Radical SAM-mediated methylation reactions

Abstract

A subset of enzymes that belong to the radical S-adenosylmethionine (SAM) superfamily is able to catalyze methylation reactions. Substrates of these enzymes are distinct from the nucleophilic substrates that undergo methylation by a polar mechanism. Recently, activities of several radical SAM methylating enzymes have been reconstituted in vitro and their mechanisms of catalysis investigated. The RNA modifying enzymes RlmN and Cfr catalyze methylation via a methyl synthase mechanism. These enzymes use SAM in two distinct roles: as a source of a methyl group transferred to a conserved cysteine and as a source of 5'-deoxyadenosyl radical (5'-dA). Hydrogen atom abstraction by this species generates a thiomethylene radical which adds into the RNA substrate, forming an enzyme-substrate covalent adduct. In another recent study, methylation of the indole moiety of tryptophan by the radical SAM and cobalamin-binding domain enzyme TsrM has been reconstituted. Methylcobalamin serves as an intermediate methyl donor in TsrM, and is proposed to transfer the methyl group as a methyl radical. Interestingly, despite the presence of the radical SAM motif, no reductive cleavage of SAM has been observed in this methylation. These important reconstitutions set the stage for further studies on mechanisms of radical methylation.

Figure 1

Selected molecules that contain methyl groups or their derivatives introduced by radical SAM methylating enzymes. Groups introduced by these enzymes are shown in red. Polytheonamides A and B differ only in the absolute configuration of the sulfoxide [58].

Figure 2

Summary of labeling experiments used to elucidate the mechanism of methylation by radical SAM methyl synthases RlmN [12,42]. Experiments in panels A and B were performed under multiple turnover conditions, whereas experiments in panels C–E were performed under single turnover conditions. SDT = sodium dithionite. Flv = flavodoxin. Flx = flavodoxin reductase. R₁ = nucleotides 2447–2778, 23S rRNA. R₂ = nucleotides 2500–2506, 23S rRNA. R₃ = nucleotides 2018–2788, 23S rRNA. The RlmN substrate adenosine is in position 2503 in all pictured RNA constructs.

Figure 3

Proposed mechanism of RNA methylation by RlmN [12]. The covalent intermediate, trapped by mutagenesis of Cys118 to Ala [13], is shown in the inset. SAM = S-adenosyl-L-methionine. SAH = S-adenosyl-L-homocysteine. 5′-dA^• = 5′-deoxyadenosyl radical.

Figure 4

Proposed mechanism of the C2 methylation of the indole moiety of tryptophan by TsrM [30]. The Trp substrate is putatively coordinated by the iron-sulfur cluster. Reduction of Cob(II)alamin by the reduced [4Fe-4S] cluster may result in transient formation of the nucleophilic Co(I), which may react with SAM to regenerate methylcobalamin cofactor. Following addition of the methyl radical, oxidation of the Trp radical might be achieved by the oxidized cluster. SAM = S-adenosyl-L-methionine. SAH = S-adenosyl-L-homocysteine.