1
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Can M, Abernathy MJ, Wiley S, Griffith C, James CD, Xiong J, Guo Y, Hoffman BM, Ragsdale SW, Sarangi R. Characterization of Methyl- and Acetyl-Ni Intermediates in Acetyl CoA Synthase Formed during Anaerobic CO 2 and CO Fixation. J Am Chem Soc 2023; 145:13696-13708. [PMID: 37306669 PMCID: PMC10311460 DOI: 10.1021/jacs.3c01772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Indexed: 06/13/2023]
Abstract
The Wood-Ljungdahl Pathway is a unique biological mechanism of carbon dioxide and carbon monoxide fixation proposed to operate through nickel-based organometallic intermediates. The most unusual steps in this metabolic cycle involve a complex of two distinct nickel-iron-sulfur proteins: CO dehydrogenase and acetyl-CoA synthase (CODH/ACS). Here, we describe the nickel-methyl and nickel-acetyl intermediates in ACS completing the characterization of all its proposed organometallic intermediates. A single nickel site (Nip) within the A cluster of ACS undergoes major geometric and redox changes as it transits the planar Nip, tetrahedral Nip-CO and planar Nip-Me and Nip-Ac intermediates. We propose that the Nip intermediates equilibrate among different redox states, driven by an electrochemical-chemical (EC) coupling process, and that geometric changes in the A-cluster linked to large protein conformational changes control entry of CO and the methyl group.
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Affiliation(s)
- Mehmet Can
- Department
of Biochemistry, Faculty of Pharmacy, Ankara
Medipol University, Ankara 06050, Turkey
| | - Macon J. Abernathy
- Stanford
Synchrotron Radiation Lightsource, SLAC
National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Seth Wiley
- Biosciences
Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Claire Griffith
- Department
of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Christopher D. James
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Jin Xiong
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Yisong Guo
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Brian M. Hoffman
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Stephen W. Ragsdale
- Department
of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Ritimukta Sarangi
- Stanford
Synchrotron Radiation Lightsource, SLAC
National Accelerator Laboratory, Menlo Park, California 94025, United States
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2
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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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3
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Moody JD, Hill S, Lundahl MN, Saxton AJ, Galambas A, Broderick WE, Lawrence CM, Broderick JB. Computational engineering of previously crystallized pyruvate formate-lyase activating enzyme reveals insights into SAM binding and reductive cleavage. J Biol Chem 2023; 299:104791. [PMID: 37156396 PMCID: PMC10267522 DOI: 10.1016/j.jbc.2023.104791] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/21/2023] [Accepted: 04/23/2023] [Indexed: 05/10/2023] Open
Abstract
Radical S-adenosyl-l-methionine (SAM) enzymes are ubiquitous in nature and carry out a broad variety of difficult chemical transformations initiated by hydrogen atom abstraction. Although numerous radical SAM (RS) enzymes have been structurally characterized, many prove recalcitrant to crystallization needed for atomic-level structure determination using X-ray crystallography, and even those that have been crystallized for an initial study can be difficult to recrystallize for further structural work. We present here a method for computationally engineering previously observed crystallographic contacts and employ it to obtain more reproducible crystallization of the RS enzyme pyruvate formate-lyase activating enzyme (PFL-AE). We show that the computationally engineered variant binds a typical RS [4Fe-4S]2+/+ cluster that binds SAM, with electron paramagnetic resonance properties indistinguishable from the native PFL-AE. The variant also retains the typical PFL-AE catalytic activity, as evidenced by the characteristic glycyl radical electron paramagnetic resonance signal observed upon incubation of the PFL-AE variant with reducing agent, SAM, and PFL. The PFL-AE variant was also crystallized in the [4Fe-4S]2+ state with SAM bound, providing a new high-resolution structure of the SAM complex in the absence of substrate. Finally, by incubating such a crystal in a solution of sodium dithionite, the reductive cleavage of SAM is triggered, providing us with a structure in which the SAM cleavage products 5'-deoxyadenosine and methionine are bound in the active site. We propose that the methods described herein may be useful in the structural characterization of other difficult-to-resolve proteins.
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Affiliation(s)
- James D Moody
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, USA; Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Sarah Hill
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Maike N Lundahl
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Aubrianna J Saxton
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, USA
| | - Amanda Galambas
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - William E Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - C Martin Lawrence
- 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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4
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Zhang X, Wang Z, Li Z, Shaik S, Wang B. [4Fe–4S]-Mediated Proton-Coupled Electron Transfer Enables the Efficient Degradation of Chloroalkenes by Reductive Dehalogenases. ACS Catal 2023. [DOI: 10.1021/acscatal.2c06306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Xuan Zhang
- State Key Laboratory Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Zikuan Wang
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der Ruhr 45470, Germany
| | - Zhen Li
- State Key Laboratory Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Sason Shaik
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Binju Wang
- State Key Laboratory Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
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5
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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: 9] [Impact Index Per Article: 9.0] [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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6
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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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7
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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: 20] [Impact Index Per Article: 10.0] [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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8
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Zhou S, Wei WJ, Liao RZ. QM/MM Study of the Mechanism of the Noncanonical S-Cγ Bond Scission in S-Adenosylmethionine Catalyzed by the CmnDph2 Radical Enzyme. Top Catal 2022. [DOI: 10.1007/s11244-021-01420-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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9
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Feng JQ, Wang BJ. Super-exchange and exchange-enhanced reactivity in Fe4S4-mediated activation of SAM by radical SAM enzymes. CHINESE J CHEM PHYS 2021. [DOI: 10.1063/1674-0068/cjcp2108134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Jian-qiang Feng
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Bin-ju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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10
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Feng J, Shaik S, Wang B. Spin‐Regulated Electron Transfer and Exchange‐Enhanced Reactivity in Fe
4
S
4
‐Mediated Redox Reaction of the Dph2 Enzyme During the Biosynthesis of Diphthamide. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202107008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Jianqiang Feng
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Sason Shaik
- Institute of Chemistry The Hebrew University of Jerusalem Jerusalem 9190401 Israel
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
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11
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Feng J, Shaik S, Wang B. Spin-Regulated Electron Transfer and Exchange-Enhanced Reactivity in Fe 4 S 4 -Mediated Redox Reaction of the Dph2 Enzyme During the Biosynthesis of Diphthamide. Angew Chem Int Ed Engl 2021; 60:20430-20436. [PMID: 34302311 DOI: 10.1002/anie.202107008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Indexed: 11/06/2022]
Abstract
The [4Fe-4S]-dependent radical S-adenosylmethionine (SAM) proteins is one of large families of redox enzymes that are able to carry a panoply of challenging transformations. Despite the extensive studies of structure-function relationships of radical SAM (RS) enzymes, the electronic state-dependent reactivity of the [4Fe-4S] cluster in these enzymes remains elusive. Using combined MD simulations and QM/MM calculations, we deciphered the electronic state-dependent reactivity of the [4Fe-4S] cluster in Dph2, a key enzyme involved in the biosynthesis of diphthamide. Our calculations show that the reductive cleavage of the S-C(γ) bond is highly dependent on the electronic structure of [4Fe-4S]. Interestingly, the six electronic states can be classified into a low-energy and a high-energy groups, which are correlated with the net spin of Fe4 atom ligated to SAM. Due to the driving force of Fe4-C(γ) bonding, the net spin on the Fe4 moiety dictate the shift of the opposite spin electron from the Fe1-Fe2-Fe3 block to SAM. Such spin-regulated electron transfer results in the exchange-enhanced reactivity in the lower-energy group compared with those in the higher-energy group. This reactivity principle provides fundamental mechanistic insights into reactivities of [4Fe-4S] cluster in RS enzymes.
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Affiliation(s)
- Jianqiang Feng
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Sason Shaik
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
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12
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Blue TC, Davis KM. Computational Approaches: An Underutilized Tool in the Quest to Elucidate Radical SAM Dynamics. Molecules 2021; 26:molecules26092590. [PMID: 33946806 PMCID: PMC8124187 DOI: 10.3390/molecules26092590] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 12/30/2022] Open
Abstract
Enzymes are biological catalysts whose dynamics enable their reactivity. Visualizing conformational changes, in particular, is technically challenging, and little is known about these crucial atomic motions. This is especially problematic for understanding the functional diversity associated with the radical S-adenosyl-L-methionine (SAM) superfamily whose members share a common radical mechanism but ultimately catalyze a broad range of challenging reactions. Computational chemistry approaches provide a readily accessible alternative to exploring the time-resolved behavior of these enzymes that is not limited by experimental logistics. Here, we review the application of molecular docking, molecular dynamics, and density functional theory, as well as hybrid quantum mechanics/molecular mechanics methods to the study of these enzymes, with a focus on understanding the mechanistic dynamics associated with turnover.
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13
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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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14
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Bím D, Alonso-Gil S, Srnec M. From Synthetic to Biological Fe 4 S 4 Complexes: Redox Properties Correlated to Function of Radical S-Adenosylmethionine Enzymes. Chempluschem 2020; 85:2534-2541. [PMID: 33245201 DOI: 10.1002/cplu.202000663] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/02/2020] [Indexed: 11/10/2022]
Abstract
By employing the computational protocol for calculation of reduction potentials of the Fe4 S4 -containing species validated using a representative series of well-defined synthetic complexes, we focused on redox properties of two prototypical radical SAM enzymes to reveal how they transform SAM into the reactive 5'-deoxyadenosyl radical, and how they tune this radical for its proper biological function. We found the reduction potential of SAM is indeed elevated by 0.3-0.4 V upon coordination to Fe4 S4 , which was previously speculated in the literature. This makes a generation of 5'-deoxyadenosyl radical from SAM less endergonic (by ca. 7-9 kcal mol-1 ) and hence more feasible in both enzymes as compared to the identical process in water. Furthermore, our calculations indicate that the enzyme-bound 5'-deoxyadenosyl radical has a significantly lower reduction potential than in referential aqueous solution, which may help the enzymes to suppress potential side redox reactions and simultaneously elevate its proton-philic character, which may, in turn, promote the radical hydrogen-atom abstraction ability.
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Affiliation(s)
- Daniel Bím
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, Prague, 8 182 23, Czech Republic
| | - Santiago Alonso-Gil
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, Prague, 8 182 23, Czech Republic
| | - Martin Srnec
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, Prague, 8 182 23, Czech Republic
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15
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Yang H, Impano S, Shepard EM, James CD, Broderick WE, Broderick JB, Hoffman BM. Photoinduced Electron Transfer in a Radical SAM Enzyme Generates an S-Adenosylmethionine Derived Methyl Radical. J Am Chem Soc 2019; 141:16117-16124. [PMID: 31509404 DOI: 10.1021/jacs.9b08541] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Radical SAM (RS) enzymes use S-adenosyl-l-methionine (SAM) and a [4Fe-4S] cluster to initiate a broad spectrum of radical transformations throughout all kingdoms of life. We report here that low-temperature photoinduced electron transfer from the [4Fe-4S]1+ cluster to bound SAM in the active site of the hydrogenase maturase RS enzyme, HydG, results in specific homolytic cleavage of the S-CH3 bond of SAM, rather than the S-C5' bond as in the enzyme-catalyzed (thermal) HydG reaction. This result is in stark contrast to a recent report in which photoinduced ET in the RS enzyme pyruvate formate-lyase activating enzyme cleaved the S-C5' bond to generate a 5'-deoxyadenosyl radical, and provides the first direct evidence for homolytic S-CH3 bond cleavage in a RS enzyme. Photoinduced ET in HydG generates a trapped •CH3 radical, as well as a small population of an organometallic species with an Fe-CH3 bond, denoted ΩM. The •CH3 radical is surprisingly found to exhibit rotational diffusion in the HydG active site at temperatures as low as 40 K, and is rapidly quenched: whereas 5'-dAdo• is stable indefinitely at 77 K, •CH3 quenches with a half-time of ∼2 min at this temperature. The rapid quenching and rotational/translational freedom of •CH3 shows that enzymes would be unable to harness this radical as a regio- and stereospecific H atom abstractor during catalysis, in contrast to the exquisite control achieved with the enzymatically generated 5'-dAdo•.
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Affiliation(s)
- Hao Yang
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States
| | - Stella Impano
- 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
| | - Christopher D James
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , 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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16
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Radical SAM enzymes: surprises along the path to understanding mechanism. J Biol Inorg Chem 2019; 24:769-776. [DOI: 10.1007/s00775-019-01706-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 08/16/2019] [Indexed: 10/26/2022]
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17
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Radical S-adenosylmethionine maquette chemistry: Cx3Cx2C peptide coordinated redox active [4Fe–4S] clusters. J Biol Inorg Chem 2019; 24:793-807. [DOI: 10.1007/s00775-019-01708-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 08/14/2019] [Indexed: 10/26/2022]
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18
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Henthorn J, Arias RJ, Koroidov S, Kroll T, Sokaras D, Bergmann U, Rees DC, DeBeer S. Localized Electronic Structure of Nitrogenase FeMoco Revealed by Selenium K-Edge High Resolution X-ray Absorption Spectroscopy. J Am Chem Soc 2019; 141:13676-13688. [PMID: 31356071 PMCID: PMC6716209 DOI: 10.1021/jacs.9b06988] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Indexed: 11/28/2022]
Abstract
The size and complexity of Mo-dependent nitrogenase, a multicomponent enzyme capable of reducing dinitrogen to ammonia, have made a detailed understanding of the FeMo cofactor (FeMoco) active site electronic structure an ongoing challenge. Selective substitution of sulfur by selenium in FeMoco affords a unique probe wherein local Fe-Se interactions can be directly interrogated via high-energy resolution fluorescence detected X-ray absorption spectroscopic (HERFD XAS) and extended X-ray absorption fine structure (EXAFS) studies. These studies reveal a significant asymmetry in the electronic distribution of the FeMoco, suggesting a more localized electronic structure picture than is typically assumed for iron-sulfur clusters. Supported by experimental small molecule model data in combination with time dependent density functional theory (TDDFT) calculations, the HERFD XAS data is consistent with an assignment of Fe2/Fe6 as an antiferromagnetically coupled diferric pair. HERFD XAS and EXAFS have also been applied to Se-substituted CO-inhibited MoFe protein, demonstrating the ability of these methods to reveal electronic and structural changes that occur upon substrate binding. These results emphasize the utility of Se HERFD XAS and EXAFS for selectively probing the local electronic and geometric structure of FeMoco.
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Affiliation(s)
- Justin
T. Henthorn
- Max
Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, D-45470 Mülheim an der
Ruhr, Germany
| | - Renee J. Arias
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Sergey Koroidov
- PULSE
Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Thomas Kroll
- Stanford
Synchrotron Radiation Lightsource, SLAC
National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Dimosthenis Sokaras
- Stanford
Synchrotron Radiation Lightsource, SLAC
National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Uwe Bergmann
- PULSE
Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Douglas C. Rees
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
- Howard
Hughes Medical Institute, California Institute
of Technology, Pasadena, California 91125, United States
| | - Serena DeBeer
- Max
Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, D-45470 Mülheim an der
Ruhr, Germany
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19
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Yang H, McDaniel EC, Impano S, Byer AS, Jodts RJ, Yokoyama K, Broderick WE, Broderick JB, Hoffman BM. The Elusive 5'-Deoxyadenosyl Radical: Captured and Characterized by Electron Paramagnetic Resonance and Electron Nuclear Double Resonance Spectroscopies. J Am Chem Soc 2019; 141:12139-12146. [PMID: 31274303 DOI: 10.1021/jacs.9b05926] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The 5'-deoxyadenosyl radical (5'-dAdo·) abstracts a substrate H atom as the first step in radical-based transformations catalyzed by adenosylcobalamin-dependent and radical S-adenosyl-l-methionine (RS) enzymes. Notwithstanding its central biological role, 5'-dAdo· has eluded characterization despite efforts spanning more than a half-century. Here, we report generation of 5'-dAdo· in a RS enzyme active site at 12 K using a novel approach involving cryogenic photoinduced electron transfer from the [4Fe-4S]+ cluster to the coordinated S-adenosylmethionine (SAM) to induce homolytic S-C5' bond cleavage. We unequivocally reveal the structure of this long-sought radical species through the use of electron paramagnetic resonance (EPR) and electron nuclear double resonance (ENDOR) spectroscopies with isotopic labeling, complemented by density-functional computations: a planar C5' (2pπ) radical (∼70% spin occupancy); the C5'(H)2 plane is rotated by ∼37° (experiment)/39° (DFT) relative to the C5'-C4'-(C4'-H) plane, placing a C5'-H antiperiplanar to the ribose-ring oxygen, which helps stabilize the radical against elimination of the 4'-H. The agreement between φ from experiment and in vacuo DFT indicates that the conformation is intrinsic to 5-dAdo· itself, and not determined by its environment.
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Affiliation(s)
- Hao Yang
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States
| | - Elizabeth C McDaniel
- Department of Chemistry and Biochemistry , Montana State University , Bozeman , Montana 59717 , United States
| | - Stella Impano
- Department of Chemistry and Biochemistry , Montana State University , Bozeman , Montana 59717 , United States
| | - Amanda S Byer
- Department of Chemistry and Biochemistry , Montana State University , Bozeman , Montana 59717 , United States
| | - Richard J Jodts
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States
| | - Kenichi Yokoyama
- Department of Biochemistry , Duke University , Durham , North Carolina 27710 , 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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20
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Lupan A, Silaghi-Dumitrescu R, King RB. Tetracapped tetrahedral ruthenium-sulfur clusters related to iron-sulfur structural units in metalloenzymes. Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2017.10.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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21
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Dong G, Cao L, Ryde U. Insight into the reaction mechanism of lipoyl synthase: a QM/MM study. J Biol Inorg Chem 2018; 23:221-229. [PMID: 29204715 PMCID: PMC5816104 DOI: 10.1007/s00775-017-1522-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 11/28/2017] [Indexed: 11/26/2022]
Abstract
Lipoyl synthase (LipA) catalyses the final step of the biosynthesis of the lipoyl cofactor by insertion of two sulfur atoms at the C6 and C8 atoms of the protein-bound octanoyl substrate. In this reaction, two [4Fe4S] clusters and two molecules of S-adenosyl-L-methionine are used. One of the two FeS clusters is responsible for the generation of a powerful oxidant, the 5'-deoxyadenosyl radical (5'-dA•). The other (the auxiliary cluster) is the source of both sulfur atoms that are inserted into the substrate. In this paper, the spin state of the FeS clusters and the reaction mechanism is investigated by the combined quantum mechanical and molecular mechanics approach. The calculations show that the ground state of the two FeS clusters, both in the [4Fe4S]2+ oxidation state, is a singlet state with antiferromagnetically coupled high-spin Fe ions and that there is quite a large variation of the energies of the various broken-symmetry states, up to 40 kJ/mol. For the two S-insertion reactions, the highest energy barrier is found for the hydrogen-atom abstraction from the octanoyl substrate by 5'-dA•. The formation of 5'-dA• is very facile for LipA, with an energy barrier of 6 kJ/mol for the first S-insertion reaction and without any barrier for the second S-insertion reaction. In addition, the first S ion attack on the C6 radical of octanoyl was found to take place directly by the transfer of the H6 from the substrate to 5'-dA•, whereas for the second S-insertion reaction, a C8 radical intermediate was formed with a rate-limiting barrier of 71 kJ/mol.
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Affiliation(s)
- Geng Dong
- Department of Theoretical Chemistry, Chemical Centre, Lund University, P.O. Box 124, 221 00, Lund, Sweden.
| | - Lili Cao
- Department of Theoretical Chemistry, Chemical Centre, Lund University, P.O. Box 124, 221 00, Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Chemical Centre, Lund University, P.O. Box 124, 221 00, Lund, Sweden
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22
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Bame J, Hoeck C, Carrington MJ, Butts CP, Jäger CM, Croft AK. Improved NOE fitting for flexible molecules based on molecular mechanics data – a case study with S-adenosylmethionine. Phys Chem Chem Phys 2018; 20:7523-7531. [DOI: 10.1039/c7cp07265a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using the important biomolecule S-adenosyl methionine as an exemplar, we provide a new, enhanced approach for fitting MD data to high-accuracy NOE data, providing improvements in structure determination.
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Affiliation(s)
- Jessica Bame
- University of Bristol
- School of Chemistry
- Clifton
- Bristol BS8 1TS
- UK
| | - Casper Hoeck
- University of Bristol
- School of Chemistry
- Clifton
- Bristol BS8 1TS
- UK
| | - Matthew J. Carrington
- University of Nottingham
- Department of Chemical and Environmental Engineering
- University Park
- Nottingham
- UK
| | - Craig P. Butts
- University of Bristol
- School of Chemistry
- Clifton
- Bristol BS8 1TS
- UK
| | - Christof M. Jäger
- University of Nottingham
- Department of Chemical and Environmental Engineering
- University Park
- Nottingham
- UK
| | - Anna K. Croft
- University of Nottingham
- Department of Chemical and Environmental Engineering
- University Park
- Nottingham
- UK
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23
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Grove TL, Himes PM, Hwang S, Yumerefendi H, Bonanno JB, Kuhlman B, Almo SC, Bowers AA. Structural Insights into Thioether Bond Formation in the Biosynthesis of Sactipeptides. J Am Chem Soc 2017; 139:11734-11744. [PMID: 28704043 PMCID: PMC6443407 DOI: 10.1021/jacs.7b01283] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Sactipeptides are ribosomally synthesized peptides that contain a characteristic thioether bridge (sactionine bond) that is installed posttranslationally and is absolutely required for their antibiotic activity. Sactipeptide biosynthesis requires a unique family of radical SAM enzymes, which contain multiple [4Fe-4S] clusters, to form the requisite thioether bridge between a cysteine and the α-carbon of an opposing amino acid through radical-based chemistry. Here we present the structure of the sactionine bond-forming enzyme CteB, from Clostridium thermocellum ATCC 27405, with both SAM and an N-terminal fragment of its peptidyl-substrate at 2.04 Å resolution. CteB has the (β/α)6-TIM barrel fold that is characteristic of radical SAM enzymes, as well as a C-terminal SPASM domain that contains two auxiliary [4Fe-4S] clusters. Importantly, one [4Fe-4S] cluster in the SPASM domain exhibits an open coordination site in absence of peptide substrate, which is coordinated by a peptidyl-cysteine residue in the bound state. The crystal structure of CteB also reveals an accessory N-terminal domain that has high structural similarity to a recently discovered motif present in several enzymes that act on ribosomally synthesized and post-translationally modified peptides (RiPPs), known as a RiPP precursor peptide recognition element (RRE). This crystal structure is the first of a sactionine bond forming enzyme and sheds light on structures and mechanisms of other members of this class such as AlbA or ThnB.
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Affiliation(s)
- Tyler L. Grove
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Paul M. Himes
- Division of Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Eshelman School of Pharmacy, Chapel Hill, North Carolina, USA
| | - Sungwon Hwang
- Division of Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Eshelman School of Pharmacy, Chapel Hill, North Carolina, USA
| | - Hayretin Yumerefendi
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jeffrey B. Bonanno
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Steven C. Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Albert A Bowers
- Division of Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Eshelman School of Pharmacy, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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24
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Yen TH, He ZC, Lee GH, Tseng MC, Shen YH, Tseng TW, Liaw WF, Chiang MH. Reduced thione ligation is preferred over neutral phosphine ligation in diiron biomimics regarding electronic functionality: a spectroscopic and computational investigation. Chem Commun (Camb) 2017; 53:332-335. [DOI: 10.1039/c6cc08042a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Sulfur means superiority: effective electronic communication and buffering by sulfur ligation.
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Affiliation(s)
- Tao-Hung Yen
- Institute of Chemistry
- Academia Sinica
- Taipei 115
- Taiwan
- Molecular Science Technology Program
| | - Zong-Cheng He
- Department of Chemical Engineering and Biotechnology
- National Taipei University of Technology
- Taipei 106
- Taiwan
| | - Gene-Hsiang Lee
- Instrumentation Center
- National Taiwan University
- Taipei 106
- Taiwan
| | | | - Yu-Hsuan Shen
- Department of Chemistry
- National Taiwan University
- Taipei 106
- Taiwan
| | - Tien-Wen Tseng
- Department of Chemical Engineering and Biotechnology
- National Taipei University of Technology
- Taipei 106
- Taiwan
| | - Wen-Feng Liaw
- Department of Chemistry
- National Tsing Hua University
- Hsinchu 300
- Taiwan
| | - Ming-Hsi Chiang
- Institute of Chemistry
- Academia Sinica
- Taipei 115
- Taiwan
- Molecular Science Technology Program
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25
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Kline CD, Blackburn NJ. Substrate-Induced Carbon Monoxide Reactivity Suggests Multiple Enzyme Conformations at the Catalytic Copper M-Center of Peptidylglycine Monooxygenase. Biochemistry 2016; 55:6652-6661. [PMID: 27933800 DOI: 10.1021/acs.biochem.6b00845] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The present study uses CO as a surrogate for oxygen to probe how substrate binding triggers oxygen activation in peptidylglycine monooygenase (PHM). Infrared stretching frequencies (ν(C ≡ O)) of the carbonyl (CO) adducts of copper proteins are sensitive markers of Cu(I) coordination and are useful in probing oxygen reactivity because the electronic properties of O2 and CO are similar. The carbonyl chemistry has been explored using PHM WT and a number of active site variants in the absence and presence of peptidyl substrates. We have determined that upon carbonylation (i) a major CO band at 2092 cm-1 and a second minor CO band at 2063 cm-1 are observed in the absence of peptide substrate Ac-YVG; (ii) the presence of peptide substrate amplifies the minor CO band and causes it to partially interconvert with the CO band at 2092 cm-1; (iii) the substrate-induced CO band is associated with a second conformer at CuM; and (iv) the CuH-site mutants, which are inactive, fail to generate any substrate-induced CO bands. The total intensity of both bands is constant, suggesting that the Cu(I)M-site partitions between the two carbonylated enzyme states. Together, these data provide evidence for two conformers at CuM, one of which is induced by binding of the peptide substrate with the implication that this represents the conformation that also allows binding and activation of O2.
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Affiliation(s)
- Chelsey D Kline
- Institute of Environmental Health, Oregon Health and Science University , 3181 S.W. Sam Jackson Park Road, Portland, Oregon 97239, United States
| | - Ninian J Blackburn
- Institute of Environmental Health, Oregon Health and Science University , 3181 S.W. Sam Jackson Park Road, Portland, Oregon 97239, United States
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26
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Abstract
Radical S-adenosylmethionine (SAM) enzymes catalyze an astonishing array of complex and chemically challenging reactions across all domains of life. Of approximately 114,000 of these enzymes, 8 are known to be present in humans: MOCS1, molybdenum cofactor biosynthesis; LIAS, lipoic acid biosynthesis; CDK5RAP1, 2-methylthio-N(6)-isopentenyladenosine biosynthesis; CDKAL1, methylthio-N(6)-threonylcarbamoyladenosine biosynthesis; TYW1, wybutosine biosynthesis; ELP3, 5-methoxycarbonylmethyl uridine; and RSAD1 and viperin, both of unknown function. Aberrations in the genes encoding these proteins result in a variety of diseases. In this review, we summarize the biochemical characterization of these 8 radical S-adenosylmethionine enzymes and, in the context of human health, describe the deleterious effects that result from such genetic mutations.
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Affiliation(s)
- Bradley J Landgraf
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Erin L McCarthy
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Squire J Booker
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802.,The Howard Hughes Medical Institute, The Pennsylvania State University, University Park, Pennsylvania 16802;
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27
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Selvaraj B, Buckel W, Golding BT, Ullmann GM, Martins BM. Structure and Function of 4-Hydroxyphenylacetate Decarboxylase and Its Cognate Activating Enzyme. J Mol Microbiol Biotechnol 2016; 26:76-91. [DOI: 10.1159/000440882] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
4-Hydroxyphenylacetate decarboxylase (4Hpad) is the prototype of a new class of Fe-S cluster-dependent glycyl radical enzymes (Fe-S GREs) acting on aromatic compounds. The two-enzyme component system comprises a decarboxylase responsible for substrate conversion and a dedicated activating enzyme (4Hpad-AE). The decarboxylase uses a glycyl/thiyl radical dyad to convert 4-hydroxyphenylacetate into <i>p</i>-cresol (4-methylphenol) by a biologically unprecedented Kolbe-type decarboxylation. In addition to the radical dyad prosthetic group, the decarboxylase unit contains two [4Fe-4S] clusters coordinated by an extra small subunit of unknown function. 4Hpad-AE reductively cleaves S-adenosylmethionine (SAM or AdoMet) at a site-differentiated [4Fe-4S]<sup>2+/+</sup> cluster (RS cluster) generating a transient 5′-deoxyadenosyl radical that produces a stable glycyl radical in the decarboxylase by the abstraction of a hydrogen atom. 4Hpad-AE binds up to two auxiliary [4Fe-4S] clusters coordinated by a ferredoxin-like insert that is C-terminal to the RS cluster-binding motif. The ferredoxin-like domain with its two auxiliary clusters is not vital for SAM-dependent glycyl radical formation in the decarboxylase, but facilitates a longer lifetime for the radical. This review describes the 4Hpad and cognate AE families and focuses on the recent advances and open questions concerning the structure, function and mechanism of this novel Fe-S-dependent class of GREs.
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28
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Density functional theory calculations on the active site of biotin synthase: mechanism of S transfer from the Fe2S2 cluster and the role of 1st and 2nd sphere residues. J Biol Inorg Chem 2015; 20:1147-62. [DOI: 10.1007/s00775-015-1296-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 09/02/2015] [Indexed: 10/23/2022]
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29
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Hover BM, Yokoyama K. C-Terminal glycine-gated radical initiation by GTP 3',8-cyclase in the molybdenum cofactor biosynthesis. J Am Chem Soc 2015; 137:3352-9. [PMID: 25697423 DOI: 10.1021/ja512997j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The molybdenum cofactor (Moco) is an essential redox cofactor found in all kingdoms of life. Genetic mutations in the human Moco biosynthetic enzymes lead to a fatal metabolic disorder, Moco deficiency (MoCD). Greater than 50% of all human MoCD patients have mutations in MOCS1A, a radical S-adenosyl-l-methionine (SAM) enzyme involved in the conversion of guanosine 5'-triphosphate (GTP) into cyclic pyranopterin monophosphate. In MOCS1A, one of the frequently affected locations is the GG motif constituted of two consecutive Gly at the C-terminus. The GG motif is conserved among all MOCS1A homologues, but its role in catalysis or the mechanism by which its mutation causes MoCD was unknown. Here, we report the functional characterization of the GG motif using MoaA, a bacterial homologue of MOCS1A, as a model. Our study elucidated that the GG motif is essential for the activity of MoaA to produce 3',8-cH2GTP from GTP (GTP 3',8-cyclase), and that synthetic peptides corresponding to the C-terminal region of wt-MoaA rescue the GTP 3',8-cyclase activity of the GG-motif mutants. Further biochemical characterization suggested that the C-terminal tail containing the GG motif interacts with the SAM-binding pocket of MoaA, and is essential for the binding of SAM and subsequent radical initiation. In sum, these observations suggest that the C-terminal tail of MoaA provides an essential mechanism to trigger the free radical reaction, impairment of which results in the complete loss of catalytic function of the enzyme, and causes MoCD.
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Affiliation(s)
- Bradley M Hover
- Department of Biochemistry, Duke University Medical Center , Durham, North Carolina 27710, United States
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30
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Jarrett JT. The biosynthesis of thiol- and thioether-containing cofactors and secondary metabolites catalyzed by radical S-adenosylmethionine enzymes. J Biol Chem 2014; 290:3972-9. [PMID: 25477512 DOI: 10.1074/jbc.r114.599308] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Sulfur atoms are present as thiol and thioether functional groups in amino acids, coenzymes, cofactors, and various products of secondary metabolic pathways. The biosynthetic pathways for several sulfur-containing biomolecules require the substitution of sulfur for hydrogen at unreactive aliphatic or electron-rich aromatic carbon atoms. Examples discussed in this review include biotin, lipoic acid, methylthioether modifications found in some nucleic acids and proteins, and thioether cross-links found in peptide natural products. Radical S-adenosyl-L-methionine (SAM) enzymes use an iron-sulfur cluster to catalyze the reduction of SAM to methionine and a highly reactive 5'-deoxyadenosyl radical; this radical can abstract hydrogen atoms at unreactive positions, facilitating the introduction of a variety of functional groups. Radical SAM enzymes that catalyze sulfur insertion reactions contain a second iron-sulfur cluster that facilitates the chemistry, either by donating the cluster's endogenous sulfide or by binding and activating exogenous sulfide or sulfur-containing substrates. The use of radical chemistry involving iron-sulfur clusters is an efficient anaerobic route to the generation of carbon-sulfur bonds in cofactors, secondary metabolites, and other natural products.
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Affiliation(s)
- Joseph T Jarrett
- From the Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii 96822
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31
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Stich TA, Myers WK, Britt RD. Paramagnetic intermediates generated by radical S-adenosylmethionine (SAM) enzymes. Acc Chem Res 2014; 47:2235-43. [PMID: 24991701 PMCID: PMC4139163 DOI: 10.1021/ar400235n] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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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Broderick JB, Duffus B, Duschene KS, Shepard EM. Radical S-adenosylmethionine enzymes. Chem Rev 2014; 114:4229-317. [PMID: 24476342 PMCID: PMC4002137 DOI: 10.1021/cr4004709] [Citation(s) in RCA: 589] [Impact Index Per Article: 58.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Indexed: 12/22/2022]
Affiliation(s)
- Joan B. Broderick
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Benjamin
R. Duffus
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Kaitlin S. Duschene
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Eric M. Shepard
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
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Shisler KA, Broderick JB. Glycyl radical activating enzymes: structure, mechanism, and substrate interactions. Arch Biochem Biophys 2014; 546:64-71. [PMID: 24486374 PMCID: PMC4083501 DOI: 10.1016/j.abb.2014.01.020] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 01/20/2014] [Accepted: 01/21/2014] [Indexed: 11/20/2022]
Abstract
The glycyl radical enzyme activating enzymes (GRE-AEs) are a group of enzymes that belong to the radical S-adenosylmethionine (SAM) superfamily and utilize a [4Fe-4S] cluster and SAM to catalyze H-atom abstraction from their substrate proteins. GRE-AEs activate homodimeric proteins known as glycyl radical enzymes (GREs) through the production of a glycyl radical. After activation, these GREs catalyze diverse reactions through the production of their own substrate radicals. The GRE-AE pyruvate formate lyase activating enzyme (PFL-AE) is extensively characterized and has provided insights into the active site structure of radical SAM enzymes including GRE-AEs, illustrating the nature of the interactions with their corresponding substrate GREs and external electron donors. This review will highlight research on PFL-AE and will also discuss a few GREs and their respective activating enzymes.
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Affiliation(s)
- Krista A Shisler
- Department of Chemistry & Biochemistry and the Astrobiology Biogeocatalysis Research Center, Montana State University, Bozeman, MT 59717, United States
| | - Joan B Broderick
- Department of Chemistry & Biochemistry and the Astrobiology Biogeocatalysis Research Center, Montana State University, Bozeman, MT 59717, United States.
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Silver SC, Gardenghi DJ, Naik SG, Shepard EM, Huynh BH, Szilagyi RK, Broderick JB. Combined Mössbauer spectroscopic, multi-edge X-ray absorption spectroscopic, and density functional theoretical study of the radical SAM enzyme spore photoproduct lyase. J Biol Inorg Chem 2014; 19:465-83. [PMID: 24532333 PMCID: PMC4089880 DOI: 10.1007/s00775-014-1104-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 01/13/2014] [Indexed: 11/30/2022]
Abstract
Spore photoproduct lyase (SPL), a member of the radical S-adenosyl-L-methionine (SAM) superfamily, catalyzes the direct reversal of the spore photoproduct, a thymine dimer specific to bacterial spores, to two thymines. SPL requires SAM and a redox-active [4Fe-4S] cluster for catalysis. Mössbauer analysis of anaerobically purified SPL indicates the presence of a mixture of cluster states with the majority (40 %) as [2Fe-2S](2+) clusters and a smaller amount (15 %) as [4Fe-4S](2+) clusters. On reduction, the cluster content changes to primarily (60 %) [4Fe-4S](+). The speciation information from Mössbauer data allowed us to deconvolute iron and sulfur K-edge X-ray absorption spectra to uncover electronic (X-ray absorption near-edge structure, XANES) and geometric (extended X-ray absorption fine structure, EXAFS) structural features of the Fe-S clusters, and their interactions with SAM. The iron K-edge EXAFS data provide evidence for elongation of a [2Fe-2S] rhomb of the [4Fe-4S] cluster on binding SAM on the basis of an Fe···Fe scatterer at 3.0 Å. The XANES spectra of reduced SPL in the absence and presence of SAM overlay one another, indicating that SAM is not undergoing reductive cleavage. The X-ray absorption spectroscopy data for SPL samples and data for model complexes from the literature allowed the deconvolution of contributions from [2Fe-2S] and [4Fe-4S] clusters to the sulfur K-edge XANES spectra. The analysis of pre-edge features revealed electronic changes in the Fe-S clusters as a function of the presence of SAM. The spectroscopic findings were further corroborated by density functional theory calculations that provided insights into structural and electronic perturbations that can be correlated by considering the role of SAM as a catalyst or substrate.
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Affiliation(s)
| | | | | | | | - Boi Hanh Huynh
- Department of Physics, Emory University, Atlanta, Georgia 30322
| | - Robert K. Szilagyi
- NAI Astrobiology Biogeocatalysis Research Center, Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT, 59718
| | - Joan B. Broderick
- NAI Astrobiology Biogeocatalysis Research Center, Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT, 59718
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35
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Selvaraj B, Pierik AJ, Bill E, Martins BM. 4-Hydroxyphenylacetate decarboxylase activating enzyme catalyses a classical S-adenosylmethionine reductive cleavage reaction. J Biol Inorg Chem 2013; 18:633-43. [DOI: 10.1007/s00775-013-1008-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 05/14/2013] [Indexed: 10/26/2022]
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Bernadotte S, Atkins AJ, Jacob CR. Origin-independent calculation of quadrupole intensities in X-ray spectroscopy. J Chem Phys 2013. [PMID: 23205980 DOI: 10.1063/1.4766359] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
For electronic excitations in the ultraviolet and visible range of the electromagnetic spectrum, the intensities are usually calculated within the dipole approximation, which assumes that the oscillating electric field is constant over the length scale of the transition. For the short wavelengths used in hard X-ray spectroscopy, the dipole approximation may not be adequate. In particular, for metal K-edge X-ray absorption spectroscopy (XAS), it becomes necessary to include higher-order contributions. In quantum-chemical approaches to X-ray spectroscopy, these so-called quadrupole intensities have so far been calculated by including contributions depending on the square of the electric-quadrupole and magnetic-dipole transition moments. However, the resulting quadrupole intensities depend on the choice of the origin of the coordinate system. Here, we show that for obtaining an origin-independent theory, one has to include all contributions that are of the same order in the wave vector consistently. This leads to two additional contributions depending on products of the electric-dipole and electric-octupole and of the electric-dipole and magnetic-quadrupole transition moments, respectively. We have implemented such an origin-independent calculation of quadrupole intensities in XAS within time-dependent density-functional theory, and demonstrate its usefulness for the calculation of metal and ligand K-edge XAS spectra of transition metal complexes.
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Affiliation(s)
- Stephan Bernadotte
- Karlsruhe Institute of Technology (KIT), Center for Functional Nanostructures, Wolfgang-Gaede-Str. 1a, 76131 Karlsruhe, Germany
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Atkins AJ, Bauer M, Jacob CR. The chemical sensitivity of X-ray spectroscopy: high energy resolution XANES versus X-ray emission spectroscopy of substituted ferrocenes. Phys Chem Chem Phys 2013; 15:8095-105. [PMID: 23579736 DOI: 10.1039/c3cp50999k] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
X-ray spectroscopy at the metal K-edge is an important tool for understanding catalytic processes and provides insight into the geometric and electronic structures of transition metal complexes. In particular, X-ray emission-based methods such as high-energy resolution fluorescence detection (HERFD), X-ray absorption near-edge spectroscopy (XANES) and valence-to-core X-ray emission spectroscopy (V2C-XES) hold the promise of providing increased chemical sensitivity compared to conventional X-ray absorption spectroscopy. Here, we explore the ability of HERFD-XANES and V2C-XES spectroscopy to distinguish substitutions beyond the directly coordinated atoms for the example of ferrocene and selected ferrocene derivatives. The experimental spectra are assigned and interpreted through the use of density functional theory (DFT) calculations. We find that while the pre-edge peaks in the HERFD-XANES spectra are affected by substituents at the cyclopentadienyl ring containing π-bonds [A. J. Atkins, Ch. R. Jacob and M. Bauer, Chem.-Eur. J., 2012, 18, 7021], the V2C-XES spectra are virtually unchanged. The pre-edge in HERFD-XANES probes the weak transition to unoccupied metal d-orbitals, while the V2C-XES spectra are determined by dipole-allowed transitions from occupied ligand orbitals to the 1s core hole. The latter turn out to be less sensitive to changes beyond the first coordination shell.
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Affiliation(s)
- Andrew J Atkins
- Karlsruhe Institute of Technology (KIT), Center for Functional Nanostructures and Institute of Physical Chemistry, Wolfgang-Gaede-Str. 1a, 76131 Karlsruhe, Germany
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Shisler KA, Broderick JB. Emerging themes in radical SAM chemistry. Curr Opin Struct Biol 2012; 22:701-10. [PMID: 23141873 DOI: 10.1016/j.sbi.2012.10.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Revised: 10/11/2012] [Accepted: 10/11/2012] [Indexed: 12/21/2022]
Abstract
Enzymes in the radical SAM (RS) superfamily catalyze a wide variety of reactions through unique radical chemistry. The characteristic markers of the superfamily include a [4Fe-4S] cluster coordinated to the protein via a cysteine triad motif, typically CX(3)CX(2)C, with the fourth iron coordinated by S-adenosylmethionine (SAM). The SAM serves as a precursor for a 5'-deoxyadenosyl radical, the central intermediate in nearly all RS enzymes studied to date. The SAM-bound [4Fe-4S] cluster is located within a partial or full triosephosphate isomerase (TIM) barrel where the radical chemistry occurs protected from the surroundings. In addition to the TIM barrel and a RS [4Fe-4S] cluster, many members of the superfamily contain additional domains and/or additional Fe-S clusters. Recently characterized superfamily members are providing new examples of the remarkable range of reactions that can be catalyzed, as well as new structural and mechanistic insights into these fascinating reactions.
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Affiliation(s)
- Krista A Shisler
- Department of Chemistry & Biochemistry and the Astrobiology Biogeocatalysis Research Center, Montana State University, Bozeman, MT 59717, United States
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Klysubun W, Sombunchoo P, Deenan W, Kongmark C. Performance and status of beamline BL8 at SLRI for X-ray absorption spectroscopy. JOURNAL OF SYNCHROTRON RADIATION 2012; 19:930-936. [PMID: 23093751 DOI: 10.1107/s0909049512040381] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 09/24/2012] [Indexed: 06/01/2023]
Abstract
Beamline BL8 of the Synchrotron Light Research Institute (Thailand) is routinely operated for X-ray absorption spectroscopy (XAS) in an intermediate photon energy range (1.25-10 keV). The photon energy is scanned by using a double-crystal monochromator, the crystal pair of which can be interchanged among KTP(011), InSb(111), Si(111) and Ge(220). The experimental set-up conveniently facilitates XAS measurements in transmission and fluorescence-yield modes at several K-edges of elements ranging from magnesium to zinc. Instrumentation and specification of the beamline and the XAS station are described, together with the determination of the available photon flux [0.1-6 × 10(10) photon s(-1) (100 mA)(-1)], energy resolution (1-5 × 10(-4)) and stability of photon energy calibration (0.07 eV), representing the beamline performance. Data quality and accuracy of XANES and EXAFS measured at BL8 are compared with those of other well established beamlines. A noted distinction of BL8 is its relatively high sensitivity for studying phosphorous, sulfur and chlorine in diluted systems and its maximum beam size of 14 mm (width) × 1 mm (height), which is suitable for bulk characterization.
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Affiliation(s)
- Wantana Klysubun
- Synchrotron Light Research Institute, Muang, Nakhon Ratchasima 30000, Thailand.
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40
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Daly SR, Keith JM, Batista ER, Boland KS, Clark DL, Kozimor SA, Martin RL. Sulfur K-edge X-ray Absorption Spectroscopy and Time-Dependent Density Functional Theory of Dithiophosphinate Extractants: Minor Actinide Selectivity and Electronic Structure Correlations. J Am Chem Soc 2012; 134:14408-22. [DOI: 10.1021/ja303999q] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Scott R. Daly
- Los Alamos National Laboratory, Los Alamos,
New Mexico 87545, United States
| | - Jason M. Keith
- Los Alamos National Laboratory, Los Alamos,
New Mexico 87545, United States
| | - Enrique R. Batista
- Los Alamos National Laboratory, Los Alamos,
New Mexico 87545, United States
| | - Kevin S. Boland
- Los Alamos National Laboratory, Los Alamos,
New Mexico 87545, United States
| | - David L. Clark
- Los Alamos National Laboratory, Los Alamos,
New Mexico 87545, United States
| | - Stosh A. Kozimor
- Los Alamos National Laboratory, Los Alamos,
New Mexico 87545, United States
| | - Richard L. Martin
- Los Alamos National Laboratory, Los Alamos,
New Mexico 87545, United States
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