Mechanistic Investigation of 1,2-Diol Dehydration of Paromamine Catalyzed by the Radical S-Adenosyl-l-methionine Enzyme AprD4

Abstract

AprD4 is a radical S-adenosyl-L-methionine (SAM) enzyme catalyzing C3′-deoxygenation of paromamine to form 4′oxo-lividamine. It is the only 1,2-diol dehydratase in the radical SAM enzyme superfamily that has been identified and characterized in vitro. The AprD4 catalyzed 1,2-diol dehydration is a key step in the biosynthesis of several C3′-deoxy-aminoglycosides. While the regiochemistry of the hydrogen atom abstraction catalyzed by AprD4 has been established, the mechanism of the subsequent chemical transformation remains not fully understood. To investigate the mechanism, several substrate analogues were synthesized and their fates upon incubation with AprD4 were analyzed. The results support a mechanism involving formation of a ketyl radical intermediate followed by direct elimination of the C3′-hydroxyl group rather than that of a gem-diol intermediate generated via 1,2migration of the C3′-hydroxyl group to C4′. The stereochemistry of hydrogen atom incorporation after radical-mediated dehydration was also established.

A Unified Strategy to Access 2- and 4-Deoxygenated Sugars Enabled by Manganese-Promoted 1,2-Radical Migration

“…Our approach is inspired by nature, where sugar deoxygenation can be achieved in a single enzymatic step, through a radical 1,2-migration or “spin center shift” mechanism (Figure C). Though well-established for the conversion of ribose to deoxyribose by ribonucleotide reductase (RNR), − methods that promote similar radical migrations outside the context of an enzyme are extremely rare. − We envisioned that an analogous redox isomerization of pyranose substrates would reveal deoxyketopyranoside intermediates amenable to subsequent diversification to deoxygenated rare sugars (Figure D).…”

Mechanistic investigation of B12-independent glycerol dehydratase and its activating enzyme GD-AE

“…The mechanism of this B12-independent GD is in line with mechanisms proposed for several other dehydratases with a ketyl radical involved, such as 1,2-propanediol dehydratase, 24 ribonucleotide reductase, 25,26 hydroxyacyl-CoA dehydratases, 27 and the newly reported deoxygenase AprD4 of paromanine. 28…”

Selective Biocatalytic Defunctionalization of Raw Materials

“…A vicinal diol dehydration of paromamine catalyzed by AprD4, an enzyme dependent on S ‐adenosyl‐ l ‐methionine (SAM), leads to the deoxygenation of paromamine at C3’ and is key for the biosynthetic route to C3’‐deoxy‐aminoglycosides [89] …”

“…[88] A vicinal diol dehydration of paromamine catalyzed by AprD4, an enzyme dependent on S-adenosyl-l-methionine (SAM), leads to the deoxygenation of paromamine at C3' and is key for the biosynthetic route to C3'-deoxy-aminoglycosides. [89] Unsaturated sugars, which can be formed by novel biocatalytic dehydration reactions, open interesting opportunities for synthesizing bioactive natural products. Forming exocyclic C=C bonds is a valuable synthetic tool and of interest for synthesizing bioactive exo-glycal-containing natural products.…”