these may extend to additional RS enzymes catalyzing the post-translational modification of ribosomally encoded peptides.
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Affiliation(s)
- Ian Barr
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, United States
| | - Troy A. Stich
- Department of Chemistry, University of California, Davis, California 95695, United States
| | - Anthony Gizzi
- Department of Biochemistry, Albert Einstein School of Medicine, Bronx, NY 10461, United States
| | - Tyler Grove
- Department of Biochemistry, Albert Einstein School of Medicine, Bronx, NY 10461, United States
| | - Jeffrey B. Bonanno
- Department of Biochemistry, Albert Einstein School of Medicine, Bronx, NY 10461, United States
| | - John A. Latham
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, United States
| | - Tyler Chung
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, United States
| | - Carrie M. Wilmot
- Department of Biochemistry, Molecular Biology, and Biophysics, and The Biotechnology Institute, University of Minnesota, St. Paul, MN 55108, United States
| | - R. David Britt
- Department of Chemistry, University of California, Davis, California 95695, United States
| | - Steven C. Almo
- Department of Biochemistry, Albert Einstein School of Medicine, Bronx, NY 10461, United States
| | - Judith P. Klinman
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, United States
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13
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Marchiori DA, Oyala PH, Debus RJ, Stich TA, Britt RD. Structural Effects of Ammonia Binding to the Mn4CaO5 Cluster of Photosystem II. J Phys Chem B 2018; 122:1588-1599. [DOI: 10.1021/acs.jpcb.7b11101] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- David A. Marchiori
- Department
of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Paul H. Oyala
- Department
of Chemistry, University of California, Davis, Davis, California 95616, United States
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Richard J. Debus
- Department
of Biochemistry, University of California, Riverside, Riverside, California 92521, United States
| | - Troy A. Stich
- 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
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14
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Abstract
A simple exchange reaction between [AriPr4Sn(μ-Cl)]2 (1) and sodium azide afforded the doubly bridged Sn(II) azide, [AriPr4Sn(μ-N3)]2 (2) (AriPr4 = C6H3-2,6(C6H3-2,6-iPr2)2) in 85% yield. Photolysis of a diethyl ether solution of 2 for ca. 16 h yielded an azepinyl-substituted insertion product, [C6H3-2-(C6H3-2,6-iPr2)-6-(C6H3N-3,7-iPr2)Sn]2 (3). The reaction of the Lewis acid, B(C6F5)3 (BCF), or the Lewis base, pyridine, with 2 dissociates the dimer to afford the corresponding complexed monomeric Sn(II) azide, AriPr4SnN3BCF (4) in which BCF coordinates the α-nitrogen, or AriPr4Sn(pyridine)N3 (6) in which pyridine coordinates to the tin atom. Photolysis of 4 in diethyl ether for 12 h results in the insertion of the α-nitrogen of the azide group into one of the B-C bonds of the BCF acceptor to yield the tin(II) amide, AriPr4SnN(C6F5)B(C6F5)2 (5). In contrast, photolysis of 6 for over 36 h afforded no apparent reaction. A highly reactive Sn nitride intermediate, AriPr4Sn≡N, is proposed as part of the mechanistic pathway for the formation of 3 and 5 as a result of trapping the tin-centered radical isomers. This was effected by immediate freezing the samples of 2 or 4 after ca. 30 min of UV photolysis and recording their electron paramagnetic resonance spectra. These exhibited a rhombic g tensor of [g1, g2, g3] = [2.029, 1.978, 1.933]. This radical intermediate could be related to the valence isomers of the nitride [-SnIV≡N] intermediate, in isomeric equilibrium with the nitrene [-SnII-N] and nitridyl [-SnIII═N·] forms, but with the spin density on the nitrogen being quenched, possibly by the H atom abstraction to form an S = 1/2 species of formula -Sn·═N(H).
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Affiliation(s)
- Shuai Wang
- Department of Chemistry, University of California Davis , 1 Shields Avenue, Davis, California 95616, United States
| | - Lizhi Tao
- Department of Chemistry, University of California Davis , 1 Shields Avenue, Davis, California 95616, United States
| | - Troy A Stich
- Department of Chemistry, University of California Davis , 1 Shields Avenue, Davis, California 95616, United States
| | - Marilyn M Olmstead
- Department of Chemistry, University of California Davis , 1 Shields Avenue, Davis, California 95616, United States
| | - R David Britt
- Department of Chemistry, University of California Davis , 1 Shields Avenue, Davis, California 95616, United States
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15
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Soldatova AV, Romano CA, Tao L, Stich TA, Casey WH, Britt RD, Tebo BM, Spiro TG. Mn(II) Oxidation by the Multicopper Oxidase Complex Mnx: A Coordinated Two-Stage Mn(II)/(III) and Mn(III)/(IV) Mechanism. J Am Chem Soc 2017; 139:11381-11391. [PMID: 28712303 DOI: 10.1021/jacs.7b02772] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The bacterial manganese oxidase MnxG of the Mnx protein complex is unique among multicopper oxidases (MCOs) in carrying out a two-electron metal oxidation, converting Mn(II) to MnO2 nanoparticles. The reaction occurs in two stages: Mn(II) → Mn(III) and Mn(III) → MnO2. In a companion study , we show that the electron transfer from Mn(II) to the low-potential type 1 Cu of MnxG requires an activation step, likely forming a hydroxide bridge at a dinuclear Mn(II) site. Here we study the second oxidation step, using pyrophosphate (PP) as a Mn(III) trap. PP chelates Mn(III) produced by the enzyme and subsequently allows it to become a substrate for the second stage of the reaction. EPR spectroscopy confirms the presence of Mn(III) bound to the enzyme. The Mn(III) oxidation step does not involve direct electron transfer to the enzyme from Mn(III), which is shown by kinetic measurements to be excluded from the Mn(II) binding site. Instead, Mn(III) is proposed to disproportionate at an adjacent polynuclear site, thereby allowing indirect oxidation to Mn(IV) and recycling of Mn(II). PP plays a multifaceted role, slowing the reaction by complexing both Mn(II) and Mn(III) in solution, and also inhibiting catalysis, likely through binding at or near the active site. An overall mechanism for Mnx-catalyzed MnO2 production from Mn(II) is presented.
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Affiliation(s)
- Alexandra V Soldatova
- Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195, United States
| | - Christine A Romano
- Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University , Portland, Oregon 97239, United States
| | | | | | | | | | - Bradley M Tebo
- Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University , Portland, Oregon 97239, United States
| | - Thomas G Spiro
- Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195, United States
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16
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Soldatova AV, Tao L, Romano CA, Stich TA, Casey WH, Britt RD, Tebo BM, Spiro TG. Mn(II) Oxidation by the Multicopper Oxidase Complex Mnx: A Binuclear Activation Mechanism. J Am Chem Soc 2017; 139:11369-11380. [PMID: 28712284 DOI: 10.1021/jacs.7b02771] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The bacterial protein complex Mnx contains a multicopper oxidase (MCO) MnxG that, unusually, catalyzes the two-electron oxidation of Mn(II) to MnO2 biomineral, via a Mn(III) intermediate. Although Mn(III)/Mn(II) and Mn(IV)/Mn(III) reduction potentials are expected to be high, we find a low reduction potential, 0.38 V (vs Normal Hydrogen Electrode, pH 7.8), for the MnxG type 1 Cu2+, the electron acceptor. Indeed the type 1 Cu2+ is not reduced by Mn(II) in the absence of molecular oxygen, indicating that substrate oxidation requires an activation step. We have investigated the enzyme mechanism via electronic absorption spectroscopy, using chemometric analysis to separate enzyme-catalyzed MnO2 formation from MnO2 nanoparticle aging. The nanoparticle aging time course is characteristic of nucleation and particle growth; rates for these processes followed expected dependencies on Mn(II) concentration and temperature, but exhibited different pH optima. The enzymatic time course is sigmoidal, signaling an activation step, prior to turnover. The Mn(II) concentration and pH dependence of a preceding lag phase indicates weak Mn(II) binding. The activation step is enabled by a pKa > 8.6 deprotonation, which is assigned to Mn(II)-bound H2O; it induces a conformation change (consistent with a high activation energy, 106 kJ/mol) that increases Mn(II) affinity. Mnx activation is proposed to decrease the Mn(III/II) reduction potential below that of type 1 Cu(II/I) by formation of a hydroxide-bridged binuclear complex, Mn(II)(μ-OH)Mn(II), at the substrate site. Turnover is found to depend cooperatively on two Mn(II) and is enabled by a pKa 7.6 double deprotonation. It is proposed that turnover produces a Mn(III)(μ-OH)2Mn(III) intermediate that proceeds to the enzyme product, likely Mn(IV)(μ-O)2Mn(IV) or an oligomer, which subsequently nucleates MnO2 nanoparticles. We conclude that Mnx exploits manganese polynuclear chemistry in order to facilitate an otherwise difficult oxidation reaction, as well as biomineralization. The mechanism of the Mn(III/IV) conversion step is elucidated in an accompanying paper .
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Affiliation(s)
- Alexandra V Soldatova
- Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195, United States
| | | | - Christine A Romano
- Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University , Portland, Oregon 97239, United States
| | | | | | | | - Bradley M Tebo
- Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University , Portland, Oregon 97239, United States
| | - Thomas G Spiro
- Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195, United States
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17
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Tao L, Stich TA, Liou SH, Soldatova AV, Delgadillo DA, Romano CA, Spiro TG, Goodin DB, Tebo BM, Casey WH, Britt RD. Copper Binding Sites in the Manganese-Oxidizing Mnx Protein Complex Investigated by Electron Paramagnetic Resonance Spectroscopy. J Am Chem Soc 2017; 139:8868-8877. [DOI: 10.1021/jacs.7b02277] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | | | | | - Alexandra V. Soldatova
- Department
of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, United States
| | - David A. Delgadillo
- Department of Chemistry & Chemical Biology, University of California, 5200 North Lake Road, Merced, California 95343, United States
| | - Christine A. Romano
- Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Thomas G. Spiro
- Department
of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, United States
| | | | - Bradley M. Tebo
- Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University, Portland, Oregon 97239, United States
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18
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Stich TA, McAlpin JG, Wall RM, Rigsby ML, Britt RD. Electron Paramagnetic Resonance Characterization of Dioxygen-Bridged Cobalt Dimers with Relevance to Water Oxidation. Inorg Chem 2016; 55:12728-12736. [PMID: 27989208 DOI: 10.1021/acs.inorgchem.6b01954] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A variety of metal oxides can catalyze the oxidation of water to molecular oxygen when polarized by a sufficiently high electrochemical potential. Minimizing the overpotential and increasing the rate of the oxygen-evolving reaction (OER) are key goals in making such materials a component of viable energy storage devices. However, the structural factors that imbue the metal oxides with their catalytic power are difficult to assess as these solids contain many distinct metal-ion sites, have a varying amount of defect sites within the lattice, and can be composed of multiple phases. In the present study, we determined the magnetic properties for a series of dimeric cobalt complexes in which the two metal centers are bridged by a dioxygen moiety. Our spectroscopically validated electronic structure description indicates that each species is best described as two Co(III) ions that are bound to a μ-η1η1 superoxide ligand. Intriguingly, we found evidence that the two compounds that possess oxygen-evolving activity coordinate the superoxide ion in an unusual, nonplanar fashion. It appears as if the intermediately long Co···Co distance of 3.9 Å is responsible for the unusual superoxide binding geometry. This structural factor may be an important element in the design of solid-state OER catalysts.
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Affiliation(s)
- Troy A Stich
- Department of Chemistry, University of California , 1 Shields Avenue, Davis, California 95616-0935, United States
| | - J Gregory McAlpin
- Department of Chemistry, University of California , 1 Shields Avenue, Davis, California 95616-0935, United States
| | - Ryan M Wall
- Department of Chemistry, University of California , 1 Shields Avenue, Davis, California 95616-0935, United States
| | - Matthew L Rigsby
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706-1322, United States
| | - R David Britt
- Department of Chemistry, University of California , 1 Shields Avenue, Davis, California 95616-0935, United States
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19
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Stich TA, Gagnon DM, Anderson BL, Nocera DG, Britt RD. EPR Spectroscopic Characterization of a Jahn‐Teller Distorted (
C
3
v
→
C
s
) Four‐Coordinate Chromium(V) Oxo Species. Isr J Chem 2016. [DOI: 10.1002/ijch.201600036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Troy A. Stich
- Department of Chemistry University of California One Shields Avenue Davis CA 95616 USA
| | - Derek M. Gagnon
- Department of Chemistry University of California One Shields Avenue Davis CA 95616 USA
| | - Bryce L. Anderson
- Department of Chemistry and Chemical Biology Harvard University 12 Oxford Street Cambridge MA 02138 USA
| | - Daniel G. Nocera
- Department of Chemistry and Chemical Biology Harvard University 12 Oxford Street Cambridge MA 02138 USA
| | - R. David Britt
- Department of Chemistry University of California One Shields Avenue Davis CA 95616 USA
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20
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Wagner CL, Tao L, Thompson EJ, Stich TA, Guo J, Fettinger JC, Berben LA, Britt RD, Nagase S, Power PP. Dispersion‐Force‐Assisted Disproportionation: A Stable Two‐Coordinate Copper(II) Complex. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605061] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Clifton L. Wagner
- Department of Chemistry University of California, Davis One Shield Avenue Davis CA 95616 USA
| | - Lizhi Tao
- Department of Chemistry University of California, Davis One Shield Avenue Davis CA 95616 USA
| | - Emily J. Thompson
- Department of Chemistry University of California, Davis One Shield Avenue Davis CA 95616 USA
| | - Troy A. Stich
- Department of Chemistry University of California, Davis One Shield Avenue Davis CA 95616 USA
| | - Jingdong Guo
- Fukui Institute for Fundamental Chemistry Kyoto University Takano Nishi-Hiraki-cho 34-4, Sakyo-ku Kyoto, 606–8103 Japan
| | - James C. Fettinger
- Department of Chemistry University of California, Davis One Shield Avenue Davis CA 95616 USA
| | - Louise A. Berben
- Department of Chemistry University of California, Davis One Shield Avenue Davis CA 95616 USA
| | - R. David Britt
- Department of Chemistry University of California, Davis One Shield Avenue Davis CA 95616 USA
| | - Shigeru Nagase
- Fukui Institute for Fundamental Chemistry Kyoto University Takano Nishi-Hiraki-cho 34-4, Sakyo-ku Kyoto, 606–8103 Japan
| | - Philip P. Power
- Department of Chemistry University of California, Davis One Shield Avenue Davis CA 95616 USA
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21
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Wagner CL, Tao L, Thompson EJ, Stich TA, Guo J, Fettinger JC, Berben LA, Britt RD, Nagase S, Power PP. Dispersion‐Force‐Assisted Disproportionation: A Stable Two‐Coordinate Copper(II) Complex. Angew Chem Int Ed Engl 2016; 55:10444-7. [DOI: 10.1002/anie.201605061] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Indexed: 12/22/2022]
Affiliation(s)
- Clifton L. Wagner
- Department of Chemistry University of California, Davis One Shield Avenue Davis CA 95616 USA
| | - Lizhi Tao
- Department of Chemistry University of California, Davis One Shield Avenue Davis CA 95616 USA
| | - Emily J. Thompson
- Department of Chemistry University of California, Davis One Shield Avenue Davis CA 95616 USA
| | - Troy A. Stich
- Department of Chemistry University of California, Davis One Shield Avenue Davis CA 95616 USA
| | - Jingdong Guo
- Fukui Institute for Fundamental Chemistry Kyoto University Takano Nishi-Hiraki-cho 34-4, Sakyo-ku Kyoto, 606–8103 Japan
| | - James C. Fettinger
- Department of Chemistry University of California, Davis One Shield Avenue Davis CA 95616 USA
| | - Louise A. Berben
- Department of Chemistry University of California, Davis One Shield Avenue Davis CA 95616 USA
| | - R. David Britt
- Department of Chemistry University of California, Davis One Shield Avenue Davis CA 95616 USA
| | - Shigeru Nagase
- Fukui Institute for Fundamental Chemistry Kyoto University Takano Nishi-Hiraki-cho 34-4, Sakyo-ku Kyoto, 606–8103 Japan
| | - Philip P. Power
- Department of Chemistry University of California, Davis One Shield Avenue Davis CA 95616 USA
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22
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Oyala PH, Ravichandran KR, Funk MA, Stucky PA, Stich TA, Drennan CL, Britt RD, Stubbe J. Biophysical Characterization of Fluorotyrosine Probes Site-Specifically Incorporated into Enzymes: E. coli Ribonucleotide Reductase As an Example. J Am Chem Soc 2016; 138:7951-64. [PMID: 27276098 PMCID: PMC4929525 DOI: 10.1021/jacs.6b03605] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
Fluorinated tyrosines
(FnY’s, n = 2
and 3) have been site-specifically incorporated into E. coli class Ia ribonucleotide reductase (RNR) using the
recently evolved M. jannaschii Y-tRNA synthetase/tRNA
pair. Class Ia RNRs require four redox active Y’s, a stable
Y radical (Y·) in the β subunit (position 122 in E. coli), and three transiently oxidized Y’s (356
in β and 731 and 730 in α) to initiate the radical-dependent
nucleotide reduction process. FnY (3,5;
2,3; 2,3,5; and 2,3,6) incorporation in place of Y122-β
and the X-ray structures of each resulting β with a diferric
cluster are reported and compared with wt-β2 crystallized under
the same conditions. The essential diferric-FnY· cofactor is self-assembled from apo FnY-β2, Fe2+, and O2 to produce ∼1
Y·/β2 and ∼3 Fe3+/β2. The FnY· are stable and active in nucleotide
reduction with activities that vary from 5% to 85% that of wt-β2.
Each FnY·-β2 has been characterized
by 9 and 130 GHz electron paramagnetic resonance and high-field electron
nuclear double resonance spectroscopies. The hyperfine interactions
associated with the 19F nucleus provide unique signatures
of each FnY· that are readily distinguishable
from unlabeled Y·’s. The variability of the abiotic FnY pKa’s
(6.4 to 7.8) and reduction potentials (−30 to +130 mV relative
to Y at pH 7.5) provide probes of enzymatic reactions proposed to
involve Y·’s in catalysis and to investigate the importance
and identity of hopping Y·’s within redox active proteins
proposed to protect them from uncoupled radical chemistry.
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Affiliation(s)
- Paul H Oyala
- Department of Chemistry, University of California, Davis , One Shields Avenue, Davis, California 95616, United States
| | | | | | - Paul A Stucky
- Department of Chemistry, University of California, Davis , One Shields Avenue, Davis, California 95616, United States
| | - Troy A Stich
- Department of Chemistry, University of California, Davis , One Shields Avenue, Davis, California 95616, United States
| | - Catherine L Drennan
- Howard Hughes Medical Institute, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - R David Britt
- Department of Chemistry, University of California, Davis , One Shields Avenue, Davis, California 95616, United States
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23
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Tao L, Stich TA, Butterfield CN, Romano CA, Spiro TG, Tebo BM, Casey WH, Britt RD. Mn(II) Binding and Subsequent Oxidation by the Multicopper Oxidase MnxG Investigated by Electron Paramagnetic Resonance Spectroscopy. J Am Chem Soc 2015; 137:10563-75. [DOI: 10.1021/jacs.5b04331] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
| | | | - Cristina N. Butterfield
- Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Christine A. Romano
- Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Thomas G. Spiro
- Department
of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, United States
| | - Bradley M. Tebo
- Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University, Portland, Oregon 97239, United States
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24
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Oyala PH, Stich TA, Debus RJ, Britt RD. Ammonia Binds to the Dangler Manganese of the Photosystem II Oxygen-Evolving Complex. J Am Chem Soc 2015; 137:8829-37. [DOI: 10.1021/jacs.5b04768] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Paul H. Oyala
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Troy A. Stich
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Richard J. Debus
- Department of Biochemistry, University of California, Riverside, Riverside, California 92521, United States
| | - R. David Britt
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
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25
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Oyala PH, Stich TA, Britt RD. Metal ion oxidation state assignment based on coordinating ligand hyperfine interaction. Photosynth Res 2015; 124:7-18. [PMID: 25663565 DOI: 10.1007/s11120-015-0086-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 01/12/2015] [Indexed: 06/04/2023]
Abstract
In exchange-coupled mixed-valence spin systems, the magnitude and sign of the effective ligand hyperfine interaction (HFI) can be useful in determining the formal oxidation state of the coordinating metal ion, as well as provide information about the coordination geometry. This is due to the fact that the observed ligand HFI is a function of the projection factor (Clebsch-Gordon coefficient) that maps the site spin value S i of the local paramagnetic center onto the total spin of the exchange-coupled system, S T. Recently, this relationship has been successfully exploited in identifying the oxidation state of the Mn ion coordinated by the sole nitrogenous ligand to the oxygen-evolving complex in certain states of photosystem II. The origin and evolution of these efforts is described.
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Affiliation(s)
- Paul H Oyala
- Department of Chemistry, University of California-Davis, One Shields Avenue, Davis, CA, 95616, USA
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Parthasarathy A, Stich TA, Lohner ST, Lesnefsky A, Britt RD, Spormann AM. Biochemical and EPR-spectroscopic investigation into heterologously expressed vinyl chloride reductive dehalogenase (VcrA) from Dehalococcoides mccartyi strain VS. J Am Chem Soc 2015; 137:3525-32. [PMID: 25686300 PMCID: PMC4516053 DOI: 10.1021/ja511653d] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Reductive dehalogenases play a critical role in the microbial detoxification of aquifers contaminated with chloroethenes and chlorethanes by catalyzing the reductive elimination of a halogen. We report here the first heterologous production of vinyl chloride reductase VcrA from Dehalococcoides mccartyi strain VS. Heterologously expressed VcrA was reconstituted to its active form by addition of hydroxocobalamin/adenosylcobalamin, Fe(3+), and sulfide in the presence of mercaptoethanol. The kinetic properties of reconstituted VcrA catalyzing vinyl chloride reduction with Ti(III)-citrate as reductant and methyl viologen as mediator were similar to those obtained previously for VcrA as isolated from D. mccartyi strain VS. VcrA was also found to catalyze a novel reaction, the environmentally important dihaloelimination of 1,2-dichloroethane to ethene. Electron paramagnetic resonance (EPR) spectroscopic studies with reconstituted VcrA in the presence of mercaptoethanol revealed the presence of Cob(II)alamin. Addition of Ti(III)-citrate resulted in the appearance of a new signal characteristic of a reduced [4Fe-4S] cluster and the disappearance of the Cob(II)alamin signal. UV-vis absorption spectroscopy of Ti(III)citrate-treated samples revealed the formation of two new absorption maxima characteristic of Cob(I)alamin. No evidence for the presence of a [3Fe-4S] cluster was found. We postulate that during the reaction cycle of VcrA, a reduced [4Fe-4S] cluster reduces Co(II) to Co(I) of the enzyme-bound cobalamin. Vinyl chloride reduction to ethene would be initiated when Cob(I)alamin transfers an electron to the substrate, generating a vinyl radical as a potential reaction intermediate.
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Affiliation(s)
- Anutthaman Parthasarathy
- Departments of Chemical Engineering and Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
| | - Troy A. Stich
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Svenja T. Lohner
- Departments of Chemical Engineering and Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
| | - Ann Lesnefsky
- Departments of Chemical Engineering and Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
| | - R. David Britt
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Alfred M. Spormann
- Departments of Chemical Engineering and Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
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Gagnon DM, Brophy MB, Bowman SEJ, Stich TA, Drennan CL, Britt RD, Nolan EM. Manganese binding properties of human calprotectin under conditions of high and low calcium: X-ray crystallographic and advanced electron paramagnetic resonance spectroscopic analysis. J Am Chem Soc 2015; 137:3004-16. [PMID: 25597447 DOI: 10.1021/ja512204s] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The antimicrobial protein calprotectin (CP), a hetero-oligomer of the S100 family members S100A8 and S100A9, is the only identified mammalian Mn(II)-sequestering protein. Human CP uses Ca(II) ions to tune its Mn(II) affinity at a biologically unprecedented hexahistidine site that forms at the S100A8/S100A9 interface, and the molecular basis for this phenomenon requires elucidation. Herein, we investigate the remarkable Mn(II) coordination chemistry of human CP using X-ray crystallography as well as continuous-wave (CW) and pulse electron paramagnetic resonance (EPR) spectroscopies. An X-ray crystallographic structure of Mn(II)-CP containing one Mn(II), two Ca(II), and two Na(I) ions per CP heterodimer is reported. The CW EPR spectrum of Ca(II)- and Mn(II)-bound CP prepared with a 10:0.9:1 Ca(II):Mn(II):CP ratio is characterized by an unusually low zero-field splitting of 485 MHz (E/D = 0.30) for the S = 5/2 Mn(II) ion, consistent with the high symmetry of the His6 binding site observed crystallographically. Results from electron spin-echo envelope modulation and electron-nuclear double resonance experiments reveal that the six Mn(II)-coordinating histidine residues of Ca(II)- and Mn(II)-bound CP are spectroscopically equivalent. The observed (15)N (I = 1/2) hyperfine couplings (A) arise from two distinct classes of nitrogen atoms: the coordinating ε-nitrogen of the imidazole ring of each histidine ligand (A = [3.45, 3.71, 5.91] MHz) and the distal δ-nitrogen (A = [0.11, 0.18, 0.42] MHz). In the absence of Ca(II), the binding affinity of CP for Mn(II) drops by two to three orders of magnitude and coincides with Mn(II) binding at the His6 site as well as other sites. This study demonstrates the role of Ca(II) in enabling high-affinity and specific binding of Mn(II) to the His6 site of human calprotectin.
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Affiliation(s)
- Derek M Gagnon
- Department of Chemistry, University of California , Davis, California 95616, United States
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Oyala PH, Stich TA, Stull JA, Yu F, Pecoraro VL, Britt RD. Pulse electron paramagnetic resonance studies of the interaction of methanol with the S2 state of the Mn4O5Ca cluster of photosystem II. Biochemistry 2014; 53:7914-28. [PMID: 25441091 DOI: 10.1021/bi501323h] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The binding of the substrate analogue methanol to the catalytic Mn4CaO5 cluster of the water-oxidizing enzyme photosystem II is known to alter the electronic structure properties of the oxygen-evolving complex without retarding O2-evolution under steady-state illumination conditions. We report the binding mode of (13)C-labeled methanol determined using 9.4 GHz (X-band) hyperfine sublevel-correlation (HYSCORE) and 34 GHz (Q-band) electron spin-echo electron nuclear double resonance (ESE-ENDOR) spectroscopies. These results are compared to analogous experiments on a mixed-valence Mn(III)Mn(IV) complex (2-OH-3,5-Cl2-salpn)2Mn(III)Mn(IV) (salpn = N,N'-bis(3,5-dichlorosalicylidene)-1,3-diamino-2-hydroxypropane) in which methanol ligates to the Mn(III) ion ( Larson et al. (1992) J. Am. Chem. Soc. , 114 , 6263 ). In the mixed-valence Mn(III,IV) complex, the hyperfine coupling to the (13)C of the bound methanol (Aiso = 0.65 MHz, T = 1.25 MHz) is appreciably larger than that observed for (13)C methanol associated with the Mn4CaO5 cluster poised in the S2 state, where only a weak dipolar hyperfine interaction (Aiso = 0.05 MHz, T = 0.27 MHz) is observed. An evaluation of the (13)C hyperfine interaction using the X-ray structure coordinates of the Mn4CaO5 cluster indicates that methanol does not bind as a terminal ligand to any of the manganese ions in the oxygen-evolving complex. We favor methanol binding in place of a water ligand to the Ca(2+) in the Mn4CaO5 cluster or in place of one of the waters that form hydrogen bonds with the oxygen bridges of the cluster.
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Affiliation(s)
- Paul H Oyala
- Department of Chemistry, University of California-Davis , One Shields Avenue, Davis, California 95616, United States
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Myers WK, Stich TA, Suess DLM, Kuchenreuther JM, Swartz JR, Britt RD. The cyanide ligands of [FeFe] hydrogenase: pulse EPR studies of (13)C and (15)N-labeled H-cluster. J Am Chem Soc 2014; 136:12237-40. [PMID: 25133957 PMCID: PMC4156861 DOI: 10.1021/ja507046w] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
The
two cyanide ligands in the assembled cluster of [FeFe] hydrogenase
originate from exogenous l-tyrosine. Using selectively labeled
tyrosine substrates, the cyanides were isotopically labeled via a
recently developed in vitro maturation procedure
allowing advanced electron paramagnetic resonance techniques to probe
the electronic structure of the catalytic core of the enzyme. The
ratio of the isotropic 13C hyperfine interactions for the
two CN– ligands—a reporter of spin density
on their respective coordinating iron ions—collapses from ≈5.8
for the Hox form of hydrogenase to <2 for the CO-inhibited
form. Additionally, when the maturation was carried out using [15N]-tyrosine, no features previously ascribed to the nitrogen
of the bridging dithiolate ligand were observed suggesting that this
bridge is not sourced from tyrosine.
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Affiliation(s)
- William K Myers
- Department of Chemistry, University of California, Davis , Davis, California 95616 United States
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Abstract
A [4Fe-4S](+) cluster reduces a bound S-adenosylmethionine (SAM) molecule, cleaving it into methionine and a 5'-deoxyadenosyl radical (5'-dA(•)). This step initiates the varied chemistry catalyzed by each of the so-called radical SAM enzymes. The strongly oxidizing 5'-dA(•) is quenched by abstracting a H-atom from a target species. In some cases, this species is an exogenous molecule of substrate, for example, L-tyrosine in the [FeFe] hydrogenase maturase, HydG. In other cases, the target is a proteinaceous residue as in all the glycyl radical forming enzymes. The generation of this initial radical species and the subsequent chemistry involving downstream radical intermediates is meticulously controlled by the enzyme so as to prevent unwanted reactions. But the manner in which this control is exerted is unknown. Electron paramagnetic resonance (EPR) spectroscopy has proven to be a valuable tool used to gain insight into these mechanisms. In this Account, we summarize efforts to trap such radical intermediates in radical SAM enzymes and highlight four examples in which EPR spectroscopic results have shed significant light on the corresponding mechanism. For lysine 2,3-aminomutase, nearly each possible intermediate, from an analogue of the initial 5'-dA(•) to the product radical L-β-lysine, has been explored. A paramagnetic intermediate observed in biotin synthase is shown to involve an auxiliary [FeS] cluster whose bridging sulfide is a co-substrate for the final step in the biosynthesis of vitamin B7. In HydG, the L-tyrosine substrate is converted in unprecedented fashion to a 4-oxidobenzyl radical on the way to generating CO and CN(-) ligands for the [FeFe] cluster of hydrogenase. And finally, EPR has confirmed a mechanistic proposal for the antibiotic resistance protein Cfr, which methylates the unactivated sp(2)-hybridized C8-carbon of an adenosine base of 23S ribosomal RNA. These four systems provide just a brief survey of the ever-growing set of radical SAM enzymes. The diverse chemistries catalyzed by these enzymes make them an intriguing target for continuing study, and EPR spectroscopy, in particular, seems ideally placed to contribute to our understanding.
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Affiliation(s)
- Troy A. Stich
- Department of Chemistry, University of California, One Shields
Avenue, Davis, California 95616, United States
| | - William K. Myers
- Department of Chemistry, University of California, One Shields
Avenue, Davis, California 95616, United States
| | - R. David Britt
- Department of Chemistry, University of California, One Shields
Avenue, Davis, California 95616, United States
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Kuchenreuther JM, Myers WK, Suess DLM, Stich TA, Pelmenschikov V, Shiigi SA, Cramer SP, Swartz JR, Britt RD, George SJ. The HydG enzyme generates an Fe(CO)2(CN) synthon in assembly of the FeFe hydrogenase H-cluster. Science 2014; 343:424-7. [PMID: 24458644 DOI: 10.1126/science.1246572] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Three iron-sulfur proteins--HydE, HydF, and HydG--play a key role in the synthesis of the [2Fe](H) component of the catalytic H-cluster of FeFe hydrogenase. The radical S-adenosyl-L-methionine enzyme HydG lyses free tyrosine to produce p-cresol and the CO and CN(-) ligands of the [2Fe](H) cluster. Here, we applied stopped-flow Fourier transform infrared and electron-nuclear double resonance spectroscopies to probe the formation of HydG-bound Fe-containing species bearing CO and CN(-) ligands with spectroscopic signatures that evolve on the 1- to 1000-second time scale. Through study of the (13)C, (15)N, and (57)Fe isotopologs of these intermediates and products, we identify the final HydG-bound species as an organometallic Fe(CO)2(CN) synthon that is ultimately transferred to apohydrogenase to form the [2Fe](H) component of the H-cluster.
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Affiliation(s)
- Jon M Kuchenreuther
- Department of Chemistry, University of California, Davis, Davis, CA 95616, USA
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Stull JA, Stich TA, Hurst JK, Britt RD. Electron Paramagnetic Resonance Analysis of a Transient Species Formed During Water Oxidation Catalyzed by the Complex Ion [(bpy)2Ru(OH2)]2O4+. Inorg Chem 2013; 52:4578-86. [DOI: 10.1021/ic4001158] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Jamie A. Stull
- Department of Chemistry, University of California−Davis, One Shields
Avenue, Davis, California 95616, United States
| | - Troy A. Stich
- Department of Chemistry, University of California−Davis, One Shields
Avenue, Davis, California 95616, United States
| | - James K. Hurst
- Department of Chemistry, Washington State University, Pullman, Washington 99164-4630, United
States
| | - R. David Britt
- Department of Chemistry, University of California−Davis, One Shields
Avenue, Davis, California 95616, United States
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Cotruvo JA, Stich TA, Britt RD, Stubbe J. Mechanism of assembly of the dimanganese-tyrosyl radical cofactor of class Ib ribonucleotide reductase: enzymatic generation of superoxide is required for tyrosine oxidation via a Mn(III)Mn(IV) intermediate. J Am Chem Soc 2013; 135:4027-39. [PMID: 23402532 DOI: 10.1021/ja312457t] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ribonucleotide reductases (RNRs) utilize radical chemistry to reduce nucleotides to deoxynucleotides in all organisms. In the class Ia and Ib RNRs, this reaction requires a stable tyrosyl radical (Y(•)) generated by oxidation of a reduced dinuclear metal cluster. The Fe(III)2-Y(•) cofactor in the NrdB subunit of the class Ia RNRs can be generated by self-assembly from Fe(II)2-NrdB, O2, and a reducing equivalent. By contrast, the structurally homologous class Ib enzymes require a Mn(III)2-Y(•) cofactor in their NrdF subunit. Mn(II)2-NrdF does not react with O2, but it binds the reduced form of a conserved flavodoxin-like protein, NrdIhq, which, in the presence of O2, reacts to form the Mn(III)2-Y(•) cofactor. Here we investigate the mechanism of assembly of the Mn(III)2-Y(•) cofactor in Bacillus subtilis NrdF. Cluster assembly from Mn(II)2-NrdF, NrdI(hq), and O2 has been studied by stopped flow absorption and rapid freeze quench EPR spectroscopies. The results support a mechanism in which NrdI(hq) reduces O2 to O2(•-) (40-48 s(-1), 0.6 mM O2), the O2(•-) channels to and reacts with Mn(II)2-NrdF to form a Mn(III)Mn(IV) intermediate (2.2 ± 0.4 s(-1)), and the Mn(III)Mn(IV) species oxidizes tyrosine to Y(•) (0.08-0.15 s(-1)). Controlled production of O2(•-) by NrdIhq during class Ib RNR cofactor assembly both circumvents the unreactivity of the Mn(II)2 cluster with O2 and satisfies the requirement for an "extra" reducing equivalent in Y(•) generation.
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Affiliation(s)
- Joseph A Cotruvo
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
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Kanady JS, Tran R, Stull JA, Lu L, Stich TA, Day MW, Yano J, Britt RD, Agapie T. Role of Oxido Incorporation and Ligand Lability in Expanding Redox Accessibility of Structurally Related Mn 4 Clusters. Chem Sci 2013; 4:3986-3996. [PMID: 24163730 DOI: 10.1039/c3sc51406d] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Photosystem II supports four manganese centers through nine oxidation states from manganese(II) during assembly through to the most oxidized state before O2 formation and release. The protein-based carboxylate and imidazole ligands allow for significant changes of the coordination environment during the incorporation of hydroxido and oxido ligands upon oxidation of the metal centers. We report the synthesis and characterization of a series of tetramanganese complexes in four of the six oxidation states from MnII3MnIII to MnIII2 MnIV2 with the same ligand framework (L) by incorporating four oxido ligands. A 1,3,5-triarylbenzene framework appended with six pyridyl and three alkoxy groups was utilized along with three acetate anions to access tetramanganese complexes, Mn4O x , with x = 1, 2, 3, and 4. Alongside two previously reported complexes, four new clusters in various states were isolated and characterized by crystallography, and four were observed electrochemically, thus accessing the eight oxidation states from MnII4 to MnIIIMnIV3. This structurally related series of compounds was characterized by EXAFS, XANES, EPR, magnetism, and cyclic voltammetry. Similar to the ligands in the active site of the protein, the ancillary ligand (L) is preserved throughout the series and changes its binding mode between the low and high oxido-content clusters. Implications for the rational assembly and properties of high oxidation state metal-oxido clusters are presented.
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Affiliation(s)
- Jacob S Kanady
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd MC 127-72, Pasadena CA 91125, USA
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35
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Fugate CJ, Stich TA, Kim EG, Myers WK, Britt RD, Jarrett JT. 9-Mercaptodethiobiotin is generated as a ligand to the [2Fe-2S]+ cluster during the reaction catalyzed by biotin synthase from Escherichia coli. J Am Chem Soc 2012; 134:9042-5. [PMID: 22607542 PMCID: PMC3418058 DOI: 10.1021/ja3012963] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Biotin synthase catalyzes formation of the thiophane ring through stepwise substitution of a sulfur atom for hydrogen atoms at the C9 and C6 positions of dethiobiotin. Biotin synthase is a radical S-adenosylmethionine (SAM) enzyme that reductively cleaves S-adenosylmethionine, generating 5'-deoxyadenosyl radicals that initially abstract a hydrogen atom from the C9 position of dethiobiotin. We have proposed that the resulting dethiobiotinyl radical is quenched by the μ-sulfide of the nearby [2Fe-2S](2+) cluster, resulting in coupled formation of 9-mercaptodethiobiotin and a reduced [2Fe-2S](+) cluster. This reduced FeS cluster is observed by electron paramagnetic resonance spectroscopy as a mixture of two orthorhombic spin systems. In the present work, we use isotopically labeled 9-mercaptodethiobiotin and enzyme to probe the ligand environment of the [2Fe-2S](+) cluster in this reaction intermediate. Hyperfine sublevel correlation spectroscopy (HYSCORE) spectra exhibit strong cross-peaks demonstrating strong isotropic coupling of the nuclear spin with the paramagnetic center. The hyperfine coupling constants are consistent with a structural model for the reaction intermediate in which 9-mercaptodethiobiotin is covalently coordinated to the remnant [2Fe-2S](+) cluster.
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Affiliation(s)
- Corey J. Fugate
- Department of Chemistry, University of Hawai’i at Manoa, Honolulu, Hawai’i 96822, United States
| | - Troy A. Stich
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Esther G. Kim
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - William K. Myers
- 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
| | - Joseph T. Jarrett
- Department of Chemistry, University of Hawai’i at Manoa, Honolulu, Hawai’i 96822, United States
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Bigi JP, Harman WH, Lassalle-Kaiser B, Robles DM, Stich TA, Yano J, Britt RD, Chang CJ. A high-spin iron(IV)-oxo complex supported by a trigonal nonheme pyrrolide platform. J Am Chem Soc 2012; 134:1536-42. [PMID: 22214221 DOI: 10.1021/ja207048h] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report the generation and characterization of a new high-spin iron(IV)-oxo complex supported by a trigonal nonheme pyrrolide platform. Oxygen-atom transfer to [(tpa(Mes))Fe(II)](-) (tpa(Ar) = tris(5-arylpyrrol-2-ylmethyl)amine) in acetonitrile solution affords the Fe(III)-alkoxide product [(tpa(Mes2MesO))Fe(III)](-) resulting from intramolecular C-H oxidation with no observable ferryl intermediates. In contrast, treatment of the phenyl derivative [(tpa(Ph))Fe(II)](-) with trimethylamine N-oxide in acetonitrile solution produces the iron(IV)-oxo complex [(tpa(Ph))Fe(IV)(O)](-) that has been characterized by a suite of techniques, including mass spectrometry as well as UV-vis, FTIR, Mössbauer, XAS, and parallel-mode EPR spectroscopies. Mass spectral, FTIR, and optical absorption studies provide signatures for the iron-oxo chromophore, and Mössbauer and XAS measurements establish the presence of an Fe(IV) center. Moreover, the Fe(IV)-oxo species gives parallel-mode EPR features indicative of a high-spin, S = 2 system. Preliminary reactivity studies show that the high-spin ferryl tpa(Ph) complex is capable of mediating intermolecular C-H oxidation as well as oxygen-atom transfer chemistry.
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Affiliation(s)
- Julian P Bigi
- Department of Chemistry, University of California Berkeley, Berkeley, California 94720, USA
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37
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Sheng Y, Stich TA, Barnese K, Gralla EB, Cascio D, Britt RD, Cabelli DE, Valentine JS. Comparison of two yeast MnSODs: mitochondrial Saccharomyces cerevisiae versus cytosolic Candida albicans. J Am Chem Soc 2011; 133:20878-89. [PMID: 22077216 DOI: 10.1021/ja2077476] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Human MnSOD is significantly more product-inhibited than bacterial MnSODs at high concentrations of superoxide (O(2)(-)). This behavior limits the amount of H(2)O(2) produced at high [O(2)(-)]; its desirability can be explained by the multiple roles of H(2)O(2) in mammalian cells, particularly its role in signaling. To investigate the mechanism of product inhibition in MnSOD, two yeast MnSODs, one from Saccharomyces cerevisiae mitochondria (ScMnSOD) and the other from Candida albicans cytosol (CaMnSODc), were isolated and characterized. ScMnSOD and CaMnSODc are similar in catalytic kinetics, spectroscopy, and redox chemistry, and they both rest predominantly in the reduced state (unlike most other MnSODs). At high [O(2)(-)], the dismutation efficiencies of the yeast MnSODs surpass those of human and bacterial MnSODs, due to very low level of product inhibition. Optical and parallel-mode electron paramagnetic resonance (EPR) spectra suggest the presence of two Mn(3+) species in yeast Mn(3+)SODs, including the well-characterized 5-coordinate Mn(3+) species and a 6-coordinate L-Mn(3+) species with hydroxide as the putative sixth ligand (L). The first and second coordination spheres of ScMnSOD are more similar to bacterial than to human MnSOD. Gln154, an H-bond donor to the Mn-coordinated solvent molecule, is slightly further away from Mn in yeast MnSODs, which may result in their unusual resting state. Mechanistically, the high efficiency of yeast MnSODs could be ascribed to putative translocation of an outer-sphere solvent molecule, which could destabilize the inhibited complex and enhance proton transfer from protein to peroxide. Our studies on yeast MnSODs indicate the unique nature of human MnSOD in that it predominantly undergoes the inhibited pathway at high [O(2)(-)].
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Affiliation(s)
- Yuewei Sheng
- Department of Chemistry and Biochemistry, University of California Los Angeles, 420 Westwood Plaza, Los Angeles, California 90095, USA
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McAlpin JG, Stich TA, Ohlin CA, Surendranath Y, Nocera DG, Casey WH, Britt RD. Electronic Structure Description of a [Co(III)3Co(IV)O4] Cluster: A Model for the Paramagnetic Intermediate in Cobalt-Catalyzed Water Oxidation. J Am Chem Soc 2011; 133:15444-52. [DOI: 10.1021/ja202320q] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | - C. André Ohlin
- School of Chemistry, Monash University, Vic 3800, Australia
| | - Yogesh Surendranath
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Daniel G. Nocera
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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39
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Stich TA, Yeagle GJ, Service RJ, Debus RJ, Britt RD. Ligation of D1-His332 and D1-Asp170 to the manganese cluster of photosystem II from Synechocystis assessed by multifrequency pulse EPR spectroscopy. Biochemistry 2011; 50:7390-404. [PMID: 21790179 DOI: 10.1021/bi2010703] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Multifrequency electron spin-echo envelope modulation (ESEEM) spectroscopy is used to ascertain the nature of the bonding interactions of various active site amino acids with the Mn ions that compose the oxygen-evolving cluster (OEC) in photosystem II (PSII) from the cyanobacterium Synechocystis sp. PCC 6803 poised in the S(2) state. Spectra of natural isotopic abundance PSII ((14)N-PSII), uniformly (15)N-labeled PSII ((15)N-PSII), and (15)N-PSII containing (14)N-histidine ((14)N-His/(15)N-PSII) are compared. These complementary data sets allow for a precise determination of the spin Hamiltonian parameters of the postulated histidine nitrogen interaction with the Mn ions of the OEC. These results are compared to those from a similar study on PSII isolated from spinach. Upon mutation of His332 of the D1 polypeptide to a glutamate residue, all isotopically sensitive spectral features vanish. Additional K(a)- and Q-band ESEEM experiments on the D1-D170H site-directed mutant give no indication of new (14)N-based interactions.
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Affiliation(s)
- Troy A Stich
- Department of Chemistry, University of California at Davis, Davis, California 95616, United States
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Barnese K, Sheng Y, Stich TA, Gralla EB, Britt RD, Cabelli DE, Valentine JS. Investigation of the highly active manganese superoxide dismutase from Saccharomyces cerevisiae. J Am Chem Soc 2011; 132:12525-7. [PMID: 20726524 DOI: 10.1021/ja104179r] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Manganese superoxide dismutase (MnSOD) from different species differs in its efficiency in removing high concentrations of superoxide (O(2)(-)), due to different levels of product inhibition. Human MnSOD exhibits a substantially higher level of product inhibition than the MnSODs from bacteria. In order to investigate the mechanism of product inhibition and whether it is a feature common to eukaryotic MnSODs, we purified MnSOD from Saccharomyces cerevisiae (ScMnSOD). It was a tetramer with 0.6 equiv of Mn per monomer. The catalytic activity of ScMnSOD was investigated by pulse radiolysis and compared with human and two bacterial (Escherichia coli and Deinococcus radiodurans) MnSODs. To our surprise, ScMnSOD most efficiently facilitates removal of high concentrations of O(2)(-) among these MnSODs. The gating value k(2)/k(3) that characterizes the level of product inhibition scales as ScMnSOD > D. radiodurans MnSOD > E. coli MnSOD > human MnSOD. While most MnSODs rest as the oxidized form, ScMnSOD was isolated in the Mn(2+) oxidation state as revealed by its optical and electron paramagnetic resonance spectra. This finding poses the possibility of elucidating the origin of product inhibition by comparing human MnSOD with ScMnSOD.
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Affiliation(s)
- Kevin Barnese
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
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Ellis PD, Sears JA, Yang P, Dupuis M, Boron TT, Pecoraro VL, Stich TA, Britt RD, Lipton AS. Solid-state (55)Mn NMR spectroscopy of bis(μ-oxo)dimanganese(IV) [Mn(2)O(2)(salpn)(2)], a model for the oxygen evolving complex in photosystem II. J Am Chem Soc 2010; 132:16727-9. [PMID: 21058720 DOI: 10.1021/ja1054252] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have examined the antiferromagneticly coupled bis(μ-oxo)dimanganese(IV) complex [Mn(2)O(2)(salpn)(2)] (1) with (55)Mn solid-state NMR at cryogenic temperatures and first-principle theory. The extracted values of the (55)Mn quadrupole coupling constant, C(Q), and its asymmetry parameter, η(Q), for 1 are 24.7 MHz and 0.43, respectively. Further, there was a large anisotropic contribution to the shielding of each Mn(4+), i.e. a Δσ of 3375 ppm. Utilizing broken symmetry density functional theory, the predicted values of the electric field gradient (EFG) or equivalently the C(Q) and η(Q) at ZORA, PBE QZ4P all electron level of theory are 23.4 MHz and 0.68, respectively, in good agreement with experimental observations.
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Affiliation(s)
- Paul D Ellis
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battlelle Boulevard, Richland, Washington 99352, United States, USA
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Stich TA, Whittaker JW, Britt RD. Multifrequency EPR studies of manganese catalases provide a complete description of proteinaceous nitrogen coordination. J Phys Chem B 2010; 114:14178-88. [PMID: 20055466 PMCID: PMC3418057 DOI: 10.1021/jp908064y] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Pulse electron paramagnetic resonance (EPR) spectroscopy is employed at two very different excitation frequencies, 9.77 and 30.67 GHz, in the study of the nitrogen coordination environment of the Mn(III)Mn(IV) state of the dimanganese-containing catalases from Lactobacillus plantarum and Thermus thermophilus. Consistent with previous studies, the lower-frequency results reveal one unique histidine nitrogen-Mn cluster interaction. For the first time, a second, more strongly hyperfine-coupled (14)N atom is unambiguously observed through the use of higher frequency/higher field EPR spectroscopy. The low excitation frequency spectral features are rationalized as arising from the interaction of a histidine nitrogen that is bound to the Mn(IV) ion, and the higher excitation frequency features are attributed to the histidine nitrogen bound to the Mn(III) ion. These results allow for the computation of intrinsic hyperfine coupling constants, which range from 2.2 to 2.9 MHz, for sp(2)-hybridized nitrogens coordinating equatorially to high-valence Mn ions. The relevance of these findings is discussed in the context of recent results from analogous higher frequency EPR studies of the Mn cluster in photosystem II and other exchange-coupled, transition metal-containing systems.
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Affiliation(s)
- Troy A. Stich
- Department of Chemistry, University of California–Davis, One Shields Avenue, Davis, CA 95616
| | - James W. Whittaker
- Department of Science and Engineering, School of Medicine, Oregon Health and Science University, 20000 N.W. Walker Road, Beaverton, OR 97006
| | - R. David Britt
- Department of Chemistry, University of California–Davis, One Shields Avenue, Davis, CA 95616
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Bender G, Stich TA, Yan L, Britt RD, Cramer SP, Ragsdale SW. Infrared and EPR spectroscopic characterization of a Ni(I) species formed by photolysis of a catalytically competent Ni(I)-CO intermediate in the acetyl-CoA synthase reaction. Biochemistry 2010; 49:7516-23. [PMID: 20669901 DOI: 10.1021/bi1010128] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Acetyl-CoA synthase (ACS) catalyzes the synthesis of acetyl-CoA from CO, coenzyme A (CoA), and a methyl group from the CH(3)-Co(3+) site in the corrinoid iron-sulfur protein (CFeSP). These are the key steps in the Wood-Ljungdahl pathway of anaerobic CO and CO(2) fixation. The active site of ACS is the A-cluster, which is an unusual nickel-iron-sulfur cluster. There is significant evidence for the catalytic intermediacy of a CO-bound paramagnetic Ni species, with an electronic configuration of [Fe(4)S(4)](2+)-(Ni(p)(+)-CO)-(Ni(d)(2+)), where Ni(p) and Ni(d) represent the Ni centers in the A-cluster that are proximal and distal to the [Fe(4)S(4)](2+) cluster, respectively. This well-characterized Ni(p)(+)-CO intermediate is often called the NiFeC species. Photolysis of the Ni(p)(+)-CO state generates a novel Ni(p)(+) species (A(red)*) with a rhombic electron paramagnetic resonance spectrum (g values of 2.56, 2.10, and 2.01) and an extremely low (1 kJ/mol) barrier for recombination with CO. We suggest that the photolytically generated A(red)* species is (or is similar to) the Ni(p)(+) species that binds CO (to form the Ni(p)(+)-CO species) and the methyl group (to form Ni(p)-CH(3)) in the ACS catalytic mechanism. The results provide support for a binding site (an "alcove") for CO near Ni(p), indicated by X-ray crystallographic studies of the Xe-incubated enzyme. We propose that, during catalysis, a resting Ni(p)(2+) state predominates over the active Ni(p)(+) species (A(red)*) that is trapped by the coupling of a one-electron transfer step to the binding of CO, which pulls the equilibrium toward Ni(p)(+)-CO formation.
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Affiliation(s)
- Güneş Bender
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-0606, USA
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McAlpin JG, Surendranath Y, Dinca M, Stich TA, Stoian SA, Casey WH, Nocera DG, Britt RD. EPR evidence for Co(IV) species produced during water oxidation at neutral pH. J Am Chem Soc 2010; 132:6882-3. [PMID: 20433197 DOI: 10.1021/ja1013344] [Citation(s) in RCA: 327] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Thin-film water oxidation catalysts (Co-Pi) prepared by electrodeposition from phosphate electrolyte and Co(NO(3))(2) have been characterized by electron paramagnetic resonance (EPR) spectroscopy. Co-Pi catalyst films exhibit EPR signals corresponding to populations of both Co(II) and Co(IV). As the deposition voltage is increased into the region where water oxidation prevails, the population of Co(IV) rises and the population of Co(II) decreases. The changes in the redox speciation of the film can also be induced, in part, by prolonged water oxidation catalysis in the absence of additional catalyst deposition. These results provide spectroscopic evidence for the formation of Co(IV) species during water oxidation catalysis at neutral pH.
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Affiliation(s)
- J Gregory McAlpin
- Department of Chemistry, University of California, 1 Shields Avenue, Davis, California 95616-0935, USA
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Stull JA, Stich TA, Service RJ, Debus RJ, Mandal SK, Armstrong WH, Britt RD. 13C ENDOR reveals that the D1 polypeptide C-terminus is directly bound to Mn in the photosystem II oxygen evolving complex. J Am Chem Soc 2010; 132:446-7. [PMID: 20038096 DOI: 10.1021/ja908688t] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Antiferromagnetically coupled Mn(III)Mn(IV) dimers have been commonly used to study biological systems that exhibit complex exchange interactions. Such is the case for the oxygen evolving complex (OEC) in photosystem II (PSII), where we have studied whether the C-terminal carboxylate of D1-Ala344 is directly bound to the Mn cluster. To probe these protein-derived carboxylate hyperfine interactions, which give direct bonding information, Q-band (34 GHz) Mims ENDOR was performed on a Mn(III)Mn(IV) dimer ([Mn(III)Mn(IV)(mu-O)(2)mu-OAc(TACN)(2)](BPh(4))(2)) (1) that was labeled with (13)C (I = (1)/(2)) at the carboxylate position of the acetate bridge. A(dip) is computed based on atomic coordinates from available X-ray crystal structures to be [-2.4, -0.8, 3.2] MHz. The value for A(iso) was determined based on simulation of the experimental ENDOR data, for complex 1 A(iso) = -1 MHz. Similar studies were then performed on PSII from Synechocystis sp. PCC 6803, in which all alanine-derived C=O groups are labeled with (13)C including the C-terminal alpha-COO(-) group of D1 (Ala344), as well as PSII proteins uniformly labeled with (13)C. Using recent X-ray crystallography data from T. elongatus the values for A(dip) were calculated and simulations of the experimental data led to A(iso) values of 1.2, 1, and 2 MHz, respectively. We infer from complex 1 that an A(iso) significantly larger than 1.2 MHz for a Mn-coordinating carboxylate moiety is unlikely. Therefore, we support the closer arrangement of Ala344 suggested by the Loll and Guskov structures and conclude that the C-terminal carboxylate of D1 polypeptide is directly bound to the Mn cluster.
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Affiliation(s)
- Jamie A Stull
- Department of Chemistry, University of California-Davis, Davis, California 95616, USA
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Ni C, Stich TA, Long GJ, Power PP. Unusual magnetic properties of a two-coordinate heteroleptic linear cobalt(ii) complex. Chem Commun (Camb) 2010; 46:4466-8. [DOI: 10.1039/c001483d] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Merrill WA, Stich TA, Brynda M, Yeagle GJ, Fettinger JC, De Hont R, Reiff WM, Schulz CE, Britt RD, Power PP. Direct spectroscopic observation of large quenching of first-order orbital angular momentum with bending in monomeric, two-coordinate Fe(II) primary amido complexes and the profound magnetic effects of the absence of Jahn- and Renner-Teller distortions in rigorously linear coordination. J Am Chem Soc 2009; 131:12693-702. [PMID: 19670870 PMCID: PMC2768349 DOI: 10.1021/ja903439t] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The monomeric iron(II) amido derivatives Fe{N(H)Ar*}(2) (1), Ar* = C(6)H(3)-2,6-(C(6)H(2)-2,4,6-Pr(i)(3))(2), and Fe{N(H)Ar(#)}(2) (2), Ar(#) = C(6)H(3)-2,6-(C(6)H(2)-2,4,6-Me(3))(2), were synthesized and studied in order to determine the effects of geometric changes on their unusual magnetic properties. The compounds, which are the first stable homoleptic primary amides of iron(II), were obtained by the transamination of Fe{N(SiMe(3))(2)}(2), with HN(SiMe(3))(2) elimination, by the primary amines H(2)NAr* or H(2)NAr(#). X-ray crystallography showed that they have either strictly linear (1) or bent (2, N-Fe-N = 140.9(2) degrees ) iron coordination. Variable temperature magnetization and applied magnetic field Mossbauer spectroscopy studies revealed a very large dependence of the magnetic properties on the metal coordination geometry. At ambient temperature, the linear 1 displayed an effective magnetic moment in the range 7.0-7.50 mu(B), consistent with essentially free ion magnetism. There is a very high internal orbital field component, H(L) approximately 170 T which is only exceeded by a H(L) approximately 203 T of Fe{C(SiMe(3))(3)}(2). In contrast, the strongly bent 2 displayed a significantly lower mu(eff) value in the range 5.25-5.80 mu(B) at ambient temperature and a much lower orbital field H(L) value of 116 T. The data for the two amido complexes demonstrate a very large quenching of the orbital magnetic moment upon bending the linear geometry. In addition, a strong correlation of H(L) with overall formal symmetry is confirmed. ESR spectroscopy supports the existence of large orbital magnetic moments in 1 and 2, and DFT calculations provide good agreement with the physical data.
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Ni C, Ellis BD, Stich TA, Fettinger JC, Long GJ, Britt RD, Power PP. Reduction of terphenyl iron(ii) or cobalt(ii) halides in the presence of trimethylphosphine: an unusual triple dehydrogenation of an alkyl group. Dalton Trans 2009:5401-5. [DOI: 10.1039/b904647j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Stich TA, Seravalli J, Venkateshrao S, Spiro TG, Ragsdale SW, Brunold TC. Spectroscopic studies of the corrinoid/iron-sulfur protein from Moorella thermoacetica. J Am Chem Soc 2007; 128:5010-20. [PMID: 16608335 PMCID: PMC2764033 DOI: 10.1021/ja054690o] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Methyl transfer reactions are important in a number of biochemical pathways. An important class of methyltransferases uses the cobalt cofactor cobalamin, which receives a methyl group from an appropriate methyl donor protein to form an intermediate organometallic methyl-Co bond that subsequently is cleaved by a methyl acceptor. Control of the axial ligation state of cobalamin influences both the mode (i.e., homolytic vs heterolytic) and the rate of Co-C bond cleavage. Here we have studied the axial ligation of a corrinoid iron-sulfur protein (CFeSP) that plays a key role in energy generation and cell carbon synthesis by anaerobic microbes, such as methanogenic archaea and acetogenic bacteria. This protein accepts a methyl group from methyltetrahydrofolate forming Me-Co(3+)CFeSP that then donates a methyl cation (Me) from Me-Co(3+)CFeSP to a nickel site on acetyl-CoA synthase. To unambiguously establish the binding scheme of the corrinoid cofactor in the CFeSP, we have combined resonance Raman, magnetic circular dichroism, and EPR spectroscopic methods with computational chemistry. Our results clearly demonstrate that the Me-Co3+ and Co2+ states of the CFeSP have an axial water ligand like the free MeCbi+ and Co(2+)Cbi+ cofactors; however, the Co-OH2 bond length is lengthened by about 0.2 angstroms for the protein-bound cofactor. Elongation of the Co-OH2 bond of the CFeSP-bound cofactor is proposed to make the cobalt center more "Co1+-like", a requirement to facilitate heterolytic Co-C bond cleavage.
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Affiliation(s)
- Troy A Stich
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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Stich TA, Lahiri S, Yeagle G, Dicus M, Brynda M, Gunn A, Aznar C, Derose VJ, Britt RD. Multifrequency Pulsed EPR Studies of Biologically Relevant Manganese(II) Complexes. Appl Magn Reson 2007; 31:321-341. [PMID: 22190766 PMCID: PMC3242439 DOI: 10.1007/bf03166263] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Electron paramagnetic resonance studies at multiple frequencies (MF EPR) can provide detailed electronic structure descriptions of unpaired electrons in organic radicals, inorganic complexes, and metalloenzymes. Analysis of these properties aids in the assignment of the chemical environment surrounding the paramagnet and provides mechanistic insight into the chemical reactions in which these systems take part. Herein, we present results from pulsed EPR studies performed at three different frequencies (9, 31, and 130 GHz) on [Mn(II)(H(2)O)(6)](2+), Mn(II) adducts with the nucleotides ATP and GMP, and the Mn(II)-bound form of the hammerhead ribozyme (MnHH). Through line shape analysis and interpretation of the zero-field splitting values derived from successful simulations of the corresponding continuous-wave and field-swept echo-detected spectra, these data are used to exemplify the ability of the MF EPR approach in distinguishing the nature of the first ligand sphere. A survey of recent results from pulsed EPR, as well as pulsed electron-nuclear double resonance and electron spin echo envelope modulation spectroscopic studies applied to Mn(II)-dependent systems, is also presented.
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Affiliation(s)
- T A Stich
- Department of Chemistry, University of California-Davis, Davis, California, USA
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