1
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Ma TT, Huang GZ, Wang XH, Liang Y, Li RH, Wang B, Yao SJ, Liao JP, Li SL, Yan Y, Lan YQ. Photochromic radical states in 3D covalent organic frameworks with zyg topology for enhanced photocatalysis. Natl Sci Rev 2024; 11:nwae177. [PMID: 38883289 PMCID: PMC11173181 DOI: 10.1093/nsr/nwae177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 04/25/2024] [Accepted: 05/02/2024] [Indexed: 06/18/2024] Open
Abstract
Covalent-organic frameworks (COFs) with photoinduced donor-acceptor (D-A) radical pairs show enhanced photocatalytic activity in principle. However, achieving long-lived charge separation in COFs proves challenging due to the rapid charge recombination. Here, we develop a novel strategy by combining [6 + 4] nodes to construct zyg-type 3D COFs, first reported in COF chemistry. This structure type exhibits a fused Olympic-rings-like shape, which provides a platform for stabilizing the photoinduced D-A radical pairs. The zyg-type COFs containing catalytically active moieties such as triphenylamine and phenothiazine (PTZ) show superior photocatalytic production rates of hydrogen peroxide (H2O2). Significantly, the photochromic radical states of these COFs show up to 400% enhancement in photocatalytic activity compared to the parent states, achieving a remarkable H2O2 synthesis rate of 3324 μmol g-1 h-1, which makes the PTZ-COF one of the best crystalline porous photocatalysts in H2O2 production. This work will shed light on the synthesis of efficient 3D COF photocatalysts built on topologies that can facilitate photogenerating D-A radical pairs for enhanced photocatalysis.
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Affiliation(s)
- Tian-Tian Ma
- School of Chemistry, South China Normal University, Guangzhou 510006, China
| | - Guo-Zhang Huang
- Department of Chemistry, Guangdong Provincial Key Laboratory of Catalytic Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xiao-Han Wang
- School of Chemistry, South China Normal University, Guangzhou 510006, China
| | - Yan Liang
- School of Chemistry, South China Normal University, Guangzhou 510006, China
| | - Run-Han Li
- School of Chemistry, South China Normal University, Guangzhou 510006, China
| | - Bin Wang
- School of Chemistry, South China Normal University, Guangzhou 510006, China
| | - Su-Juan Yao
- School of Chemistry, South China Normal University, Guangzhou 510006, China
| | - Jia-Peng Liao
- School of Chemistry, South China Normal University, Guangzhou 510006, China
| | - Shun-Li Li
- School of Chemistry, South China Normal University, Guangzhou 510006, China
| | - Yong Yan
- School of Chemistry, South China Normal University, Guangzhou 510006, China
| | - Ya-Qian Lan
- School of Chemistry, South China Normal University, Guangzhou 510006, China
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2
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Cheek LE, Zhu W. Structural features and substrate engagement in peptide-modifying radical SAM enzymes. Arch Biochem Biophys 2024; 756:110012. [PMID: 38663796 DOI: 10.1016/j.abb.2024.110012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 05/04/2024]
Abstract
In recent years, the biological significance of ribosomally synthesized, post-translationally modified peptides (RiPPs) and the intriguing chemistry catalyzed by their tailoring enzymes has garnered significant attention. A subgroup of bacterial radical S-adenosylmethionine (rSAM) enzymes can activate C-H bonds in peptides, which leads to the production of a diverse range of RiPPs. The remarkable ability of these enzymes to facilitate various chemical processes, to generate and harbor high-energy radical species, and to accommodate large substrates with a high degree of flexibility is truly intriguing. The wide substrate scope and diversity of the chemistry performed by rSAM enzymes raise one question: how does the protein environment facilitate these distinct chemical conversions while sharing a similar structural fold? In this review, we discuss recent advances in the field of RiPP-rSAM enzymes, with a particular emphasis on domain architectures and substrate engagements identified by biophysical and structural characterizations. We provide readers with a comparative analysis of six examples of RiPP-rSAM enzymes with experimentally characterized structures. Linking the structural elements and the nature of rSAM-catalyzed RiPP production will provide insight into the functional engineering of enzyme activity to harness their catalytic power in broader applications.
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Affiliation(s)
- Lilly E Cheek
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, 32306, USA
| | - Wen Zhu
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, 32306, USA.
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3
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Yang H, Ho MB, Lundahl MN, Mosquera MA, Broderick WE, Broderick JB, Hoffman BM. ENDOR Spectroscopy Reveals the "Free" 5'-Deoxyadenosyl Radical in a Radical SAM Enzyme Active Site Actually is Chaperoned by Close Interaction with the Methionine-Bound [4Fe-4S] 2+ Cluster. J Am Chem Soc 2024; 146:3710-3720. [PMID: 38308759 DOI: 10.1021/jacs.3c09428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2024]
Abstract
1/2H and 13C hyperfine coupling constants to 5'-deoxyadenosyl (5'-dAdo•) radical trapped within the active site of the radical S-adenosyl-l-methionine (SAM) enzyme, pyruvate formate lyase-activating enzyme (PFL-AE), both in the absence of substrate and the presence of a reactive peptide-model of the PFL substrate, are completely characteristic of a classical organic free radical whose unpaired electron is localized in the 2pπ orbital of the sp2 C5'-carbon (J. Am. Chem. Soc. 2019, 141, 12139-12146). However, prior electron-nuclear double resonance (ENDOR) measurements had indicated that this 5'-dAdo• free radical is never truly "free": tight van der Waals contact with its target partners and active-site residues guide it in carrying out the exquisitely precise, regioselective reactions that are hallmarks of RS enzymes. Here, our understanding of how the active site chaperones 5'-dAdo• is extended through the finding that this apparently unexceptional organic free radical has an anomalous g-tensor and exhibits significant 57Fe, 13C, 15N, and 2H hyperfine couplings to the adjacent, isotopically labeled, methionine-bound [4Fe-4S]2+ cluster cogenerated with 5'-dAdo• during homolytic cleavage of cluster-bound SAM. The origin of the 57Fe couplings through nonbonded radical-cluster contact is illuminated by a formal exchange-coupling model and broken symmetry-density functional theory computations. Incorporation of ENDOR-derived distances from C5'(dAdo•) to labeled-methionine as structural constraints yields a model for active-site positioning of 5'-dAdo• with a short, nonbonded C5'-Fe distance (∼3 Å). This distance involves substantial motion of 5'-dAdo• toward the unique Fe of the [4Fe-4S]2+ cluster upon S-C(5') bond-cleavage, plausibly an initial step toward formation of the Fe-C5' bond of the organometallic complex, Ω, the central intermediate in catalysis by radical-SAM enzymes.
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Affiliation(s)
- Hao Yang
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Madeline B Ho
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Maike N Lundahl
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Martín A Mosquera
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - William E Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Joan B Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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4
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Omeiri J, Martin L, Usclat A, Cherrier MV, Nicolet Y. Maturation of the [FeFe]-Hydrogenase: Direct Transfer of the (κ 3 -cysteinate)Fe II (CN)(CO) 2 Complex B from HydG to HydE. Angew Chem Int Ed Engl 2023; 62:e202314819. [PMID: 37962296 DOI: 10.1002/anie.202314819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 11/15/2023]
Abstract
[FeFe]-hydrogenases efficiently catalyze the reversible oxidation of molecular hydrogen. Their prowess stems from the intricate H-cluster, combining a [Fe4 S4 ] center with a binuclear iron center ([2Fe]H ). In the latter, each iron atom is coordinated by a CO and CN ligand, connected by a CO and an azadithiolate ligand. The synthesis of this active site involves a unique multiprotein assembly, featuring radical SAM proteins HydG and HydE. HydG initiates the transformation of L-tyrosine into cyanide and carbon monoxide to generate complex B, which is subsequently transferred to HydE to continue the biosynthesis of the [2Fe]H -subcluster. Due to its instability, complex B isolation for structural or spectroscopic characterization has been elusive thus far. Nevertheless, the use of a biomimetic analogue of complex B allowed circumvention of the need for the HydG protein during in vitro functional investigations, implying a similar structure for complex B. Herein, we used the HydE protein as a nanocage to encapsulate and stabilize the complex B product generated by HydG. Using X-ray crystallography, we successfully determined its structure at 1.3 Å resolution. Furthermore, we demonstrated that complex B is directly transferred from HydG to HydE, thus not being released into the solution post-synthesis, highlighting a transient interaction between the two proteins.
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Affiliation(s)
- Juneina Omeiri
- Univ. Grenoble-Alpes, CEA, CNRS, IBS, Metalloproteins Unit, 38000, Grenoble, France
| | - Lydie Martin
- Univ. Grenoble-Alpes, CEA, CNRS, IBS, Metalloproteins Unit, 38000, Grenoble, France
| | - Anthony Usclat
- Univ. Grenoble-Alpes, CEA, CNRS, IBS, Metalloproteins Unit, 38000, Grenoble, France
| | - Mickael V Cherrier
- Univ. Grenoble-Alpes, CEA, CNRS, IBS, Metalloproteins Unit, 38000, Grenoble, France
| | - Yvain Nicolet
- Univ. Grenoble-Alpes, CEA, CNRS, IBS, Metalloproteins Unit, 38000, Grenoble, France
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5
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Lundahl MN, Yang H, Broderick WE, Hoffman BM, Broderick JB. Pyruvate formate-lyase activating enzyme: The catalytically active 5'-deoxyadenosyl radical caught in the act of H-atom abstraction. Proc Natl Acad Sci U S A 2023; 120:e2314696120. [PMID: 37956301 PMCID: PMC10665898 DOI: 10.1073/pnas.2314696120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 10/03/2023] [Indexed: 11/15/2023] Open
Abstract
Enzymes of the radical S-adenosyl-l-methionine (radical SAM, RS) superfamily, the largest in nature, catalyze remarkably diverse reactions initiated by H-atom abstraction. Glycyl radical enzyme activating enzymes (GRE-AEs) are a growing class of RS enzymes that generate the catalytically essential glycyl radical of GREs, which in turn catalyze essential reactions in anaerobic metabolism. Here, we probe the reaction of the GRE-AE pyruvate formate-lyase activating enzyme (PFL-AE) with the peptide substrate RVSG734YAV, which mimics the site of glycyl radical formation on the native substrate, pyruvate formate-lyase. Time-resolved freeze-quench electron paramagnetic resonance spectroscopy shows that at short mixing times reduced PFL-AE + SAM reacts with RVSG734YAV to form the central organometallic intermediate, Ω, in which the adenosyl 5'C is covalently bound to the unique iron of the [4Fe-4S] cluster. Freeze-trapping the reaction at longer times reveals the formation of the peptide G734• glycyl radical product. Of central importance, freeze-quenching at intermediate times reveals that the conversion of Ω to peptide glycyl radical is not concerted. Instead, homolysis of the Ω Fe-C5' bond generates the nominally "free" 5'-dAdo• radical, which is captured here by freeze-trapping. During cryoannealing at 77 K, the 5'-dAdo• directly abstracts an H-atom from the peptide to generate the G734• peptide radical trapped in the PFL-AE active site. These observations reveal the 5'-dAdo• radical to be a well-defined intermediate, caught in the act of substrate H-atom abstraction, providing new insights into the mechanistic steps of radical initiation by RS enzymes.
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Affiliation(s)
- Maike N. Lundahl
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT59717
| | - Hao Yang
- Department of Chemistry, Northwestern University, Evanston, IL60208
| | - William E. Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT59717
| | - Brian M. Hoffman
- Department of Chemistry, Northwestern University, Evanston, IL60208
| | - Joan B. Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT59717
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6
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Jodts RJ, Wittkop M, Ho MB, Broderick WE, Broderick JB, Hoffman BM, Mosquera MA. Computational Description of Alkylated Iron-Sulfur Organometallic Clusters. J Am Chem Soc 2023; 145:13879-13887. [PMID: 37307050 PMCID: PMC10573082 DOI: 10.1021/jacs.3c03062] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The radical S-adenosyl methionine (SAM) enzyme superfamily has widespread roles in hydrogen atom abstraction reactions of crucial biological importance. In these enzymes, reductive cleavage of SAM bound to a [4Fe-4S]1+ cluster generates the 5'-deoxyadenosyl radical (5'-dAdo•) which ultimately abstracts an H atom from the substrate. However, overwhelming experimental evidence has surprisingly revealed an obligatory organometallic intermediate Ω exhibiting an Fe-C5'-adenosyl bond, whose properties are the target of this theoretical investigation. We report a readily applied, two-configuration version of broken symmetry DFT, denoted 2C-DFT, designed to allow the accurate description of the hyperfine coupling constants and g-tensors of an alkyl group bound to a multimetallic iron-sulfur cluster. This approach has been validated by the excellent agreement of its results both with those of multiconfigurational complete active space self-consistent field computations for a series of model complexes and with the results from electron nuclear double-resonance/electron paramagnetic resonance spectroscopic studies for the crystallographically characterized complex, M-CH3, a [4Fe-4S] cluster with a Fe-CH3 bond. The likewise excellent agreement between spectroscopic results and 2C-DFT computations for Ω confirm its identity as an organometallic complex with a bond between an Fe of the [4Fe-4S] cluster and C5' of the deoxyadenosyl moiety, as first proposed.
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Affiliation(s)
- Richard J. Jodts
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208
| | - M Wittkop
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717
| | - Madeline B. Ho
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208
| | - William E. Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717
| | - Joan B. Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717
| | - Brian M. Hoffman
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208
| | - Martín A. Mosquera
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717
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7
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Abstract
Radical S-adenosylmethionine (SAM) enzymes use a site-differentiated [4Fe-4S] cluster and SAM to initiate radical reactions through liberation of the 5'-deoxyadenosyl (5'-dAdo•) radical. They form the largest enzyme superfamily, with more than 700,000 unique sequences currently, and their numbers continue to grow as a result of ongoing bioinformatics efforts. The range of extremely diverse, highly regio- and stereo-specific reactions known to be catalyzed by radical SAM superfamily members is remarkable. The common mechanism of radical initiation in the radical SAM superfamily is the focus of this review. Most surprising is the presence of an organometallic intermediate, Ω, exhibiting an Fe-C5'-adenosyl bond. Regioselective reductive cleavage of the SAM S-C5' bond produces 5'-dAdo• to form Ω, with the regioselectivity originating in the Jahn-Teller effect. Ω liberates the free 5'-dAdo• as the catalytically active intermediate through homolysis of the Fe-C5' bond, in analogy to Co-C5' bond homolysis in B12, which was once viewed as biology's choice of radical generator.
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Affiliation(s)
- Brian M Hoffman
- Department of Chemistry, Northwestern University, Evanston, Illinois, USA
| | - William E Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA;
| | - Joan B Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA;
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8
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Tang C, Song L, Zhou K, Ren P, Zhao E, He Z. Manipulating D-A interaction to achieve stable photoinduced organic radicals in triphenylphosphine crystals. Chem Sci 2023; 14:1871-1877. [PMID: 36819874 PMCID: PMC9930928 DOI: 10.1039/d2sc05753k] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/18/2023] [Indexed: 01/19/2023] Open
Abstract
New strategies for the design and synthesis of stable organic radicals without additives are highly desirable. Herein, we design a series of donor-acceptor structured triarylphosphines and disclose the fast color change triggered by UV-irradiation in the crystalline state. Photoinduced organic radicals are undoubtedly verified and proved to be the reason for the color change by time-dependent and quantitative electron paramagnetic resonance analysis, X-ray crystallographic analysis, and theoretical calculations. It is revealed that the intrinsic symmetry breaking of peripheral architecture helps to form continuous molecular chains by donor-acceptor counterpart pairing. Intermolecular electron-transfer occurs among molecular chains and results in radical ion pairs upon photoirradiation.
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Affiliation(s)
- Chunlin Tang
- School of Science, Harbin Institute of Technology Shenzhen Guangdong 518055 China
| | - Lijuan Song
- School of Science, Harbin Institute of Technology Shenzhen Guangdong 518055 China
| | - Kang Zhou
- Hoffmann Institute of Advanced Materials, Shenzhen PolytechnicShenzhenGuangdong 518055China
| | - Peng Ren
- School of Science, Harbin Institute of Technology Shenzhen Guangdong 518055 China
| | - Engui Zhao
- School of Science, Harbin Institute of Technology Shenzhen Guangdong 518055 China
| | - Zikai He
- School of Science, Harbin Institute of Technology Shenzhen Guangdong 518055 China .,School of Chemical Engineering and Technology, Harbin Institute of Technology Harbin Heilongjiang 150001 China
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9
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Broderick JB, Broderick WE, Hoffman BM. Radical SAM enzymes: Nature's choice for radical reactions. FEBS Lett 2023; 597:92-101. [PMID: 36251330 PMCID: PMC9894703 DOI: 10.1002/1873-3468.14519] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 10/05/2022] [Indexed: 02/04/2023]
Abstract
Enzymes that use a [4Fe-4S]1+ cluster plus S-adenosyl-l-methionine (SAM) to initiate radical reactions (radical SAM) form the largest enzyme superfamily, with over half a million members across the tree of life. This review summarizes recent work revealing the radical SAM reaction pathway, which ultimately liberates the 5'-deoxyadenosyl (5'-dAdo•) radical to perform extremely diverse, highly regio- and stereo-specific, transformations. Most surprising was the discovery of an organometallic intermediate Ω exhibiting an Fe-C5'-adenosyl bond. Ω liberates 5'-dAdo• through homolysis of the Fe-C5' bond, in analogy to Co-C5' bond homolysis in B12 , previously viewed as biology's paradigmatic radical generator. The 5'-dAdo• has been trapped and characterized in radical SAM enzymes via a recently discovered photoreactivity of the [4Fe-4S]+ /SAM complex, and has been confirmed as a catalytically active intermediate in enzyme catalysis. The regioselective SAM S-C bond cleavage to produce 5'-dAdo• originates in the Jahn-Teller effect. The simplicity of SAM as a radical precursor, and the exquisite control of 5'-dAdo• reactivity in radical SAM enzymes, may be why radical SAM enzymes pervade the tree of life, while B12 enzymes are only a few.
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Affiliation(s)
- Joan B. Broderick
- Department of Chemistry & Biochemistry, 103 CBB, Montana State University, Bozeman, MT 59717
| | - William E. Broderick
- Department of Chemistry & Biochemistry, 103 CBB, Montana State University, Bozeman, MT 59717
| | - Brian M. Hoffman
- Department of Chemistry, 2145 Sheridan Rd, Northwestern University, Evanston, IL. 60208
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10
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Ho MB, Jodts RJ, Kim Y, McSkimming A, Suess DLM, Hoffman BM. Characterization by ENDOR Spectroscopy of the Iron–Alkyl Bond in a Synthetic Counterpart of Organometallic Intermediates in Radical SAM Enzymes. J Am Chem Soc 2022; 144:17642-17650. [DOI: 10.1021/jacs.2c07155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Madeline B. Ho
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Richard J. Jodts
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Youngsuk Kim
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Alex McSkimming
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Daniel L. M. Suess
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Brian M. Hoffman
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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11
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Lundahl MN, Sarksian R, Yang H, Jodts RJ, Pagnier A, Smith DF, Mosquera MA, van der Donk WA, Hoffman BM, Broderick WE, Broderick JB. Mechanism of Radical S-Adenosyl-l-methionine Adenosylation: Radical Intermediates and the Catalytic Competence of the 5'-Deoxyadenosyl Radical. J Am Chem Soc 2022; 144:5087-5098. [PMID: 35258967 PMCID: PMC9524473 DOI: 10.1021/jacs.1c13706] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Radical S-adenosyl-l-methionine (SAM) enzymes employ a [4Fe-4S] cluster and SAM to initiate diverse radical reactions via either H-atom abstraction or substrate adenosylation. Here we use freeze-quench techniques together with electron paramagnetic resonance (EPR) spectroscopy to provide snapshots of the reaction pathway in an adenosylation reaction catalyzed by the radical SAM enzyme pyruvate formate-lyase activating enzyme on a peptide substrate containing a dehydroalanine residue in place of the target glycine. The reaction proceeds via the initial formation of the organometallic intermediate Ω, as evidenced by the characteristic EPR signal with g∥ = 2.035 and g⊥ = 2.004 observed when the reaction is freeze-quenched at 500 ms. Thermal annealing of frozen Ω converts it into a second paramagnetic species centered at giso = 2.004; this second species was generated directly using freeze-quench at intermediate times (∼8 s) and unequivocally identified via isotopic labeling and EPR spectroscopy as the tertiary peptide radical resulting from adenosylation of the peptide substrate. An additional paramagnetic species observed in samples quenched at intermediate times was revealed through thermal annealing while frozen and spectral subtraction as the SAM-derived 5'-deoxyadenosyl radical (5'-dAdo•). The time course of the 5'-dAdo• and tertiary peptide radical EPR signals reveals that the former generates the latter. These results thus support a mechanism in which Ω liberates 5'-dAdo• by Fe-C5' bond homolysis, and the 5'-dAdo• attacks the dehydroalanine residue of the peptide substrate to form the adenosylated peptide radical species. The results thus provide a picture of a catalytically competent 5'-dAdo• intermediate trapped just prior to reaction with the substrate.
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Affiliation(s)
- Maike N. Lundahl
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Raymond Sarksian
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Hao Yang
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Richard J. Jodts
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Adrien Pagnier
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Donald F. Smith
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Martín A. Mosquera
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Wilfred A. van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Brian M. Hoffman
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - William E. Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Joan B. Broderick
- Corresponding Author: Joan B. Broderick – Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States;
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12
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Donnan PH, Mansoorabadi SO. Broken-Symmetry Density Functional Theory Analysis of the Ω Intermediate in Radical S-Adenosyl-l-methionine Enzymes: Evidence for a Near-Attack Conformer over an Organometallic Species. J Am Chem Soc 2022; 144:3381-3385. [PMID: 35170316 DOI: 10.1021/jacs.2c00678] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Radical S-adenosyl-l-methionine (SAM) enzymes are found in all domains of life and catalyze a wide range of biochemical reactions. Recently, an organometallic intermediate, Ω, has been experimentally implicated in the 5'-deoxyadenosyl radical generation mechanism of the radical SAM superfamily. In this work, we employ broken-symmetry density functional theory to evaluate several structural models of Ω. The results show that the calculated hyperfine coupling constants (HFCCs) for the proposed organometallic structure of Ω are inconsistent with the experiment. In contrast, a near-attack conformer of SAM bound to the catalytic [4Fe-4S] cluster, in which the distance between the unique iron and SAM sulfur is ∼3 Å, yields HFCCs that are all within 1 MHz of the experimental values. These results clarify the structure of the ubiquitous Ω intermediate and suggest a paradigm shift reversal regarding the mechanism of SAM cleavage by members of the radical SAM superfamily.
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Affiliation(s)
- Patrick H Donnan
- Department of Chemistry and Biochemistry, Auburn University, 179 Chemistry Building, Auburn, Alabama 36849, United States
| | - Steven O Mansoorabadi
- Department of Chemistry and Biochemistry, Auburn University, 179 Chemistry Building, Auburn, Alabama 36849, United States
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13
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The B 12-independent glycerol dehydratase activating enzyme from Clostridium butyricum cleaves SAM to produce 5'-deoxyadenosine and not 5'-deoxy-5'-(methylthio)adenosine. J Inorg Biochem 2022; 227:111662. [PMID: 34847521 PMCID: PMC8889718 DOI: 10.1016/j.jinorgbio.2021.111662] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 11/04/2021] [Accepted: 11/04/2021] [Indexed: 02/03/2023]
Abstract
Glycerol dehydratase activating enzyme (GD-AE) is a radical S-adenosyl-l-methionine (SAM) enzyme that installs a catalytically essential amino acid backbone radical onto glycerol dehydratase in bacteria under anaerobic conditions. Although GD-AE is closely homologous to other radical SAM activases that have been shown to cleave the S-C(5') bond of SAM to produce 5'-deoxyadenosine (5'-dAdoH) and methionine, GD-AE from Clostridium butyricum has been reported to instead cleave the S-C(γ) bond of SAM to yield 5'-deoxy-5'-(methylthio)adenosine (MTA). Here we re-investigate the SAM cleavage reaction catalyzed by GD-AE and show that it produces the widely observed 5'-dAdoH, and not the less conventional product MTA.
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14
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Rao G, Chen N, Marchiori DA, Wang LP, Britt RD. Accumulation and Pulse Electron Paramagnetic Resonance Spectroscopic Investigation of the 4-Oxidobenzyl Radical Generated in the Radical S-Adenosyl-l-methionine Enzyme HydG. Biochemistry 2022; 61:107-116. [PMID: 34989236 DOI: 10.1021/acs.biochem.1c00619] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The radical S-adenosyl-l-methionine (SAM) enzyme HydG cleaves tyrosine to generate CO and CN- ligands of the [FeFe] hydrogenase H-cluster, accompanied by the formation of a 4-oxidobenzyl radical (4-OB•), which is the precursor to the HydG p-cresol byproduct. Native HydG only generates a small amount of 4-OB•, limiting detailed electron paramagnetic resonance (EPR) spectral characterization beyond our initial EPR lineshape study employing various tyrosine isotopologues. Here, we show that the concentration of trapped 4-OB• is significantly increased in reactions using HydG variants, in which the "dangler Fe" to which CO and CN- bind is missing or substituted by a redox-inert Zn2+ ion. This allows for the detailed characterization of 4-OB• using high-field EPR and electron nuclear double resonance spectroscopy to extract its g-values and 1H/13C hyperfine couplings. These results are compared to density functional theory-predicted values of several 4-OB• models with different sizes and protonation states, with a best fit to the deprotonated radical anion configuration of 4-OB•. Overall, our results depict a clearer electronic structure of the transient 4-OB• radical and provide new insights into the radical SAM chemistry of HydG.
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Affiliation(s)
- Guodong Rao
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
| | - Nanhao Chen
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
| | - David A Marchiori
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
| | - Lee-Ping Wang
- 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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15
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Wang Y, Liu R, Zhou P, Wu J, Li W, Wang C, Li H, Li D, Yang J. Visible Light‐Driven Base‐Promoted Radical Cascade Difluoroalkylization‐cyclization‐iodination of 1,6‐Enynes with Ethyl Difluoroiodoacetate. European J Org Chem 2022. [DOI: 10.1002/ejoc.202101395] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yan Wang
- Ningxia University School of chemistry and chemical Engineering 539 West Helan Mountains road, Xixia District, Yinchuan 750000 Yinchuan CHINA
| | - Ruyan Liu
- Ningxia University School of Chemistry and Chemical Engineering CHINA
| | - Pengsheng Zhou
- Ningxia University School of Chemistry and Chemical Engineering CHINA
| | - Jianglong Wu
- Ningxia University School of Chemistry and Chemical Engineering CHINA
| | - Wenshuang Li
- Ningxia University School of Chemistry and Chemical Engineering CHINA
| | - Chenyu Wang
- Ningxia University School of Chemistry and Chemical Engineering CHINA
| | - Hao Li
- Ningxia University School of Chemistry and Chemical Engineering CHINA
| | - Dianjun Li
- Ningxia University State Key Laboratory of High-Efficiency Utilization of Coal and Green Chemical Engineering, School of Chemistry and Chemical Engineering CHINA
| | - Jinhui Yang
- Ningxia University State Key Laboratory of High-efficiency Utilization of Coal and Green Chemical Engineering China, Ning Xia, Yinchuan, Xixia District Ningxia University B 750021 Yinchuan CHINA
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16
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Britt RD, Rauchfuss TB. Biosynthesis of the [FeFe] hydrogenase H-cluster via a synthetic [Fe(II)(CN)(CO) 2(cysteinate)] - complex. Dalton Trans 2021; 50:12386-12391. [PMID: 34545884 DOI: 10.1039/d1dt02258j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The H-cluster of [Fe-Fe] hydrogenase consists of a [4Fe]H subcluster linked by the sulfur of a cysteine residue to an organometallic [2Fe]H subcluster that utilizes terminal CO and CN ligands to each Fe along with a bridging CO and a bridging SCH2NHCH2S azadithiolate (adt) to catalyze proton reduction or hydrogen oxidation. Three Fe-S "maturase" proteins, HydE, HydF, and HydG, are responsible for the biosynthesis of the [2Fe]H subcluster and its incorporation into the hydrogenase enzyme to form this catalytically active H-cluster. We have proposed that HydG is a bifunctional enzyme that uses S-adenosylmethione (SAM) bound to a [4Fe-4S] cluster to lyse tyrosine via a transient 5'-deoxyadenosyl radical to produce CO and CN ligands to a unique cysteine-chelated Fe(II) that is linked to a second [4Fe-4S] cluster via the cysteine sulfur. In this "synthon model", after two cycles of tyrosine lysis, the product of HydG is completed: a [Fe(CN)(CO)2(cysteinate)]- organometallic unit that is vectored directly into the synthesis of the [2Fe]H sub-cluster. However our HydG-centric synthon model is not universally accepted, so further validation is important. In this Frontiers article, we discuss recent results using a synthetic "Syn-B" complex that donates [Fe(CN)(CO)2(cysteinate)]- units that match our proposed HydG product. Can Syn-B activate hydrogenase in the absence of HydG and its tyrosine substrate? If so, since Syn-B can be synthesized with specific magnetic nuclear isotopes and with chemical substitutions, its use could allow its enzymatic conversions on the route to the H-cluster to be monitored and modeled in fresh detail.
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Affiliation(s)
- R David Britt
- Department of Chemistry, University of California Davis, Davis, CA 95616, USA.
| | - Thomas B Rauchfuss
- School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
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17
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Shepard EM, Impano S, Duffus BR, Pagnier A, Duschene KS, Betz JN, Byer AS, Galambas A, McDaniel EC, Watts H, McGlynn SE, Peters JW, Broderick WE, Broderick JB. HydG, the "dangler" iron, and catalytic production of free CO and CN -: implications for [FeFe]-hydrogenase maturation. Dalton Trans 2021; 50:10405-10422. [PMID: 34240096 DOI: 10.1039/d1dt01359a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The organometallic H-cluster of the [FeFe]-hydrogenase consists of a [4Fe-4S] cubane bridged via a cysteinyl thiolate to a 2Fe subcluster ([2Fe]H) containing CO, CN-, and dithiomethylamine (DTMA) ligands. The H-cluster is synthesized by three dedicated maturation proteins: the radical SAM enzymes HydE and HydG synthesize the non-protein ligands, while the GTPase HydF serves as a scaffold for assembly of [2Fe]H prior to its delivery to the [FeFe]-hydrogenase containing the [4Fe-4S] cubane. HydG uses l-tyrosine as a substrate, cleaving it to produce p-cresol as well as the CO and CN- ligands to the H-cluster, although there is some question as to whether these are formed as free diatomics or as part of a [Fe(CO)2(CN)] synthon. Here we show that Clostridium acetobutylicum (C.a.) HydG catalyzes formation of multiple equivalents of free CO at rates comparable to those for CN- formation. Free CN- is also formed in excess molar equivalents over protein. A g = 8.9 EPR signal is observed for C.a. HydG reconstituted to load the 5th "dangler" iron of the auxiliary [4Fe-4S][FeCys] cluster and is assigned to this "dangler-loaded" cluster state. Free CO and CN- formation and the degree of activation of [FeFe]-hydrogenase all occur regardless of dangler loading, but are increased 10-35% in the dangler-loaded HydG; this indicates the dangler iron is not essential to this process but may affect relevant catalysis. During HydG turnover in the presence of myoglobin, the g = 8.9 signal remains unchanged, indicating that a [Fe(CO)2(CN)(Cys)] synthon is not formed at the dangler iron. Mutation of the only protein ligand to the dangler iron, H272, to alanine nearly completely abolishes both free CO formation and hydrogenase activation, however results show this is not due solely to the loss of the dangler iron. In experiments with wild type and H272A HydG, and with different degrees of dangler loading, we observe a consistent correlation between free CO/CN- formation and hydrogenase activation. Taken in full, our results point to free CO/CN-, but not an [Fe(CO)2(CN)(Cys)] synthon, as essential species in hydrogenase maturation.
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Affiliation(s)
- Eric M Shepard
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Stella Impano
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Benjamin R Duffus
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Adrien Pagnier
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Kaitlin S Duschene
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Jeremiah N Betz
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Amanda S Byer
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Amanda Galambas
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Elizabeth C McDaniel
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Hope Watts
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Shawn E McGlynn
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - John W Peters
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99163, USA
| | - William E Broderick
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
| | - Joan B Broderick
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA.
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18
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Lachowicz JC, Gizzi AS, Almo SC, Grove TL. Structural Insight into the Substrate Scope of Viperin and Viperin-like Enzymes from Three Domains of Life. Biochemistry 2021; 60:2116-2129. [PMID: 34156827 PMCID: PMC8672371 DOI: 10.1021/acs.biochem.0c00958] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Viperin is a member of the radical S-adenosylmethionine superfamily and has been shown to restrict the replication of a wide range of RNA and DNA viruses. We recently demonstrated that human viperin (HsVip) catalyzes the conversion of CTP to 3'-deoxy-3',4'-didehydro-CTP (ddhCTP or ddh-synthase), which acts as a chain terminator for virally encoded RNA-dependent RNA polymerases from several flaviviruses. Viperin homologues also exist in non-chordate eukaryotes (e.g., Cnidaria and Mollusca), numerous fungi, and members of the archaeal and eubacterial domains. Recently, it was reported that non-chordate and non-eukaryotic viperin-like homologues are also ddh-synthases and generate a diverse range of ddhNTPs, including the newly discovered ddhUTP and ddhGTP. Herein, we expand on the catalytic mechanism of mammalian, fungal, bacterial, and archaeal viperin-like enzymes with a combination of X-ray crystallography and enzymology. We demonstrate that, like mammalian viperins, these recently discovered viperin-like enzymes operate through the same mechanism and can be classified as ddh-synthases. Furthermore, we define the unique chemical and physical determinants supporting ddh-synthase activity and nucleotide selectivity, including the crystallographic characterization of a fungal viperin-like enzyme that utilizes UTP as a substrate and a cnidaria viperin-like enzyme that utilizes CTP as a substrate. Together, these results support the evolutionary conservation of the ddh-synthase activity and its broad phylogenetic role in innate antiviral immunity.
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Affiliation(s)
- Jake C Lachowicz
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Anthony S Gizzi
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Steven C Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
- Department of Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Tyler L Grove
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
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19
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Impano S, Yang H, Shepard EM, Swimley R, Pagnier A, Broderick WE, Hoffman BM, Broderick JB. S-Adenosyl-l-ethionine is a Catalytically Competent Analog of S-Adenosyl-l-methione (SAM) in the Radical SAM Enzyme HydG. Angew Chem Int Ed Engl 2021; 60:4666-4672. [PMID: 33935588 PMCID: PMC8081114 DOI: 10.1002/anie.202014337] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Indexed: 01/02/2023]
Abstract
Radical S-adenosyl-l-methionine (SAM) enzymes initiate biological radical reactions with the 5'-deoxyadenosyl radical (5'-dAdo•). A [4Fe-4S]+ cluster reductively cleaves SAM to form the Ω organometallic intermediate in which the 5'-deoxyadenosyl moiety is directly bound to the unique iron of the [4Fe-4S] cluster, with subsequent liberation of 5'-dAdo•. Here we present synthesis of the SAM analog S-adenosyl-l-ethionine (SAE) and show SAE is a mechanistically-equivalent SAM-alternative for HydG, both supporting enzymatic turnover of substrate tyrosine and forming the organometallic intermediate Ω. Photolysis of SAE bound to HydG forms an ethyl radical trapped in the active site. The ethyl radical withstands prolonged storage at 77 K and its EPR signal is only partially lost upon annealing at 100 K, making it significantly less reactive than the methyl radical formed by SAM photolysis. Upon annealing above 77K, the ethyl radical adds to the [4Fe-4S]2+ cluster, generating an ethyl-[4Fe-4S]3+ organometallic species termed ΩE.
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Affiliation(s)
- Stella Impano
- Department of Chemistry & Biochemistry, ontana State University, ozeman, MT. USA. 59717
| | - Hao Yang
- Department of Chemistry, Northwestern University, Evanston, IL. USA 60208
| | - Eric M Shepard
- Department of Chemistry & Biochemistry, ontana State University, ozeman, MT. USA. 59717
| | - Ryan Swimley
- Department of Chemistry & Biochemistry, ontana State University, ozeman, MT. USA. 59717
| | - Adrien Pagnier
- Department of Chemistry & Biochemistry, ontana State University, ozeman, MT. USA. 59717
| | - William E Broderick
- Department of Chemistry & Biochemistry, ontana State University, ozeman, MT. USA. 59717
| | - Brian M Hoffman
- Department of Chemistry & Biochemistry, ontana State University, ozeman, MT. USA. 59717
| | - Joan B Broderick
- Department of Chemistry & Biochemistry, ontana State University, ozeman, MT. USA. 59717
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20
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Impano S, Yang H, Shepard EM, Swimley R, Pagnier A, Broderick WE, Hoffman BM, Broderick JB. S
‐Adenosyl‐
l
‐ethionine is a Catalytically Competent Analog of
S
‐Adenosyl‐
l
‐methionine (SAM) in the Radical SAM Enzyme HydG. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202014337] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Stella Impano
- Department of Chemistry & Biochemistry Montana State University Bozeman MT 59717 USA
| | - Hao Yang
- Department of Chemistry Northwestern University Evanston IL 60208 USA
| | - Eric M. Shepard
- Department of Chemistry & Biochemistry Montana State University Bozeman MT 59717 USA
| | - Ryan Swimley
- Department of Chemistry & Biochemistry Montana State University Bozeman MT 59717 USA
| | - Adrien Pagnier
- Department of Chemistry & Biochemistry Montana State University Bozeman MT 59717 USA
| | - William E. Broderick
- Department of Chemistry & Biochemistry Montana State University Bozeman MT 59717 USA
| | - Brian M. Hoffman
- Department of Chemistry Northwestern University Evanston IL 60208 USA
| | - Joan B. Broderick
- Department of Chemistry & Biochemistry Montana State University Bozeman MT 59717 USA
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21
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Impano S, Yang H, Jodts RJ, Pagnier A, Swimley R, McDaniel EC, Shepard EM, Broderick WE, Broderick JB, Hoffman BM. Active-Site Controlled, Jahn-Teller Enabled Regioselectivity in Reductive S-C Bond Cleavage of S-Adenosylmethionine in Radical SAM Enzymes. J Am Chem Soc 2021; 143:335-348. [PMID: 33372786 PMCID: PMC7934139 DOI: 10.1021/jacs.0c10925] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Catalysis by canonical radical S-adenosyl-l-methionine (SAM) enzymes involves electron transfer (ET) from [4Fe-4S]+ to SAM, generating an R3S0 radical that undergoes regioselective homolytic reductive cleavage of the S-C5' bond to generate the 5'-dAdo· radical. However, cryogenic photoinduced S-C bond cleavage has regioselectively yielded either 5'-dAdo· or ·CH3, and indeed, each of the three SAM S-C bonds can be regioselectively cleaved in an RS enzyme. This diversity highlights a longstanding central question: what controls regioselective homolytic S-C bond cleavage upon SAM reduction? We here provide an unexpected answer, founded on our observation that photoinduced S-C bond cleavage in multiple canonical RS enzymes reveals two enzyme classes: in one, photolysis forms 5'-dAdo·, and in another it forms ·CH3. The identity of the cleaved S-C bond correlates with SAM ribose conformation but not with positioning and orientation of the sulfonium center relative to the [4Fe-4S] cluster. We have recognized the reduced-SAM R3S0 radical is a (2E) state with its antibonding unpaired electron in an orbital doublet, which renders R3S0 Jahn-Teller (JT)-active and therefore subject to vibronically induced distortion. Active-site forces induce a JT distortion that localizes the odd electron in a single priority S-C antibond, which undergoes regioselective cleavage. In photolytic cleavage those forces act through control of the ribose conformation and are transmitted to the sulfur via the S-C5' bond, but during catalysis thermally induced conformational changes that enable ET from a cluster iron generate dominant additional forces that specifically select S-C5' for cleavage. This motion also can explain how 5'-dAdo· subsequently forms the organometallic intermediate Ω.
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Affiliation(s)
- Stella Impano
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Hao Yang
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Richard J Jodts
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Adrien Pagnier
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Ryan Swimley
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Elizabeth C McDaniel
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Eric M Shepard
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - William E Broderick
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Joan B Broderick
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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22
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Pagnier A, Yang H, Jodts RJ, James CD, Shepard EM, Impano S, Broderick WE, Hoffman BM, Broderick JB. Radical SAM Enzyme Spore Photoproduct Lyase: Properties of the Ω Organometallic Intermediate and Identification of Stable Protein Radicals Formed during Substrate-Free Turnover. J Am Chem Soc 2020; 142:18652-18660. [PMID: 32966073 DOI: 10.1021/jacs.0c08585] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Spore photoproduct lyase is a radical S-adenosyl-l-methionine (SAM) enzyme with the unusual property that addition of SAM to the [4Fe-4S]1+ enzyme absent substrate results in rapid electron transfer to SAM with accompanying homolytic S-C5' bond cleavage. Herein, we demonstrate that this unusual reaction forms the organometallic intermediate Ω in which the unique Fe atom of the [4Fe-4S] cluster is bound to C5' of the 5'-deoxyadenosyl radical (5'-dAdo•). During catalysis, homolytic cleavage of the Fe-C5' bond liberates 5'-dAdo• for reaction with substrate, but here, we use Ω formation without substrate to determine the thermal stability of Ω. The reaction of Geobacillus thermodenitrificans SPL (GtSPL) with SAM forms Ω within ∼15 ms after mixing. By monitoring the decay of Ω through rapid freeze-quench trapping at progressively longer times we find an ambient temperature decay time of the Ω Fe-C5' bond of τ ≈ 5-6 s, likely shortened by enzymatic activation as is the case with the Co-C5' bond of B12. We have further used hand quenching at times up to 10 min, and thus with multiple SAM turnovers, to probe the fate of the 5'-dAdo• radical liberated by Ω. In the absence of substrate, Ω undergoes low-probability conversion to a stable protein radical. The WT enzyme with valine at residue 172 accumulates a Val•; mutation of Val172 to isoleucine or cysteine results in accumulation of an Ile• or Cys• radical, respectively. The structures of the radical in WT, V172I, and V172C variants have been established by detailed EPR/DFT analyses.
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Affiliation(s)
- Adrien Pagnier
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, Montana. 59717, United States
| | - Hao Yang
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Richard J Jodts
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Christopher D James
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Eric M Shepard
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, Montana. 59717, United States
| | - Stella Impano
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, Montana. 59717, United States
| | - William E Broderick
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, Montana. 59717, United States
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Joan B Broderick
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, Montana. 59717, United States
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23
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McSkimming A, Sridharan A, Thompson NB, Müller P, Suess DLM. An [Fe 4S 4] 3+-Alkyl Cluster Stabilized by an Expanded Scorpionate Ligand. J Am Chem Soc 2020; 142:14314-14323. [PMID: 32692919 DOI: 10.1021/jacs.0c06334] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Alkyl-ligated iron-sulfur clusters in the [Fe4S4]3+ charge state have been proposed as short-lived intermediates in a number of enzymatic reactions. To better understand the properties of these intermediates, we have prepared and characterized the first synthetic [Fe4S4]3+-alkyl cluster. Isolation of this highly reactive species was made possible by the development of an expanded scorpionate ligand suited to the encapsulation of cuboidal clusters. Like the proposed enzymatic intermediates, this synthetic [Fe4S4]3+-alkyl cluster adopts an S = 1/2 ground state with giso > 2. Mössbauer spectroscopic studies reveal that the alkylated Fe has an unusually low isomer shift, which reflects the highly covalent Fe-C bond and the localization of Fe3+ at the alkylated site in the solid state. Paramagnetic 1H NMR studies establish that this valence localization persists in solution at physiologically relevant temperatures, an effect that has not been observed for [Fe4S4]3+ clusters outside of a protein. These findings establish the unusual electronic-structure effects imparted by the strong-field alkyl ligand and lay the foundation for understanding the electronic structures of [Fe4S4]3+-alkyl intermediates in biology.
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Affiliation(s)
- Alex McSkimming
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Arun Sridharan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Niklas B Thompson
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Peter Müller
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Daniel L M Suess
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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24
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Mariasina SS, Chang CF, Petrova OA, Efimov SV, Klochkov VV, Kechko OI, Mitkevich VA, Sergiev PV, Dontsova OA, Polshakov VI. Williams-Beuren syndrome-related methyltransferase WBSCR27: cofactor binding and cleavage. FEBS J 2020; 287:5375-5393. [PMID: 32255258 DOI: 10.1111/febs.15320] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 02/20/2020] [Accepted: 03/30/2020] [Indexed: 11/28/2022]
Abstract
Williams-Beuren syndrome, characterized by numerous physiological and mental problems, is caused by the heterozygous deletion of chromosome region 7q11.23, which results in the disappearance of 26 protein-coding genes. Protein WBSCR27 is a product of one of these genes whose biological function has not yet been established and for which structural information has been absent until now. Using NMR, we investigated the structural and functional properties of murine WBSCR27. For protein in the apo form and in a complex with S-(5'-adenosyl)-l-homocysteine (SAH), a complete NMR resonance assignment has been obtained and the secondary structure has been determined. This information allows us to attribute WBSCR27 to Class I methyltransferases. The interaction of WBSCR27 with the cofactor S-(5'-adenosyl)-l-methionine (SAM) and its metabolic products - SAH, 5'-deoxy-5'-methylthioadenosine (MTA) and 5'-deoxyadenosine (5'dAdo) - was studied by NMR and isothermal titration calorimetry. SAH binds WBSCR27 much tighter than SAM, leaving open the question of cofactor turnover in the methylation reaction. One possible answer to this question is the presence of weak but detectable nucleosidase activity for WBSCR27. We found that the enzyme catalyses the cleavage of the adenine moiety from SAH, MTA and 5'dAdo, similar to the action of bacterial SAH/MTA nucleosidases. We also found that the binding of SAM or SAH causes a significant change in the structure of WBSCR27 and in the conformational mobility of the protein fragments, which can be attributed to the substrate recognition site. This indicates that the binding of the cofactor modulates the folding of the substrate-recognizing region of the enzyme.
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Affiliation(s)
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | | | - Sergey V Efimov
- NMR Laboratory, Institute of Physics, Kazan Federal University, Russia
| | | | - Olga I Kechko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Vladimir A Mitkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Petr V Sergiev
- M.V. Lomonosov Moscow State University, Russia.,Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Olga A Dontsova
- M.V. Lomonosov Moscow State University, Russia.,Skolkovo Institute of Science and Technology, Moscow, Russia
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Rittle J. The Key Intermediate in Radical S-Adenosyl-methionine Catalysis: Caught in the Act. ACS CENTRAL SCIENCE 2019; 5:1741-1743. [PMID: 31807673 PMCID: PMC6891856 DOI: 10.1021/acscentsci.9b01024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
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