Radical SAM enzymes: Nature's choice for radical reactions

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.

[1]  B. Hoffman,et al.  Mechanism of Radical S-Adenosyl-l-methionine Adenosylation: Radical Intermediates and the Catalytic Competence of the 5'-Deoxyadenosyl Radical. , 2022, Journal of the American Chemical Society.

[2]  J. Gerlt,et al.  RadicalSAM.org: A Resource to Interpret Sequence-Function Space and Discover New Radical SAM Enzyme Chemistry , 2021, ACS bio & med chem Au.

[3]  D. Nocera,et al.  Radicals in Biology: Your Life Is in Their Hands. , 2021, Journal of the American Chemical Society.

[4]  B. Hoffman,et al.  S-Adenosyl-l-ethionine is a Catalytically Competent Analog of S-Adenosyl-l-methione (SAM) in the Radical SAM Enzyme HydG. , 2021, Angewandte Chemie.

[5]  B. Hoffman,et al.  Active-Site Controlled, Jahn-Teller Enabled Regioselectivity in Reductive S-C Bond Cleavage of S-Adenosylmethionine in Radical SAM Enzymes. , 2020, Journal of the American Chemical Society.

[6]  D. Procter,et al.  Radical C−C Bond Formation using Sulfonium Salts and Light , 2020, Advanced Synthesis & Catalysis.

[7]  R. D. Britt,et al.  Trapping and Electron Paramagnetic Resonance Characterization of the 5′dAdo• Radical in a Radical S-Adenosyl Methionine Enzyme Reaction with a Non-Native Substrate , 2019, ACS central science.

[8]  B. Hoffman,et al.  Photoinduced Electron Transfer in a Radical SAM Enzyme Generates an S-Adenosylmethionine Derived Methyl Radical. , 2019, Journal of the American Chemical Society.

[9]  A. Byer,et al.  The Elusive 5'-Deoxyadenosyl Radical: Captured and Characterized by EPR and ENDOR Spectroscopies. , 2019, Journal of the American Chemical Society.

[10]  L. Scott,et al.  Paradigm Shift for Radical S-Adenosyl-l-methionine Reactions: The Organometallic Intermediate Ω Is Central to Catalysis , 2018, Journal of the American Chemical Society.

[11]  S. Khare,et al.  Structures of the peptide-modifying radical SAM enzyme SuiB elucidate the basis of substrate recognition , 2017, Proceedings of the National Academy of Sciences.

[12]  A. Byer,et al.  Monovalent Cation Activation of the Radical SAM Enzyme Pyruvate Formate-Lyase Activating Enzyme , 2017, Journal of the American Chemical Society.

[13]  B. Hoffman,et al.  Radical SAM catalysis via an organometallic intermediate with an Fe–[5′-C]-deoxyadenosyl bond , 2016, Science.

[14]  P. Amara,et al.  Carbon-sulfur bond-forming reaction catalysed by the radical SAM enzyme HydE. , 2016, Nature chemistry.

[15]  A. Byer,et al.  Why Nature Uses Radical SAM Enzymes so Widely: Electron Nuclear Double Resonance Studies of Lysine 2,3-Aminomutase Show the 5'-dAdo• "Free Radical" Is Never Free. , 2015, Journal of the American Chemical Society.

[16]  R. Sension,et al.  Energy cascades, excited state dynamics, and photochemistry in cob(III)alamins and ferric porphyrins. , 2015, Accounts of chemical research.

[17]  J. Broderick,et al.  Radical S-Adenosylmethionine Enzymes , 2014, Chemical reviews.

[18]  C. Drennan,et al.  X-ray structure of an AdoMet radical activase reveals an anaerobic solution for formylglycine posttranslational modification , 2013, Proceedings of the National Academy of Sciences.

[19]  K. Hodgson,et al.  S K-edge XAS and DFT calculations on SAM dependent pyruvate formate-lyase activating enzyme: nature of interaction between the Fe4S4 cluster and SAM and its role in reactivity. , 2011, Journal of the American Chemical Society.

[20]  K. Warncke,et al.  Characterization of protein contributions to cobalt-carbon bond cleavage catalysis in adenosylcobalamin-dependent ethanolamine ammonia-lyase by using photolysis in the ternary complex. , 2011, Journal of the American Chemical Society.

[21]  C. Drennan,et al.  Structural insights into radical generation by the radical SAM superfamily. , 2011, Chemical reviews.

[22]  K. Warncke,et al.  Photolysis of adenosylcobalamin and radical pair recombination in ethanolamine ammonia-lyase probed on the micro- to millisecond time scale by using time-resolved optical absorption spectroscopy. , 2009, Biochemistry.

[23]  J. Broderick,et al.  Structural basis for glycyl radical formation by pyruvate formate-lyase activating enzyme , 2008, Proceedings of the National Academy of Sciences.

[24]  Adrian D Hegeman,et al.  The Radical SAM Superfamily. , 2008, Critical reviews in biochemistry and molecular biology.

[25]  H. Zipse.  Radical Stability: A Theoretical Perspective , 2006 .

[26]  Dagmar Ringe,et al.  The x-ray crystal structure of lysine-2,3-aminomutase from Clostridium subterminale. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[27]  K. Brown,et al.  Chemistry and enzymology of vitamin B12. , 2005, Chemical reviews.

[28]  Ruma Banerjee,et al.  Radical carbon skeleton rearrangements: catalysis by coenzyme B12-dependent mutases. , 2003, Chemical reviews.

[29]  P. Frey,et al.  S-Adenosylmethionine: a wolf in sheep's clothing, or a rich man's adenosylcobalamin? , 2003, Chemical reviews.

[30]  B. Hoffman,et al.  An anchoring role for FeS clusters: chelation of the amino acid moiety of S-adenosylmethionine to the unique iron site of the [4Fe-4S] cluster of pyruvate formate-lyase activating enzyme. , 2002, Journal of the American Chemical Society.

[31]  B. Hoffman,et al.  Electron-nuclear double resonance spectroscopic evidence that S-adenosylmethionine binds in contact with the catalytically active [4Fe-4S](+) cluster of pyruvate formate-lyase activating enzyme. , 2002, Journal of the American Chemical Society.

[32]  H. Fischer.  The persistent radical effect: a principle for selective radical reactions and living radical polymerizations. , 2001, Chemical reviews.

[33]  G. H. Reed,et al.  Characterization of an allylic analogue of the 5'-deoxyadenosyl radical: an intermediate in the reaction of lysine 2,3-aminomutase. , 2001, Biochemistry.

[34]  J. Broderick,et al.  Adenosylmethionine-dependent iron-sulfur enzymes: versatile clusters in a radical new role , 2001, JBIC Journal of Biological Inorganic Chemistry.

[35]  Jorge F. Reyes-Spindola,et al.  Radical SAM, a novel protein superfamily linking unresolved steps in familiar biosynthetic pathways with radical mechanisms: functional characterization using new analysis and information visualization methods. , 2001, Nucleic acids research.

[36]  P A Frey,et al.  Radical mechanisms of enzymatic catalysis. , 2001, Annual review of biochemistry.

[37]  J. Broderick,et al.  The [4Fe-4S]1+ Cluster of Pyruvate Formate-Lyase Activating Enzyme Generates the Glycyl Radical on Pyruvate Formate-Lyase: EPR-Detected Single Turnover , 2000 .

[38]  G. H. Reed,et al.  Spectroscopic Evidence for the Participation of an Allylic Analogue of the 5‘-Deoxyadenosyl Radical in the Reaction of Lysine 2,3-Aminomutase , 1999 .

[39]  B. Bui,et al.  Biotin Synthase Mechanism: Evidence for Hydrogen Transfer from the Substrate into Deoxyadenosine , 1999 .

[40]  W. Nicholson,et al.  Spore Photoproduct Lyase from Bacillus subtilis Spores Is a Novel Iron-Sulfur DNA Repair Enzyme Which Shares Features with Proteins such as Class III Anaerobic Ribonucleotide Reductases and Pyruvate-Formate Lyases , 1998, Journal of bacteriology.

[41]  J. Stubbe,et al.  Protein Radicals in Enzyme Catalysis. , 1998, Chemical reviews.

[42]  B. Tse Sum Bui,et al.  Biotin synthase, a new member of the family of enzymes which uses S-adenosylmethionine as a source of deoxyadenosyl radical. , 1997, Biochemical and biophysical research communications.

[43]  J. Stubbe,et al.  Thiyl Radicals in Ribonucleotide Reductases , 1996, Science.

[44]  J. Knappe,et al.  Adenosylmethionine-dependent synthesis of the glycyl radical in pyruvate formate-lyase by abstraction of the glycine C-2 pro-S hydrogen atom. Studies of [2H]glycine-substituted enzyme and peptides homologous to the glycine 734 site. , 1994, The Journal of biological chemistry.

[45]  J. Stubbe,et al.  Ribonucleotide reductases: radical enzymes with suicidal tendencies. , 1995, Biochemical Society transactions.

[46]  P. Frey.  Lysine 2,3‐aminomutase: is adenosylmethionine a poor man's adenosylcobalamin? , 1993, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[47]  P. Frey.  Importance of Organic Radicals in Enzymatic Cleavage of Unactivated C‐ H Bonds , 1991 .

[48]  J. Stubbe,et al.  Ribonucleotide reductases: amazing and confusing. , 1990, The Journal of biological chemistry.

[49]  D B Goodin,et al.  Identification by ENDOR of Trp191 as the free-radical site in cytochrome c peroxidase compound ES. , 1989, Science.

[50]  J. Stubbe.  Protein radical involvement in biological catalysis? , 1989, Annual review of biochemistry.

[51]  J. Stubbe,et al.  Radicals in biological catalysis. , 1988, Biochemistry.

[52]  P. Frey,et al.  The role of S-adenosylmethionine in the lysine 2,3-aminomutase reaction. , 1987, The Journal of biological chemistry.

[53]  G. Babcock,et al.  Tyrosine radicals are involved in the photosynthetic oxygen-evolving system. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[54]  H. Fischer.  Unusual selectivities of radical reactions by internal suppression of fast modes , 1986 .

[55]  B. Giese.  Radicals in organic synthesis : formation of carbon-carbon bonds , 1986 .

[56]  R. Williams.  The necessary and the desirable production of radicals in biology. , 1985, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[57]  F. A. Neugebauer,et al.  Post-translational activation introduces a free radical into pyruvate formate-lyase. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[58]  P. Reichard,et al.  Ribonucleotide reductase--a radical enzyme. , 1983, Science.

[59]  B. Sjöberg,et al.  The tyrosine free radical in ribonucleotide reductase from Escherichia coli. , 1978, The Journal of biological chemistry.

[60]  W. Pryor.  THE FORMATION OF FREE RADICALS AND THE CONSEQUENCES OF THEIR REACTIONS IN VIVO , 1978, Photochemistry and photobiology.

[61]  B. Sjöberg,et al.  Nature of the free radical in ribonucleotide reductase from Escherichia coli. , 1977, The Journal of biological chemistry.

[62]  J. Knappe,et al.  A novel reaction of S-adenosyl-L-methionine correlated with the activation of pyruvate formate-lyase. , 1976, Biochemical and biophysical research communications.

[63]  P. Reichard,et al.  Electron spin resonance of the iron-containing protein B2 from ribonucleotide reductase. , 1972, The Journal of biological chemistry.

[64]  H. A. Barker.  14 Coenzyme Bl2-Dependent Mutases Causing Carbon Chain Rearrangements , 1972 .

[65]  H. A. Barker,et al.  Lysine 2,3-aminomutase. Purification and properties of a pyridoxal phosphate and S-adenosylmethionine-activated enzyme. , 1970, The Journal of biological chemistry.

[66]  P. Frey,et al.  The role of the B12 coenzyme in the conversion of 1,2-propanediol to propionaldehyde. , 1966, The Journal of biological chemistry.

[67]  G. Catoni.  S-Adenosylmethionine; a new intermediate formed enzymatically from L-methionine and adenosinetriphosphate. , 1953, The Journal of biological chemistry.