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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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2
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Lee YH, Yeh YC, Fan PH, Zhong A, Ruszczycky MW, Liu HW. Changing Fates of the Substrate Radicals Generated in the Active Sites of the B 12-Dependent Radical SAM Enzymes OxsB and AlsB. J Am Chem Soc 2023; 145:3656-3664. [PMID: 36719327 PMCID: PMC9940012 DOI: 10.1021/jacs.2c12953] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
OxsB is a B12-dependent radical SAM enzyme that catalyzes the oxidative ring contraction of 2'-deoxyadenosine 5'-phosphate to the dehydrogenated, oxetane containing precursor of oxetanocin A phosphate. AlsB is a homologue of OxsB that participates in a similar reaction during the biosynthesis of albucidin. Herein, OxsB and AlsB are shown to also catalyze radical mediated, stereoselective C2'-methylation of 2'-deoxyadenosine monophosphate. This reaction proceeds with inversion of configuration such that the resulting product also possesses a C2' hydrogen atom available for abstraction. However, in contrast to methylation, subsequent rounds of catalysis result in C-C dehydrogenation of the newly added methyl group to yield a 2'-methylidene followed by radical addition of a 5'-deoxyadenosyl moiety to produce a heterodimer. These observations expand the scope of reactions catalyzed by B12-dependent radical SAM enzymes and emphasize the susceptibility of radical intermediates to bifurcation along different reaction pathways even within the highly organized active site of an enzyme.
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Affiliation(s)
- Yu-Hsuan Lee
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Yu-Cheng Yeh
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Po-Hsun Fan
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Aoshu Zhong
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
| | - Mark W. Ruszczycky
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
| | - Hung-wen Liu
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States; Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
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3
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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: 1] [Impact Index Per Article: 1.0] [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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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: 14] [Impact Index Per Article: 7.0] [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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Adenosylation reactions catalyzed by the radical S-adenosylmethionine superfamily enzymes. Curr Opin Chem Biol 2020; 55:86-95. [DOI: 10.1016/j.cbpa.2020.01.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/22/2019] [Accepted: 01/15/2020] [Indexed: 01/23/2023]
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Zhong Y, Ji X, Zhang Q. Radical SAM‐Dependent Adenosylation Involved in Bacteriohopanepolyol Biosynthesis
†. CHINESE J CHEM 2019. [DOI: 10.1002/cjoc.201900399] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yuting Zhong
- Department of ChemistryFudan University Shanghai 200433 China
| | - Xinjian Ji
- Department of ChemistryFudan University Shanghai 200433 China
| | - Qi Zhang
- Department of ChemistryFudan University Shanghai 200433 China
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Wu Y, Wu R, Mandalapu D, Ji X, Chen T, Ding W, Zhang Q. Radical SAM-dependent adenosylation catalyzed by l-tyrosine lyases. Org Biomol Chem 2019; 17:1809-1812. [DOI: 10.1039/c8ob02906g] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Tyrosine analogues containing an olefin moiety can be adenosylated by l-tyrosine lyases.
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Affiliation(s)
- Yujie Wu
- State Key Laboratory of Cryospheric Sciences
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering
- Northwest Institute of Eco-environment and Resource
- Chinese Academy of Sciences
- Lanzhou 730000
| | - Runze Wu
- Department of Chemistry
- Fudan University
- Shanghai 200433
- China
| | | | - Xinjian Ji
- Department of Chemistry
- Fudan University
- Shanghai 200433
- China
| | - Tuo Chen
- State Key Laboratory of Cryospheric Sciences
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering
- Northwest Institute of Eco-environment and Resource
- Chinese Academy of Sciences
- Lanzhou 730000
| | - Wei Ding
- Department of Chemistry
- Fudan University
- Shanghai 200433
- China
| | - Qi Zhang
- Department of Chemistry
- Fudan University
- Shanghai 200433
- China
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8
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Synthesis and preliminary biological evaluation of new phenolic and catecholic dehydroamino acid derivatives. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.09.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Joshi S, Mahanta N, Fedoseyenko D, Williams H, Begley TP. Aminofutalosine Synthase: Evidence for Captodative and Aryl Radical Intermediates Using β-Scission and SRN1 Trapping Reactions. J Am Chem Soc 2017; 139:10952-10955. [DOI: 10.1021/jacs.7b04209] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Sumedh Joshi
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Nilkamal Mahanta
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Dmytro Fedoseyenko
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Howard Williams
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Tadhg P. Begley
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
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Bruender NA, Grell TAJ, Dowling DP, McCarty RM, Drennan CL, Bandarian V. 7-Carboxy-7-deazaguanine Synthase: A Radical S-Adenosyl-l-methionine Enzyme with Polar Tendencies. J Am Chem Soc 2017; 139:1912-1920. [PMID: 28045519 PMCID: PMC5301278 DOI: 10.1021/jacs.6b11381] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Radical S-adenosyl-l-methionine (SAM)
enzymes are widely distributed and catalyze diverse reactions. SAM
binds to the unique iron atom of a site-differentiated [4Fe-4S] cluster
and is reductively cleaved to generate a 5′-deoxyadenosyl radical,
which initiates turnover. 7-Carboxy-7-deazaguanine (CDG) synthase
(QueE) catalyzes a key step in the biosynthesis of 7-deazapurine containing
natural products. 6-Carboxypterin (6-CP), an oxidized analogue of
the natural substrate 6-carboxy-5,6,7,8-tetrahydropterin (CPH4), is shown to be an alternate substrate for CDG synthase.
Under reducing conditions that would promote the reductive cleavage
of SAM, 6-CP is turned over to 6-deoxyadenosylpterin (6-dAP), presumably
by radical addition of the 5′-deoxyadenosine followed by oxidative
decarboxylation to the product. By contrast, in the absence of the
strong reductant, dithionite, the carboxylate of 6-CP is esterified
to generate 6-carboxypterin-5′-deoxyadenosyl ester (6-CP-dAdo
ester). Structural studies with 6-CP and SAM also reveal electron
density consistent with the ester product being formed in crystallo.
The differential reactivity of 6-CP under reducing and nonreducing
conditions highlights the ability of radical SAM enzymes to carry
out both polar and radical transformations in the same active site.
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Affiliation(s)
- Nathan A Bruender
- Department of Chemistry, University of Utah , Salt Lake City, Utah 84112, United States
| | | | | | - Reid M McCarty
- Department of Chemistry and Biochemistry, University of Arizona , Tucson, Arizona 85721, United States
| | | | - Vahe Bandarian
- Department of Chemistry, University of Utah , Salt Lake City, Utah 84112, United States
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Ji X, Li Y, Xie L, Lu H, Ding W, Zhang Q. Expanding Radical SAM Chemistry by Using Radical Addition Reactions and SAM Analogues. Angew Chem Int Ed Engl 2016; 55:11845-8. [DOI: 10.1002/anie.201605917] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Revised: 08/11/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Xinjian Ji
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Yongzhen Li
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Liqi Xie
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Haojie Lu
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Wei Ding
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
| | - Qi Zhang
- Department of Chemistry; Fudan University; Shanghai 200433 China
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12
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Ji X, Li Y, Xie L, Lu H, Ding W, Zhang Q. Expanding Radical SAM Chemistry by Using Radical Addition Reactions and SAM Analogues. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605917] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Xinjian Ji
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Yongzhen Li
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Liqi Xie
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Haojie Lu
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Wei Ding
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
| | - Qi Zhang
- Department of Chemistry; Fudan University; Shanghai 200433 China
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Abstract
Pyruvate and acetyl-CoA form the backbone of central metabolism. The nonoxidative cleavage of pyruvate to acetyl-CoA and formate by the glycyl radical enzyme pyruvate formate lyase is one of the signature reactions of mixed-acid fermentation in enterobacteria. Under these conditions, formic acid accounts for up to one-third of the carbon derived from glucose. The further metabolism of acetyl-CoA to acetate via acetyl-phosphate catalyzed by phosphotransacetylase and acetate kinase is an exemplar of substrate-level phosphorylation. Acetyl-CoA can also be used as an acceptor of the reducing equivalents generated during glycolysis, whereby ethanol is formed by the polymeric acetaldehyde/alcohol dehydrogenase (AdhE) enzyme. The metabolism of acetyl-CoA via either the acetate or the ethanol branches is governed by the cellular demand for ATP and the necessity to reoxidize NADH. Consequently, in the absence of an electron acceptor mutants lacking either branch of acetyl-CoA metabolism fail to cleave pyruvate, despite the presence of PFL, and instead reduce it to D-lactate by the D-lactate dehydrogenase. The conversion of PFL to the active, radical-bearing species is controlled by a radical-SAM enzyme, PFL-activase. All of these reactions are regulated in response to the prevalent cellular NADH:NAD+ ratio. In contrast to Escherichia coli and Salmonella species, some genera of enterobacteria, e.g., Klebsiella and Enterobacter, produce the more neutral product 2,3-butanediol and considerable amounts of CO2 as fermentation products. In these bacteria, two molecules of pyruvate are converted to α-acetolactate (AL) by α-acetolactate synthase (ALS). AL is then decarboxylated and subsequently reduced to the product 2,3-butandiol.
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14
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Mahanta N, Fedoseyenko D, Dairi T, Begley TP. Menaquinone biosynthesis: formation of aminofutalosine requires a unique radical SAM enzyme. J Am Chem Soc 2013; 135:15318-21. [PMID: 24083939 PMCID: PMC3855536 DOI: 10.1021/ja408594p] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Menaquinone (MK, vitamin K2) is a lipid-soluble molecule that participates in the bacterial electron transport chain. In mammalian cells, MK functions as an essential vitamin for the activation of various proteins involved in blood clotting and bone metabolism. Recently, a new pathway for the biosynthesis of this cofactor was discovered in Streptomyces coelicolor A3(2) in which chorismate is converted to aminofutalosine in a reaction catalyzed by MqnA and an unidentified enzyme. Here, we reconstitute the biosynthesis of aminofutalosine and demonstrate that the missing enzyme (aminofutalosine synthase, MqnE) is a radical SAM enzyme that catalyzes the addition of the adenosyl radical to the double bond of 3-[(1-carboxyvinyl)oxy]benzoic acid. This is a new reaction type in the radical SAM superfamily.
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Affiliation(s)
- Nilkamal Mahanta
- Department of Chemistry, Texas A&M University , College Station, Texas 77843, United States
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15
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Vey JL, Drennan CL. Structural insights into radical generation by the radical SAM superfamily. Chem Rev 2011; 111:2487-506. [PMID: 21370834 PMCID: PMC5930932 DOI: 10.1021/cr9002616] [Citation(s) in RCA: 183] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jessica L Vey
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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16
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Szu PH, Ruszczycky MW, Choi SH, Yan F, Liu HW. Characterization and mechanistic studies of DesII: a radical S-adenosyl-L-methionine enzyme involved in the biosynthesis of TDP-D-desosamine. J Am Chem Soc 2009; 131:14030-42. [PMID: 19746907 PMCID: PMC2780582 DOI: 10.1021/ja903354k] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
D-desosamine (1) is a 3-(N,N-dimethylamino)-3,4,6-trideoxyhexose found in a number of macrolide antibiotics including methymycin (2), neomethymycin (3), pikromycin (4), and narbomycin (5) produced by Streptomyces venezuelae . It plays an essential role in conferring biological activities to its parent aglycones. Previous genetic and biochemical studies of the biosynthesis of desosamine in S. venezuelae showed that the conversion of TDP-4-amino-4,6-dideoxy-D-glucose (8) to TDP-3-keto-4,6-dideoxy-D-glucose (9) is catalyzed by DesII, which is a member of the radical S-adenosyl-L-methionine (SAM) enzyme superfamily. Here, we report the purification and reconstitution of His(6)-tagged DesII, characterization of its [4Fe-4S] cluster using UV-vis and EPR spectroscopies, and the capability of flavodoxin, flavodoxin reductase, and NADPH to reduce the [4Fe-4S](2+) cluster. Also included are a steady-state kinetic analysis of DesII-catalyzed reaction and an investigation of the substrate flexibility of DesII. Studies of deuterium incorporation into SAM using TDP-[3-(2)H]-4-amino-4,6-dideoxy-D-glucose as the substrate provides strong evidence for direct hydrogen atom transfer to a 5'-deoxyadenosyl radical in the catalytic cycle. The fact that hydrogen atom abstraction occurs at C-3 also sheds light on the mechanism of this intriguing deamination reaction.
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Affiliation(s)
- Ping-Hui Szu
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, USA
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Ferreira PMT, Monteiro LS, Coban T, Suzen S. Comparative effect ofN-substituted dehydroamino acids and α-tocopherol on rat liver lipid peroxidation activities. J Enzyme Inhib Med Chem 2009; 24:967-71. [DOI: 10.1080/14756360802561162] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
| | - Luis S. Monteiro
- Department of Chemistry, University of Minho, 4710-057 Braga, Portugal
| | - T. Coban
- Department of Pharmaceutical Toxicology, Faculty of Pharmacy, Ankara University, 06100, Tandogan, Ankara, Turkey
| | - S. Suzen
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ankara University, 06100, Tandogan, Ankara, Turkey
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Suzen S, Gurkok G, Coban T. NovelN-acyl dehydroalanine derivatives as antioxidants: Studies on rat liver lipid peroxidation levels and DPPH free radical scavenging activity. J Enzyme Inhib Med Chem 2008; 21:179-85. [PMID: 16789432 DOI: 10.1080/14756360500533109] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
Oxidative stress has been implicated in the development of many neurodegenerative diseases such as Parkinson and Alzhemier's disease and is also responsible for aging, artherosclerosis, rheumatoid arthritis and carcinogenesis. Olefins such as dehydroalanines have been shown to inactivate free radicals by forming stabilized free radical adducts. Among these molecules N-acyl dehydroalanines react with and scavenge oxygen and hydroxyl radicals. This study describes the synthesis, characterization and in vitro effects on rat liver lipid peroxidation levels, and DPPH free radical scavenging activities of some N-acyl dehydroalanine derivatives. Compounds c, f and j slightly scavenged the level of DPPH radical at 10(-3) M concentration by about 27, 46, and 56%, respectively while compounds a, d, e, f, g, h showed a strong inhibitory effect on lipid peroxidation at 10(-3)M and 10(-4)M concentrations and inhibition was in the range of 76-90%. The possible antioxidant mechanism of the compounds was discussed.
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Affiliation(s)
- Sibel Suzen
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ankara University 06100 Tandogan, Ankara, Turkey.
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Abstract
The radical S-adenosylmethionine (SAM) superfamily currently comprises more than 2800 proteins with the amino acid sequence motif CxxxCxxC unaccompanied by a fourth conserved cysteine. The charcteristic three-cysteine motif nucleates a [4Fe-4S] cluster, which binds SAM as a ligand to the unique Fe not ligated to a cysteine residue. The members participate in more than 40 distinct biochemical transformations, and most members have not been biochemically characterized. A handful of the members of this superfamily have been purified and at least partially characterized. Significant mechanistic and structural information is available for lysine 2,3-aminomutase, pyruvate formate-lyase, coproporphyrinogen III oxidase, and MoaA required for molybdopterin biosynthesis. Biochemical information is available for spore photoproduct lyase, anaerobic ribonucleotide reductase activation subunit, lipoyl synthase, and MiaB involved in methylthiolation of isopentenyladenine-37 in tRNA. The radical SAM enzymes biochemically characterized to date have in common the cleavage of the [4Fe-4S](1 +) -SAM complex to [4Fe-4S](2 +)-Met and the 5' -deoxyadenosyl radical, which abstracts a hydrogen atom from the substrate to initiate a radical mechanism.
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Affiliation(s)
- Perry A Frey
- Department of Biochemistry, University of Madison, Wisconin-Madison, Wisconsin 53726, USA.
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20
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Marsh ENG, Patwardhan A, Huhta MS. S-adenosylmethionine radical enzymes. Bioorg Chem 2005; 32:326-40. [PMID: 15381399 DOI: 10.1016/j.bioorg.2004.06.001] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2004] [Indexed: 11/25/2022]
Abstract
The role of S-adenosylmethionine (SAM) as a precursor to organic radicals, generated by one-electron reduction of SAM and subsequent fission to form 5'-deoxyadenosyl radical and methionine, has been known for some time. Only recently, however, has it become apparent how widespread such enzymes are, and what a wide range of chemical reactions they catalyze. In the last few years several new SAM radical enzymes have been identified. Spectroscopic and kinetic investigations have begun to uncover the mechanism by which an iron sulfur cluster unique to these enzymes reduces SAM to generate adenosyl radical. Most recently, the first X-ray structures of SAM radical enzymes, coproporphyrinogen-III oxidase, and biotin synthase have been solved, providing a structural framework within which to interpret mechanistic studies.
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Affiliation(s)
- E Neil G Marsh
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA.
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Fontecave M, Ollagnier-de-Choudens S, Mulliez E. Biological radical sulfur insertion reactions. Chem Rev 2003; 103:2149-66. [PMID: 12797827 DOI: 10.1021/cr020427j] [Citation(s) in RCA: 150] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Marc Fontecave
- Laboratoire de Chimie et Biochimie des Centres Rédox Biologiques, DRDC-CB, CEA/CNRS/Université Joseph Fourier, UMR 5047, 17, Avenue des Martyrs, 38054 Grenoble Cedex 09, France.
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Frey PA, Magnusson OT. S-Adenosylmethionine: a wolf in sheep's clothing, or a rich man's adenosylcobalamin? Chem Rev 2003; 103:2129-48. [PMID: 12797826 DOI: 10.1021/cr020422m] [Citation(s) in RCA: 191] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Perry A Frey
- Department of Biochemistry, University of Wisconsin--Madison, Madison, Wisconsin 53726, USA.
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Frey PA, Booker SJ. Radical mechanisms of S-adenosylmethionine-dependent enzymes. ADVANCES IN PROTEIN CHEMISTRY 2002; 58:1-45. [PMID: 11665486 DOI: 10.1016/s0065-3233(01)58001-8] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- P A Frey
- University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
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Knappe J, Wagner AF. Stable glycyl radical from pyruvate formate-lyase and ribonucleotide reductase (III). ADVANCES IN PROTEIN CHEMISTRY 2002; 58:277-315. [PMID: 11665490 DOI: 10.1016/s0065-3233(01)58007-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Affiliation(s)
- J Knappe
- Biochemie-Zentrum Heidelberg, Ruprecht-Karls-Universität, Im Neuenheimer Feld 501, D-69120 Heidelberg, Germany
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Fontecave M, Mulliez E, Ollagnier-de-Choudens S. Adenosylmethionine as a source of 5'-deoxyadenosyl radicals. Curr Opin Chem Biol 2001; 5:506-11. [PMID: 11578923 DOI: 10.1016/s1367-5931(00)00237-4] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The combination of an iron-sulfur cluster and S-adenosylmethionine provides a novel mechanism for the initiation of radical catalysis in an unanticipated variety of metabolic processes. Molecular details of the cluster-mediated reductive cleavage of S-adenosylmethionine to methionine and, presumably, a 5'-deoxyadenosyl radical are the targets of recent studies.
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Affiliation(s)
- M Fontecave
- Laboratoire de Chimie et Biochimie des Centres Rédox Biologiques, DBMS-CB, CEA/CNRS/Université Joseph Fourier, UMR 5047, 17 Avenue des Martyrs, 38054 Grenoble, Cedex 09, France.
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Selmer T, Andrei PI. p-Hydroxyphenylacetate decarboxylase from Clostridium difficile. A novel glycyl radical enzyme catalysing the formation of p-cresol. EUROPEAN JOURNAL OF BIOCHEMISTRY 2001; 268:1363-72. [PMID: 11231288 DOI: 10.1046/j.1432-1327.2001.02001.x] [Citation(s) in RCA: 163] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The human pathogenic bacterium Clostridium difficile is a versatile organism concerning its ability to ferment amino acids. The formation of p-cresol as the main fermentation product of tyrosine by C. difficile is unique among clostridial species. The enzyme responsible for p-cresol formation is p-hydroxyphenylacetate decarboxylase. The enzyme was purified from C. difficile strain DMSZ 1296(T) and initially characterized. The N-terminal amino-acid sequence was 100% identical to an open reading frame in the unfinished genome of C. difficile strain 630. The ORF encoded a protein of the same size as the purified decarboxylase and was very similar to pyruvate formate-lyase-like proteins from Escherichia coli and Archaeoglobus fulgidus. The enzyme decarboxylated p-hydroxyphenylacetate (K(m) = 2.8 mM) and 3,4-dihydroxyphenylacetate (K(m) = 0.5 mM). It was competitively inhibited by the substrate analogues p-hydroxyphenylacetylamide and p-hydroxymandelate with K(i) values of 0.7 mM and 0.48 mM, respectively. The protein was readily and irreversibly inactivated by molecular oxygen. Although the purified enzyme was active in the presence of sodium sulfide, there are some indications for an as yet unidentified low molecular mass cofactor that is required for catalytic activity in vivo. Based on the identification of p-hydroxyphenylacetate decarboxylase as a novel glycyl radical enzyme and the substrate specificity of the enzyme, a catalytic mechanism involving ketyl radicals as intermediates is proposed.
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Affiliation(s)
- T Selmer
- Laboratorium für Mikrobiologie, Fachbereich Biologie, Philipps-Universität, Marburg, Germany.
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Yamamoto Y, Sato Y, Takahashi-Abbe S, Takahashi N, Kizaki H. Characterization of the Streptococcus mutans pyruvate formate-lyase (PFL)-activating enzyme gene by complementary reconstitution of the In vitro PFL-reactivating system. Infect Immun 2000; 68:4773-7. [PMID: 10899886 PMCID: PMC98435 DOI: 10.1128/iai.68.8.4773-4777.2000] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The act gene was identified and an act mutant as well as the pfl mutant was constructed in Streptococcus mutans. Pyruvate formate-lyase (PFL) activity was regenerated with the mixture of the respective cell extracts from these mutants by complementary reconstitution of the in vitro reactivating system. The S. mutans act gene encoded the sole enzyme able to activate the PFL protein in this organism.
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Affiliation(s)
- Y Yamamoto
- Department of Biochemistry, Tokyo Dental College, Mihama-ku, Chiba City 261-8502, Japan.
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