Radical SAM enzymes involved in the biosynthesis of purine-based natural products

Abstract

The radical S-adenosyl-l-methionine (SAM) superfamily is a widely distributed group of iron-sulfur containing proteins that exploit the reactivity of the high energy intermediate, 5'-deoxyadenosyl radical, which is produced by the reductive cleavage of SAM, to carry-out complex radical-mediated transformations. The reactions catalyzed by radical SAM enzymes range from simple group migrations to complex reactions in protein and RNA modification. This review will highlight three radical SAM enzymes that catalyze reactions involving modified guanosines in the biosynthesis pathways of the hypermodified tRNA base wybutosine; secondary metabolites of 7-deazapurine structure, including the hypermodified tRNA base queuosine; and the redox cofactor F(420). This article is part of a Special Issue entitled: Radical SAM enzymes and Radical Enzymology.

Figure 1

Radical SAM proteins catalyze reductive cleavage of SAM to generate dAdo•, which is required for catalysis.

Figure 2

Representative examples of 7-deazapurines showing the structural diversity in pyrrolopyrimidine-based metabolites.

Figure 3

In the course of biosynthesis from carbon-2 of the starting purine is retained whereas carbon-8 is lost as formate. Carbons 1–3 from ribose of the starting sugar are incorporated into the 5-membered ring and side chain of the 7-deazapurine.

Figure 4

Biosynthetic pathways leading to the hypermodified tRNA base queuosine and secondary metabolites sangivamycin/toyocamycin. Steps that have been demonstrated in vitro are denoted by solid arrows.

Figure 5

Mechanism of CDG synthase involving H-atom abstraction to generate a substrate based radical (A). In this mechanism it is assumed that the substrate radical abstracts an H-atom from the dAdo to produce the product and that SAM is regenerated. The C-6 radical can be stabilized by capto-dative effects, as illustrated in (B).

Figure 6

Mechanism for CDG synthase assuming abstraction at C-7. As in the mechanism involving abstraction at C-6 shown in Fig. 5, it is assumed that the substrate radical is quenched by H-atom transfer from dAdo and that SAM is regenerated.

Figure 7

Biosynthetic pathway leading to the hypermodified tRNA base wybutosine (yW). Unlike queuosine, all steps leading to the modified base occur on the tRNA.

Figure 8

Mechanism of action of TYW1. H-atom abstraction either by dAdo• or another radical generated by it from m¹G substrate initiates the radical cascade. A conserved Lys residue is proposed to be involved in formation of Schiff base with pyruvate.

Figure 9

Biosynthesis of coenzyme F₄₂₀. Compound 6 is an intermediate in the biosynthesis of riboflavin as well. F₄₂₀ from different organisms can have variable numbers of glutamate residues.

Figure 10

Similarity of reactions catalyzed by the radical SAM proteins HydG, ThiH, and NosL to that of DS. By analogy to HydG [69] and ThiGH [68], where p-cresol has been shown to be a product, HPP may be activated in a similar manner upon abstraction of a hydrogen atom from the ring hydroxyl and fragmentation.