Radical SAM enzymes: Nature's choice for radical reactions

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.

Comparative Study of Adenosine Analogs as Inhibitors of Protein Arginine Methyltransferases and a Clostridioides difficile-Specific DNA Adenine Methyltransferase

“…As expected, both 11a and 11b exhibit reduced inhibition of PRMT1 and PRMT3, as one of the parental compounds (7) does not significantly inhibit either of the two PRMTs. 11a has a remarkable reduction (∼116×) in inhibition of PRMT1 from that of 6e (IC 50 of 14 μM vs. 0.12 μM) (Figure 2C).…”

“…The desired compounds 11a and 11b were synthesized following the reported methods 48 (Scheme 1). Briefly, the commercially available 6chloropurine ribonucleoside reacted with 3-phenylpropylamine to yield N6-phenylpropyladenosine (7), which was then subjected to the Mitsunobu reaction to produce compound 8. Then the acetyl group of 8 was removed, followed by its substitution with Boc protected ethyl or propyl amine.…”

“…S -Adenosyl- l -methionine (SAM, SAMe, or AdoMet) is a metabolite that is biosynthesized naturally in almost all species (excepting only some obligate intracellular parasites that import it) and is the second most-used cofactor after ATP . SAM is involved in a wide range of biochemical reactions including (but not limited to) transmethylation reactions, , radical SAM reactions, − polyamine biosynthesis, and SAM-sensing riboswitches. , SAM-dependent methyltransferases (MTases) catalyze methyl transfers onto a wide variety of substrate molecules, including both macromolecules (DNA, RNA, polysaccharides, lipids, and proteins) and micromolecules (such as catechol, arsenic, histamine, nicotinamide, and thiopurine). Given the significance of epigenetic methylation of macromolecules in cancer, immunity, cardiovascular and many other diseases, as well as methylation of anticancer drugs such as thiopurine, , SAM-dependent MTases are increasingly becoming therapeutic targets. − …”

Computational Description of Alkylated Iron–Sulfur Organometallic Clusters

“…Radical S -adenosyl- l -methionine (SAM) enzymes are ubiquitous in life, comprising one of the largest enzyme superfamilies. − These enzymes catalyze the reductive cleavage of SAM by electron transfer from a [4Fe-4S] 1+ cluster to the sulfonium group of the coordinated SAM to form the highly reactive 5′-deoxyadenosyl radical (5′-dAdo•), which then ultimately abstracts a hydrogen atom from substrates. − However, rapid freeze-quench electron paramagnetic (EPR) and electron nuclear double-resonance (ENDOR) spectroscopies have shown that prior to H abstraction from the substrate, 5′-dAdo• forms an organometallic intermediate, denoted Ω, that is characterized by a direct bond between the [4Fe-4S] 3+ cluster and 5′C of 5′-dAdo (Figure , left). , Later, it was shown that photo-reductive cleavage of SAM in a broad subset of radical SAM (RS) enzymes releases either 5′-dAdo• or a methyl radical (•CH 3 ); ,, upon annealing, the latter forms an alternative organometallic species, denoted Ω Μ , which was shown by ENDOR to have a [4Fe-4S] 3+ cluster with a Fe–CH 3 bond (Figure , middle). − Inspired by these discoveries, the M–CH 3 analogue of Ω Μ (Figure , right) was synthesized and extensively characterized by crystallography as well as with Mossbauer and ENDOR spectroscopic methods, , with additional alkylated iron–sulfur clusters being synthesized and characterized. − …”

Nobel symposium #168 Visions of bio‐inorganic chemistry: metals and the molecules of life

“…Klinman [9] paints a fascinating picture of how function in metalloenzymes can be activated by dynamics and how the interplay between protein dynamics and function can be addressed using novel experimental and theoretical approaches. Broderick and Hoffman review the vast “radical SAM” family of proteins [10]. Enzymes utilizing a 4Fe‐4S cluster together with S ‐adenosyl‐methionine to perform a hugely diverse set of radical‐based chemical reactions.…”