Mechanistic and functional versatility of radical SAM enzymes

Abstract

Enzymes of the radical SAM (RS) superfamily catalyze a diverse assortment of reactions that proceed via intermediates containing unpaired electrons. The radical initiator is the common metabolite S-adenosyl-l-methionine (SAM), which is reductively cleaved to generate a 5'-deoxyadenosyl 5'-radical, a universal and obligate intermediate among enzymes within this class. A bioinformatics study that appeared in 2001 indicated that this superfamily contained over 600 members, many catalyzing reactions that were rich in novel chemical transformations. Since that seminal study, the RS superfamily has grown immensely, and new details about the scope of reactions and biochemical pathways in which its members participate have emerged. This review will highlight only a few of the most significant findings from the past 2-3 years, focusing primarily on: RS enzymes involved in complex metallocofactor maturation; characterized RS enzymes that lack the canonical CxxxCxxC motif; RS enzymes containing multiple iron-sulfur clusters; RS enzymes catalyzing reactions with compelling medical implications; and the energetics and mechanism of generating the 5'-deoxyadenosyl radical. A number of significant studies of RS enzymes will unfortunately be omitted, and it is hoped that the reader will access the relevant literature - particularly a number of superb review articles recently written on the subject - to acquire a deeper appreciation of this class of enzymes.

Figure 1.. Binding mode of SAM in radical SAM proteins

Binding of SAM (S-adenosyl-l-methionine) to the [4Fe-4S] cluster of biotin synthase. Color scheme: black, Fe; blue, N; yellow, S; red, O; grey, C. Structure prepared using Pymol Molecular Graphics System [74] from Protein Data Bank entry 1R30.

Figure 2.. Maturation of the H-cluster of the [FeFe]-hydrogenase

The structure on the left represents HydA, the hydrogenase from Desulfovibrio desulfuricans, with a [4Fe-4S] cluster bound. In the presence of HydE, HydF, HydG, and appropriate small molecules, the H-cluster is formed on HydA. Color scheme: red, iron; yellow, sulfur; grey, carbon; blue, nitrogen; black, unidentified atom (X). Structure prepared using Pymol Molecular Graphics System [74] from Protein Data Bank entry 1HFE.

Figure 3.. The reaction catalyzed by ThiC

Color-coding depicts the change in positioning of certain atoms during the rearrangement as determined by labeling experiments. AIR, 5-aminoimidazole ribonucleotide; HMP, 4-amino-5-hydroxymethyl-2-methylpyrimidine. Figure is adapted from reference [21].

Figure 4.. The reaction catalyzed by MoaA/MoaC

Numbers highlight changes in positioning of atoms during the rearrangement.

Figure 5.. The active site of MoaA

Structure of MoaA with both GTP and SAM (S-adenosyl-l-methionine) bound. Color scheme: black, Fe; blue, N; yellow, S; red, O; grey, C. Structure prepared using Pymol Molecular Graphics System [74] from Protein Data Bank entry 2FB3.

Figure 6.. The reactions catalyzed by Cfr and RlmN

SAH, S-adenosyl-homocysteine; SAM, S-adenosyl-l-methionine.

Figure 7.. Model for the reductive cleavage of SAM to generate a 5′-deoxyadenosyl radical