In this minireview, we describe the radical S-adenosylmethionine enzymes involved in the biosynthesis of thiamin, menaquinone, molybdopterin, coenzyme F 420 , and heme. Our focus is on the remarkably complex organic rearrangements involved, many of which have no precedent in organic or biological chemistry. Radical S-adenosylmethionine (SAM)2 enzymes are among the most intriguing enzymes discovered over the past 15 years. In these enzymes, reduction of SAM by a 1ϩ cluster generates the adenosyl radical, which then abstracts a hydrogen atom from the substrate. The resulting substrate radical usually undergoes a rearrangement or fragmentation reaction to give the product radical (1). Sequence analysis suggests that a large number of enzymes use the radical SAM catalytic motif (2). We are still at an early stage of defining the catalytic mechanisms and the structural enzymology of this fascinating enzyme family.This minireview focuses on the organic chemistry of the radical SAM enzymes involved in cofactor biosynthesis: thiamin (1), F 0 (2), menaquinone (3), molybdopterin (4), and heme (5) (Fig. 1). (Biotin and lipoic biosynthesis also uses radical SAM enzymology and is covered separately in another minireview in this series (42).) In contrast to iron(IV)-oxo-derived radicals, where the dominant chemistry involves radical recombination with the iron-bound oxygen (P 450 rebound rate of Ͼ10 10 s Ϫ1 ) (3), radicals formed by hydrogen atom transfer to the 5Ј-deoxyadenosyl (5Ј-dA) radical are more persistent because the reverse reaction is relatively slow. This allows time for complex rearrangements to occur. Radical SAM enzymes catalyze a remarkable range of reactions due to the high intrinsic reactivity of organic radicals, which can undergo rapid hydrogen atom abstraction, double-bond addition, and fragmentation reactions as shown in Fig. 2. Prokaryotic Thiamin Pyrimidine Synthase (ThiC)Thiamin pyrophosphate (1) is an important cofactor in carbohydrate metabolism and branched chain amino acid biosynthesis, where it plays a key role in stabilization of the acyl carbanion biosynthon. The thiamin pyrimidine synthase (ThiC) catalyzes the conversion of aminoimidazole ribotide (AIR; 6) to hydroxymethylpyrimidine phosphate (HMP-P; 8) (Fig. 3A) (4, 5). The origin of all of the atoms of the product and the fate of all of the atoms of the substrate have been determined using isotope labeling studies (6 -8). This rearrangement, as far as we can tell, is the most complex unsolved rearrangement in primary metabolism.A mechanistic proposal for this reaction is shown in Fig. 3B (5). In this proposal, radical 7 abstracts a hydrogen atom from 6 to form 10. A ␤-scission followed by N-glycosyl bond cleavage gives 12. Electrophilic addition to the aminoimidazole followed by hydrogen atom transfer gives 14. The regenerated 5Ј-dA radical (7) abstracts a hydrogen atom from 14 to form 15. Radical addition to the imine followed by ␤-scission gives 17. A second ␤-scission followed by a diol dehydratase-like rearrangement gives 20 and 21. Ra...

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This study has demonstrated the formation of the G-quadruplex structure from the G-rich sequence in the promoter region of the bcl-2 oncogene; the formation could be induced by addition of NH(4)(+) or K(+) ions. The binding affinity and stoichiometry of seven small molecules with the G-quadruplex were examined by using ESI-MS, as well as CD and UV spectroscopy. The binding-affinity order was determined to be P1 approximately = P5 > P2 > P3 approximately = P4 > P7 > P6. In particular, the small-molecule induction of the structural transition between the G-quadruplex and duplex DNA forms in this promoter region was investigated by ESI-MS. We directly observed specific binding of dehydrocorydaline (P7) and cationic porphyrin (P5) in one system consisting of the G-quadruplex and the duplex DNA, respectively. The results indicate that P7 selectively stabilizes the G-quadruplex and shifts the equilibrium toward G-quadruplex formation of the bcl-2 promoter, whereas P5 converts the G-quadruplex into the duplex DNA, which results in strong and selective binding to the duplex form. Therefore, P5 and P7 with their attractive binding specificities could be considered as precursors for pathway-specific drug design for regulation of bcl-2 oncogene transcription.

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